# Patent

## Title
Methods and compositions for assessment of pulmonary function and disorders

## Abstract

The present invention provides methods for the assessment of risk of developing lung cancer in smokers and non-smokers using analysis of genetic polymorphisms. The present invention also relates to the use of genetic polymorphisms in assessing a subject's risk of developing lung cancer. Nucleotide probes and primers, kits, and microarrays suitable for such assessment are also provided.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority to: New Zealand Application No. 540203, filed May 19, 2005; New Zealand Application No. 541787, filed Aug. 11, 2005; and New Zealand Application No. 543297, filed Oct. 28, 2005. All of the foregoing applications are incorporated by reference in their entireties.
FIELD OF THE INVENTION
The present invention is concerned with methods for assessment of pulmonary function and/or disorders, and in particular for assessing risk of developing lung cancer in smokers and non-smokers using analysis of genetic polymorphisms and altered gene expression.
BACKGROUND OF THE INVENTION
Lung cancer is the second most common cancer and has been attributed primarily to cigarette smoking. Other factors contributing to the development of lung cancer include occupational exposure, genetic factors, radon exposure, exposure to other aero-pollutants and possibly dietary factors (Alberg, A. J. et al. Epidemiology of lung cancer. Chest 123:21s-49s, (2003), herein incorporated by reference in its entirety). Non-smokers are estimated to have a one in 400 risk of lung cancer (0.25%). Smoking increases this risk by approximately 40 fold, such that smokers have a one in 10 risk of lung cancer (10%) and in long-term smokers the life-time risk of lung cancer has been reported to be as high 10-15% (Schwartz, A. G. Genetic predisposition to lung cancer. Chest 125:86s-89s, (2004), herein incorporated by reference in its entirety). Genetic factors are thought to play some part as evidenced by a weak familial tendency (among smokers) and the fact that only the minority of smokers get lung cancer. It is generally accepted that the majority of this genetic tendency comes from low penetrant high frequency polymorphisms, that is, polymorphisms which are common in the general population that in context of chronic smoking exposure contribute collectively to cancer development (Schwartz, A G. 2004; Wu, X. et al. Genetic susceptibility to tobacco-related cancer. Oncogene 23:6500-6523, (2004), each of the foregoing which is incorporated by reference in its entirety). Several epidemiological studies have reported that impaired lung function (Anthonisen, N. R. Prognosis in COPD: Results from multi-center clinical trials. Am Rev Respir Dis 140:s95-s99, (1989); Skillrud, D. M. et al. Higher risk of lung cancer in COPD: A prospective matched controlled study. Ann Int Med 105:503-507, (1986); Tockman, M. S. et al. Airways obstruction and the risk for lung cancer. Ann Int Med 106:512-518, (1987); Kuller, L. H. et al. Relation of forced expiratory volume in one second to lung cancer mortality in the MRFIT. Am J Epidmiol 132:265-274, (1990); Nomura, A. et al. Prospective study of pulmonary function and lung cancer. Am Rev Respir Dis 144:307-311, (1991); each of the foregoin which is incorporated by reference in its entirety) or symptoms of obstructive lung disease (Mayne, S. T. et al. Previous lung disease and risk of lung cancer among men and women nonsmokers. Am J Epidemiol 149:13-20, (1999), herein incorporated by reference in its entirety) are independent risk factors for lung cancer and are possibly more relevant than smoking exposure dose.
Despite advances in the treatment of airways disease, current therapies do not significantly alter the natural history of lung cancer, which can include metastasis and progressive loss of lung function causing respiratory failure and death. Although cessation of smoking can be expected to reduce this decline in lung function, it is probable that if this is not achieved at an early stage, the loss is considerable and symptoms of worsening breathlessness likely cannot be averted. Analogous to the discovery of serum cholesterol and its link to coronary artery disease, there is a need to better understand the factors that contribute to lung cancer so that tests that identify at risk subjects can be developed and that new treatments can be discovered to reduce the adverse effects of lung cancer. The early diagnosis of lung cancer or of a propensity to developing lung cancer enables a broader range of prophylactic or therapeutic treatments to be employed than can be employed in the treatment of late stage lung cancer. Such prophylactic or early therapeutic treatment is also more likely to be successful, achieve remission, improve quality of life, and/or increase lifespan.
To date, a number of biomarkers useful in the diagnosis and assessment of propensity towards developing various pulmonary disorders have been identified. These include, for example, single nucleotide polymorphisms including the following: A-82G in the promoter of the gene encoding human macrophage elastase (MMP12); T→C within codon 10 of the gene encoding transforming growth factor beta (TGFβ); C+760G of the gene encoding superoxide dismutase 3 (SOD3); T-1296C within the promoter of the gene encoding tissue inhibitor of metalloproteinase 3 (TIMP3); and polymorphisms in linkage disequilibrium with these polymorphisms, as disclosed in PCT International Application PCT/NZ02/00106 (published as WO 02/099134 and herein incorporated by reference in its entirety).
SUMMARY OF THE INVENTION
In some aspects, the present invention is primarily based on the finding that certain polymorphisms are found more often in subjects with lung cancer than in control subjects. Analysis of these polymorphisms reveals an association between polymorphisms and the subject's risk of developing lung cancer.
Thus, according to some aspects there is provided a method of determining a subject's risk of developing lung cancer including analyzing a sample from said subject for the presence or absence of one or more polymorphisms selected from the group consisting of: Asp 298 Glu in the gene encoding Nitric oxide synthase 3 (NOS3); −786 T/C in the promoter of the gene encoding NOS3; Arg 312 Gln in the gene encoding Superoxide dismutase 3 (SOD3); Ala 15 Thr in the gene encoding Anti-chymotrypsin (ACT); Asn 357 Ser A/G in the gene encoding Matrix metalloproteinase 12 (MMP12); 105 A/C in the gene encoding Interleukin-18 (IL-18); −133 G/C in the promoter of the gene encoding Interleukin-18; 874 A/T in the gene encoding Interferon gamma (IFNγ); −765 G/C in the gene encoding Cyclooxygenase 2 (COX2); −447 G/C in the gene encoding Connective tissue growth factor (CTGF); −221 C/T in the gene encoding Mucin 5AC (MUC5AC); +161 G/A in the gene encoding Mannose binding lectin 2 (MBL2); intron 1 C/T in the gene encoding Arginase 1 (Arg1); Leu 252 Val C/G in the gene encoding Insulin-like growth factor II receptor (IGF2R); and −1082 A/G in the gene encoding Interleukin 10 (IL-10), wherein the presence or absence of one or more of said polymorphisms is indicative of the subject's risk of developing lung cancer. The one or more polymorphisms can be detected directly or by detection of one or more polymorphisms which are in linkage disequilibrium with said one or more polymorphisms. Linkage disequilibrium (LD) is a phenomenon in genetics whereby two or more mutations or polymorphisms are in such close genetic proximity that they are co-inherited. This means that in genotyping, detection of one polymorphism as present implies the presence of the other. (Reich DE et al; Linkage disequilibrium in the human genome, Nature 2001, 411:199-204, herein incorporated by reference in its entirety.)
In some embodiments, the method can additionally include analyzing a sample from said subject for the presence of one or more further polymorphisms selected from the group consisting of: Arg 399 Gln G/A in the X-ray repair complementing defective in Chinese hamster 1 (XRCC1) gene; −251 A/T in the gene encoding Interleukin-8 (IL-8); A870G in the gene encoding Cyclin D (CCND1); −511 A/G in the gene encoding Interleukin 1B (IL-1B); −670G in the gene encoding FAS (Apo-1/CD95); −751 G/T in the promoter of the Xeroderma pigmentosum complementation group D (XPD) gene; Ile 462 Val A/G in the gene encoding Cytochrome P450 1A1 (CYP1A1); Ser 326 Cys G/C in the gene encoding 8-Oxoguanine DNA glycolase (OGG1); Arg 197 Gln A/G in the gene encoding N-acetyltransferase 2 (NAT2); 1019 G/C Pst I in the gene encoding Cytochrome P450 2E1 (CYP2E1); C/T Rsa I in the gene encoding Cytochrome P450 2E1; GSTM null in the gene encoding Glutathione S-transferase M (GSTM); −1607 1G/2G in the promoter of the gene encoding Matrix metalloproteinase 1 (MMP1); Gln 185 Glu G/C in the gene encoding Nibrin (NBS1); Phe 257 Ser C/T in the gene encoding REV1; and Asp 148 Glu G/T in the gene encoding Apex nuclease (APE1).
Again, detection of the one or more further polymorphisms can be carried out directly or by detection of polymorphisms in linkage disequilibrium with the one or more further polymorphisms.
In some embodiments, the presence of one or more polymorphisms selected from the group consisting of: the Asp 298 Glu TT genotype in the gene encoding NOS3; the Arg 312 Gln CG or GG genotype in the gene encoding SOD3; the Asn 357 Ser AG or GG genotype in the gene encoding MMP12; the 105 AC or CC genotype in the gene encoding IL-18; the −133 CG or GG genotype in the gene encoding IL-18; the −765 CC or CG genotype in the promoter of the gene encoding COX2; the −221 TT genotype in the gene encoding MUC5AC; the intron 1 C/T TT genotype in the gene encoding Arg1; the Leu252Val GG genotype in the gene encoding IGF2R; the −1082 GG genotype in the gene encoding IL-10; the −251 AA genotype in the gene encoding IL-8; the Arg 399 Gln AA genotype in the XRCC1 gene; the A870G GG genotype in the gene encoding CCND1; the −751 GG genotype in the promoter of the XPD gene; the Ile 462 Val AG or GG genotype in the gene encoding CYP1A1; the Ser 326 Cys GG genotype in the gene encoding OGG1; and the Phe 257 Ser CC genotype in the gene encoding REV1 can be indicative of a reduced risk of developing lung cancer.
In some embodiments, the presence of one or more polymorphisms selected from the group consisting of: the −786 TT genotype in the promoter of the gene encoding NOS3; the Ala 15 Thr GG genotype in the gene encoding ACT; the 105 AA genotype in the gene encoding IL-18; the −133 CC genotype in the promoter of the gene encoding IL-18; the 874 AA genotype in the gene encoding IFNγ; the −765 GG genotype in the promoter of the gene encoding COX2; the −447 CC or GC genotype in the gene encoding CTGF; the +161 AA or AG genotype in the gene encoding MBL2; the −511 GG genotype in the gene encoding IL-1B; the A-670G AA genotype in the gene encoding FAS; the Arg 197 Gln GG genotype in the gene encoding NAT2; the Ile462 Val AA genotype in the gene encoding CYP1A1; the 1019 G/C Pst I CC or CG genotype in the gene encoding CYP2E1; the C/T Rsa I TT or TC genotype in the gene encoding CYP2E1; the GSTM null genotype in the gene encoding GSTM; the −1607 2G/2G genotype in the promoter of the gene encoding MMP1; the Gln 185 Glu CC genotype in the gene encoding NBS1; and the Asp 148 Glu GG genotype in the gene encoding APE1, can be indicative of an increased risk of developing lung cancer.
In some embodiments, the methods of the invention are particularly useful in smokers (both current and former).
It will be appreciated that the methods of the invention identify two categories of polymorphisms—namely those associated with a reduced risk of developing lung cancer (which can be termed “protective polymorphisms”) and those associated with an increased risk of developing lung cancer (which can be termed “susceptibility polymorphisms”).
Therefore, in some embodiments, the present invention further provides a method of assessing a subject's risk of developing lung cancer, said method including: determining the presence or absence of at least one protective polymorphism associated with a reduced risk of developing lung cancer and in the absence of at least one protective polymorphism, determining the presence or absence of at least one susceptibility polymorphism associated with an increased risk of developing lung cancer. The presence of one or more of said protective polymorphisms is indicative of a reduced risk of developing lung cancer, and the absence of at least one protective polymorphism in combination with the presence of at least one susceptibility polymorphism is indicative of an increased risk of developing lung cancer.
In some embodiments, said at least one protective polymorphism is selected from the group consisting of: the Asp 298 Glu TT genotype in the gene encoding NOS3; the Arg 312 Gln CG or GG genotype in the gene encoding SOD3; the Asn 357 Ser AG or GG genotype in the gene encoding MMP12; the 105 AC or CC genotype in the gene encoding IL-18; the −133 CG or GG genotype in the gene encoding IL-18; the −765 CC or CG genotype in the promoter of the gene encoding COX2; the −221 TT genotype in the gene encoding MUC5AC; the intron 1 C/T TT genotype in the gene encoding Arg1; the Leu252Val GG genotype in the gene encoding IGF2R; the −1082 GG genotype in the gene encoding IL-10; the −251 AA genotype in the gene encoding IL-8; the Arg 399 Gln AA genotype in the XRCC1 gene; the A870G GG genotype in the gene encoding CCND1; the −751 GG genotype in the promoter of the XPD gene; the Ile 462 Val AG or GG genotype in the gene encoding CYP1A1; the Ser 326 Cys GG genotype in the gene encoding OGG1; and the Phe 257 Ser CC genotype in the gene encoding REV1.
In some embodiments, the at least one susceptibility polymorphism can be selected from the group consisting of: the −786 TT genotype in the promoter of the gene encoding NOS3; the Ala 15 Thr GG genotype in the gene encoding ACT; the 105 AA genotype in the gene encoding IL-18; the −133 CC genotype in the promoter of the gene encoding IL-18; the 874 AA genotype in the gene encoding IFNγ; the −765 GG genotype in the promoter of the gene encoding COX2; the −447 CC or GC genotype in the gene encoding CTGF; the +161 AA or AG genotype in the gene encoding MBL2; the −511 GG genotype in the gene encoding IL-1B; the A-670G AA genotype in the gene encoding FAS; the Arg 197 Gln GG genotype in the gene encoding NAT2; the Ile462 Val AA genotype in the gene encoding CYP1A1; the 1019 G/C Pst I CC or CG genotype in the gene encoding CYP2E1; the C/T Rsa I TT or TC genotype in the gene encoding CYP2E1; the GSTM null genotype in the gene encoding GSTM; the −1607 2G/2G genotype in the promoter of the gene encoding MMP1; the Gln 185 Glu CC genotype in the gene encoding NBS1; and the Asp 148 Glu GG genotype in the gene encoding APE1.
In some embodiments of the invention, the presence of two or more protective polymorphisms is indicative of a reduced risk of developing lung cancer.
In a further preferred form of some embodiments of the invention, the presence of two or more susceptibility polymorphisms is indicative of an increased risk of developing lung cancer. In still a further preferred form of the invention the presence of two or more protective polymorphims irrespective of the presence of one or more susceptibility polymorphisms is indicative of reduced risk of developing lung cancer.
In another aspect, the invention provides a method of determining a subject's risk of developing lung cancer, said method including obtaining the result of one or more genetic tests of a sample from said subject, and analyzing the result for the presence or absence of one or more polymorphisms selected from the group consisting of: Asp 298 Glu in the gene encoding Nitric oxide synthase 3 (NOS3); −786 T/C in the promoter of the gene encoding NOS3; Arg 312 Gln in the gene encoding Superoxide dismutase 3 (SOD3); Ala 15 Thr in the gene encoding Anti-chymotrypsin (ACT); Asn 357 Ser A/G in the gene encoding Matrix metalloproteinase 12 (MMP12); 105 A/C in the gene encoding Interleukin-18 (IL-18); −133 G/C in the promoter of the gene encoding Interleukin-18; 874 A/T in the gene encoding Interferon gamma (IFNγ); −765 G/C in the gene encoding Cyclooxygenase 2 (COX2); −447 G/C in the gene encoding Connective tissue growth factor (CTGF); −221 C/T in the gene encoding Mucin 5AC (MUC5AC); +161 G/A in the gene encoding Mannose binding lectin 2 (MBL2); intron 1 C/T in the gene encoding Arginase 1 (Arg1); Leu 252 Val C/G in the gene encoding Insulin-like growth factor II receptor (IGF2R); −1082 A/G in the gene encoding Interleukin 10 (IL-10); and one or more polymorphisms in linkage disequilibrium with any one or more of these polymorphisms. A result indicating the presence or absence of one or more of said polymorphisms is indicative of the subject's risk of developing lung cancer.
In a further aspect there is provided a method of determining a subject's risk of developing lung cancer including the analysis of two or more polymorphisms selected from the group consisting of: Asp 298 Glu in the gene encoding NOS3; −786 T/C in the promoter of the gene encoding NOS3; Arg 312 Gln in the gene encoding SOD3; −251 A/T in the gene encoding IL-8; Ala 15 Thr in the gene encoding ACT; Asn 357 Ser A/G in the gene encoding MMP12; 105 A/C in the gene encoding IL-18; −133 G/C in the promoter of the gene encoding IL-18; 874 A/T in the gene encoding IFNγ; Arg 399 Gln G/A in the XRCC1 gene; A870G in the gene encoding CCND1; −511 A/G in the gene encoding IL-1B; −670G in the gene encoding FAS (Apo-1/CD95); −751 G/T in the promoter of the XPD gene; Ile 462 Val A/G in the gene encoding CYP1A1; Ser 326 Cys G/C in the gene encoding OGG1; Arg 197 Gln A/G in the gene encoding NAT2; 1019 G/C Pst I in the gene encoding CYP2E1; C/T Rsa I in the gene encoding CYP2E1; GSTM null in the gene encoding GSTM; −765 C/G in the promoter of the gene encoding COX2; −1607 1G/2G in the promoter of the gene encoding MMP1; −447 G/C in the gene encoding CTGF; −221 C/T in the gene encoding MUC5AC; +161 G/A in the gene encoding MBL2; intron 1 C/T in the gene encoding Arg1; Leu 252 Val C/G in the gene encoding IGF2R; −1082 A/G in the gene encoding IL-10; Gln 185 Glu G/C in the gene encoding NBS1; Phe 257 Ser C/T in the gene encoding REV1; Asp 148 Glu G/T in the gene encoding APE1; and one or more polymorphisms in linkage disequilibrium with any one or more of these polymorphisms.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 298 of the gene encoding NOS3.
In some embodiments, the presence of glutamate at said position is indicative of an increased risk of developing lung cancer.
In some embodiments, the presence of asparagine at said position is indicative of reduced risk of developing lung cancer.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 312 in the gene encoding SOD3.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 15 in the gene encoding ACT.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 357 in the gene encoding MMP12.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 399 in the XRCC1 gene.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 462 in the gene encoding CYP1A1.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 326 in the gene encoding OGG1.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 197 in the gene encoding NAT2.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 185 in the gene encoding NBS1.
In some embodiments, the presence of glutamine at said position is indicative of an increased risk of developing lung cancer.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 257 in the gene encoding REV1.
In some embodiments, the presence of serine at said position is indicative of reduced risk of developing lung cancer.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 252 in the gene encoding IGF2R.
In some embodiments, the presence of valine at said position is indicative of reduced risk of developing lung cancer.
In various embodiments, any one or more of the above methods includes the step of analyzing the amino acid present at a position mapping to codon 148 in the, gene encoding APE1.
In some embodiments, the presence of glutamate at said position is indicative of an increased risk of developing lung cancer.
In a preferred form of the invention the methods as described herein are performed in conjunction with an analysis of one or more risk factors, including one or more epidemiological risk factors, associated with a risk of developing lung cancer. Such epidemiological risk factors include but are not limited to smoking or exposure to tobacco smoke, age, sex, and familial history of lung cancer.
In a further aspect, the invention provides for the use of at least one polymorphism in the assessment of a subject's risk of developing lung cancer, wherein said at least one polymorphism is selected from the group consisting of: Asp 298 Glu in the gene encoding Nitric oxide synthase 3 (NOS3); −786 T/C in the promoter of the gene encoding NOS3; Arg 312 Gln in the gene encoding Superoxide dismutase 3 (SOD3); Ala 15 Thr in the gene encoding Anti-chymotrypsin (ACT); Asn 357 Ser A/G in the gene encoding Matrix metalloproteinase 12 (MMP12); 105 A/C in the gene encoding Interleukin-18 (IL-18); −133 G/C in the promoter of the gene encoding Interleukin-18; 874 A/T in the gene encoding Interferon gamma (IFNγ); −765 G/C in the gene encoding Cyclooxygenase 2 (COX2); −447 G/C in the gene encoding Connective tissue growth factor (CTGF); −221 C/T in the gene encoding Mucin 5AC (MUC5AC); +161 G/A in the gene encoding Mannose binding lectin 2 (MBL2); intron 1 C/T in the gene encoding Arginase 1 (Arg1); Leu 252 Val C/G in the gene encoding Insulin-like growth factor II receptor (IGF2R); −1082 A/G in the gene encoding Interleukin 10 (IL-10); and one or more polymorphisms in linkage disequilibrium with any one of said polymorphisms.
Optionally, said use can be in conjunction with the use of at least one further polymorphism selected from the group consisting of: Arg 399 Gln G/A in the X-ray repair complementing defective in Chinese hamster 1 (XRCC1) gene; −251 A/T in the gene encoding Interleukin-8 (IL-8); A870G in the gene encoding Cyclin D (CCND1); −511 A/G in the gene encoding Interleukin 1B (IL-1B); −670G in the gene encoding FAS (Apo-1/CD95); −751 G/T in the promoter of the Xeroderma pigmentosum complementation group D (XPD) gene; Ile 462 Val A/G in the gene encoding Cytochrome P450 1A1 (CYP1A1); Ser 326 Cys G/C in the gene encoding 8-Oxoguanine DNA glycolase (OGG1); Arg 197 Gln A/G in the gene encoding N-acetyltransferase 2 (NAT2); 1019 G/C Pst I in the gene encoding Cytochrome P450 2E1 (CYP2E1); C/T Rsa I in the gene encoding Cytochrome P450 2E1; GSTM null in the gene encoding Glutathione S-transferase M (GSTM); −1607 1G/2G in the promoter of the gene encoding Matrix metalloproteinase 1 (MMP1); Gln 185 Glu G/C in the gene encoding Nibrin (NBS1); Phe 257 Ser C/T in the gene encoding REV1; Asp 148 Glu G/T in the gene encoding Apex nuclease (APE1); and one or more polymorphisms which are in linkage disequilibrium with any one or more of these polymorphisms.
In another aspect, the invention provides a set of nucleotide probes and/or primers for use in the preferred methods of the invention herein described. Preferably, the nucleotide probes and/or primers are those which span, or are able to be used to span, the polymorphic regions of the genes. Also provided are one or more nucleotide probes and/or primers including the sequence of any one of the probes and/or primers herein described, including any one including the sequence of any one of SEQ.ID. NO. 1 to 145, more preferably any one of SEQ.ID.NO. 3 to 142.
In yet a further aspect, the invention provides a nucleic acid microarray for use in the methods of the invention, which microarray includes a substrate presenting nucleic acid sequences capable of hybridizing to nucleic acid sequences which encode one or more of the susceptibility or protective polymorphisms described herein or sequences complimentary thereto.
In another aspect, the invention provides an antibody microarray for use in the methods of the invention, which microarray includes a substrate presenting antibodies capable of binding to a product of expression of a gene the expression of which is upregulated or downregulated when associated with a susceptibility or protective polymorphism as described herein.
In a further aspect, the present invention provides a method treating a subject having an increased risk of developing lung cancer including the step of replicating, genotypically or phenotypically, the presence and/or functional effect of a protective polymorphism in said subject.
In yet a further aspect, the present invention provides a method of treating a subject having an increased risk of developing lung cancer, said subject having a detectable susceptibility polymorphism which either upregulates or downregulates expression of a gene such that the physiologically active concentration of the expressed gene product is outside a range which is normal for the age and sex of the subject, said method including the step of restoring the physiologically active concentration of said product of gene expression to be within a range which is normal for the age and sex of the subject.
In a further aspect, the present invention provides a method of treating a subject having an increased risk of developing lung cancer and for whom the presence of the AA genotype at the 105 C/A polymorphism in the gene encoding IL-18 has been determined, said method including administering to said subject an agent capable of augmenting IL-18 activity in said subject.
In yet a further aspect, the present invention provides a method of treating a subject having an increased risk of developing lung cancer and for whom the presence of the CC genotype at the −133 G/C polymorphism in the promoter of the gene encoding IL-18 has been determined, said method including administering to said subject an agent capable of augmenting IL-18 activity in said subject.
In yet a further aspect, the present invention provides a method for screening for compounds that modulate the expression and/or activity of a gene, the expression of which is upregulated or downregulated when associated with a susceptibility or protective polymorphism, said method including the steps of: contacting a candidate compound with a cell including a susceptibility or protective polymorphism which has been determined to be associated with the upregulation or downregulation of expression of a gene, and measuring the expression of said gene following contact with said candidate compound. A change in the level of expression after the contacting step as compared to before the contacting step is indicative of the ability of the compound to modulate the expression and/or activity of said gene. Preferably, the cell is a human lung cell which has been pre-screened to confirm the presence of said polymorphism. Preferably, said cell includes a susceptibility polymorphism associated with upregulation of expression of said gene and said screening is for candidate compounds which downregulate expression of said gene. Alternatively, said cell includes a susceptibility polymorphism associated with downregulation of expression of said gene and said screening is for candidate compounds which upregulate expression of said gene.
In another embodiment, said cell includes a protective polymorphism associated with upregulation of expression of said gene and said screening is for candidate compounds which further upregulate expression of said gene. Alternatively, said cell includes a protective polymorphism associated with downregulation of expression of said gene and said screening is for candidate compounds which further downregulate expression of said gene.
In another aspect, the present invention provides a method for screening for compounds that modulate the expression and/or activity of a gene, the expression of which is upregulated or downregulated when associated with a susceptibility or protective polymorphism, said method includes the steps of: contacting a candidate compound with a cell including a gene, the expression of which is upregulated or downregulated when associated with a susceptibility or protective polymorphism but which in said cell the expression of which is neither upregulated nor downregulated; and measuring the expression of said gene following contact with said candidate compound. A change in the level of expression after the contacting step as compared to before the contacting step is indicative of the ability of the compound to modulate the expression and/or activity of said gene. Preferably, expression of the gene is downregulated when associated with a susceptibility polymorphism once said screening is for candidate compounds which in said cell, upregulate expression of said gene. Preferably, said cell is a human lung cell which has been pre-screened to confirm the presence, and baseline level of expression, of said gene. Alternatively, expression of the gene is upregulated when associated with a susceptibility polymorphism and said screening is for candidate compounds which, in said cell, downregulate expression of said gene.
In another embodiment, expression of the gene is upregulated when associated with a protective polymorphism and said screening is for compounds which, in said cell, upregulate expression of said gene. Alternatively, expression of the gene is downregulated when associated with a protective polymorphism and said screening is for compounds which, in said cell, downregulate expression of said gene.
In yet a further aspect, the present invention provides a method of assessing the likely responsiveness of a subject at risk of developing or suffering from lung cancer to a prophylactic or therapeutic treatment, which treatment involves restoring the physiologically active concentration of a product of gene expression to be within a range which is normal for the age and sex of the subject, which method includes detecting in said subject the presence or absence of a susceptibility polymorphism which when present either upregulates or downregulates expression of said gene such that the physiological active concentration of the expressed gene product is outside said normal range, wherein the detection of the presence of said polymorphism is indicative of the subject likely responding to said treatment.
In still a further aspect the present invention provides a method of treating a subject having an increased risk of developing lung cancer and for whom the presence of the GG genotype at the −765 C/G polymorphism present in the promoter of the gene encoding COX2 has been determined. The method includes administering to said subject an agent capable of reducing COX2 activity in said subject. In one embodiment, the agent is a COX2 inhibitor or a nonsteroidal anti-inflammatory drug (NSAID), preferably the COX2 inhibitor is selected from the group consisting of CelebrexTM (Celecoxib), BextraTM (Valdecoxib), and VioxxTM (Rofecoxib).
In yet still a further aspect the present invention provides a method of treating a subject having an increased risk of developing or cancer and for whom the presence of the 2G2G genotype at the −1607 1G/2G polymorphism in the promoter of the gene encoding MMP1 has been determined, said method including administering to the subject an agent capable of reducing MMP1 activity in the subject.
In one embodiment, the agent is an agent capable of increasing expression of or the activity of one or more tissue inhibitors of metalloproteinases (TIMPs), preferably the expression or activity of one or more of TIMP1, TIMP2, TIMP3, or TIMP4. In a further embodiment, said agent is an agent capable of reducing expression of or the activity of one or more membrane bound MMPs. In still a futher embodiment, said agent is a MMP inhibitor, preferably the MMP inhibitor is selected from the group including 4,5-dihydroxyanthaquinone-2-carboxylic acid (AQCA), anthraquinyl-mercaptoethyamine, anthraquinyl-alanine hydroxamate, and derivatives thereof.
In a further aspect, the present invention provides a kit for assessing a subject's risk of developing lung cancer, said kit including a means of analyzing a sample from said subject for the presence or absence of one or more polymorphisms disclosed herein.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 depicts a graph showing the percentage of people with lung cancer plotted against the number of protective polymorphisms.
FIG. 2 depicts a graph showing the percentage of people with lung cancer plotted against the number of susceptibility polymorphisms.
FIG. 3 depicts a graph showing the frequency of protective polymorphisms in smokers with lung cancer and in resistant smokers.
FIG. 4 depicts a graph showing the frequency of susceptibility polymorphisms in smokers with lung cancer and in resistant smokers.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
Additional biomarkers which can be used to assess a subject's risk of developing pulmonary disorders such as lung cancer, or a risk of developing lung cancer-related impaired lung function, can be desireable, particularly if the subject is a smoker. In some aspects, it is primarily to such biomarkers and their use in methods to assess risk of developing such disorders that the present invention is directed.
Using case-control studies the frequencies of several genetic variants (polymorphisms) of candidate genes in smokers who have developed lung cancer and blood donor controls have been compared. The majority of these candidate genes have confirmed (or likely) functional effects on gene expression or protein function. Specifically the frequencies of polymorphisms between blood donor controls, resistant smokers and those with lung cancer (subdivided into those with early onset and those with normal onset) have been compared. The present invention demonstrates that there are both protective and susceptibility polymorphisms present in selected candidate genes of the patients tested.
In one embodiment described herein 19 susceptibility genetic polymorphisms and 17 protective genetic polymorphisms are identified. These are as follows in Table 1A:









TABLE 1A





Gene
Polymorphism
Role







Nitric Oxide synthase 3 (NOS3)
NOS3 Asp 298 Glu
TT protective


Nitric Oxide synthase 3 (NOS3)
NOS3 −786 T/C
TT susceptibility


Superoxide dismutase 3 (SOD3)
SOD3 Arg 312 Gln
CG/GG protective


XRCC1
XRCC1 Arg 399 Gln G/A
AA protective


Interleukin-8 (IL-8)
IL-8 −251 A/T
AA protective


Anti-chymotrypsin (ACT)
ACT Ala 15 Thr
GG susceptibility


Cyclin D (CCND1)
CCND1 A870G
GG protective




AA susceptibility


Interleukin 1B (IL-1B)
IL-1B −511 A/G
GG susceptibility


FAS (Apo-1/CD95)
FAS A-670G
AA susceptibility


XPD
XPD −751 G/T
GG protective


CYP 1A1
CYP 1A1 Ile 462 Val A/G
GG/AG protective




AA susceptibility


Matrix metalloproteinase 12 (MMP12)
MMP12 Asn 357 Ser A/G
GG/AG protective


8-Oxoguanine DNA glycolase (OGG1)
OGG1 Ser 326 Cys G/C
GG protective


N-acetyltransferase 2 (NAT2)
NAT2 Arg 197 Gln A/G
GG susceptibility


CYP2E1
CYP2E1 1019 G/C Pst I
CC/CG susceptibility


CYP2E1
GYP2E1 C/T Rsa I
TT/TC susceptibility


Interleukin-18 (IL-18)
IL-18 105 A/C
AC/CC protective




AA susceptibility


Interleukin-18 (IL-18)
IL-18 −133 G/C
CG/GG protective




CC susceptibility


Glutathione S-transferase M
GSTM null
Null susceptibility


Interferon gamma (IFNγ)
IFNγ 874 A/T
AA susceptibility


Cyclooxygenase 2 (COX2)
COX2 −765 C/G
CC/CG protective




GG susceptibility


Matrix metalloproteinase 1 (MMP1)
MMP1 −1607 1G/2G
2G susceptibility


Connective tissue growth factor (CTGF)
CTGF −447 G/C
CG/CC susceptibility


Mucin 5AC (MUC5AC)
MUC5AC −221 C/T
TT protective


Mannose binding lectin 2 (MBL2)
MBL2 +161 G/A
AG/AA susceptibility


Nibrin (NBS1)
NBS1 Gln185Glu G/C
CC susceptibility


Arginase 1 (Arg1)
Arg1 intron 1 C/T
TT protective


REV1
REV1 Phe257Ser C/T
CC protective


Insulin-like growth factor II receptor (IGF2R)
IGF2R Leu252Val C/G
GG protective


Apex nuclease (Apex or APE1))
Apex Asp148Glu G/T
GG susceptibility


Interleukin 10 (IL-10)
IL-10 −1082 A/G
GG protective









A susceptibility genetic polymorphism is one which, when present, is indicative of an increased risk of developing lung cancer. In contrast, a protective genetic polymorphism is one which, when present, is indicative of a reduced risk of developing lung cancer.
As used herein, the phrase “risk of developing lung cancer” means the likelihood that a subject to whom the risk applies will develop lung cancer, and includes predisposition to, and potential onset of the disease. Accordingly, the phrase “increased risk of developing lung cancer” means that a subject having such an increased risk possesses an hereditary inclination or tendency to develop lung cancer. This does not mean that such a person will actually develop lung cancer at any time, merely that he or she has a greater likelihood of developing lung cancer compared to the general population of individuals that either does not possess a polymorphism associated with increased lung cancer or does possess a polymorphism associated with decreased lung cancer risk. Subjects with an increased risk of developing lung cancer include those with a predisposition to lung cancer, such as a tendency or predilection regardless of their lung function at the time of assessment, for example, a subject who is genetically inclined to lung cancer but who has normal lung function, those at potential risk, including subjects with a tendency to mildly reduced lung function who are likely to go on to suffer lung cancer if they keep smoking, and subjects with potential onset of lung cancer, who have a tendency to poor lung function on spirometry etc., consistent with lung cancer at the time of assessment.
Similarly, the phrase “decreased risk of developing lung cancer” means that a subject having such a decreased risk possesses an hereditary disinclination or reduced tendency to develop lung cancer. This does not mean that such a person will not develop lung cancer at any time, merely that he or she has a decreased likelihood of developing lung cancer compared to the general population of individuals that either does possess one or more polymorphisms associated with increased lung cancer, or does not possess a polymorphism associated with decreased lung cancer.
It will be understood that in the context of the present invention the term “polymorphism” means the occurrence together in the same population at a rate greater than that attributable to random mutation (usually greater than 1%) of two or more alternate forms (such as alleles or genetic markers) of a chromosomal locus that differ in nucleotide sequence or have variable numbers of repeated nucleotide units. See www “dot” ornl “dot” gov/sci/techresources/Human_Genome/publicat/97pr/09gloss “dot” html#p. Accordingly, the term “polymorphisms” is used herein contemplates genetic variations, including single nucleotide substitutions, insertions and deletions of nucleotides, repetitive sequences (such as microsatellites), and the total or partial absence of genes (eg. null mutations). As used herein, the term “polymorphisms” also includes genotypes and haplotypes. A genotype is the genetic composition at a specific locus or set of loci. A haplotype is a set of closely linked genetic markers present on one chromosome which are not easily separable by recombination, tend to be inherited together, and can be in linkage disequilibrium. A haplotype can be identified by patterns of polymorphisms such as SNPs. Similarly, in some embodiments, the term “single nucleotide polymorphism” or “SNP” in the context of the present invention includes single base nucleotide subsitutions and short deletion and insertion polymorphisms. In other embodiments, the terms only refer to single base nucleotide substitutions, deletions, and insertions.
A reduced or increased risk of a subject developing lung cancer can be diagnosed by analyzing a sample from said subject for the presence of a polymorphism selected from the group consisting of: Asp 298 Glu in the gene encoding Nitric oxide synthase 3 (NOS3); −786 T/C in the promoter of the gene encoding NOS3; Arg 312 Gln in the gene encoding Superoxide dismutase 3 (SOD3); Ala 15 Thr in the gene encoding Anti-chymotrypsin (ACT); Asn 357 Ser A/G in the gene encoding Matrix metalloproteinase 12 (MMP12); 105 A/C in the gene encoding Interleukin-18 (IL-18); −133 G/C in the promoter of the gene encoding Interleukin-18; 874 A/T in the gene encoding Interferon gamma (IFNγ); −765 G/C in the gene encoding Cyclooxygenase 2 (COX2); −447 G/C in the gene encoding Connective tissue growth factor (CTGF); −221 C/T in the gene encoding Mucin SAC (MUC5AC); +161 G/A in the gene encoding Mannose binding lectin 2 (MBL2); intron 1 C/T in the gene encoding Arginase 1 (Arg1); Leu 252 Val C/G in the gene encoding Insulin-like growth factor II receptor (IGF2R); and −1082 A/G in the gene encoding Interleukin 10 (IL-10), or one or more polymorphisms which are in linkage disequilibrium with any one or more of the above group.
These polymorphisms can also be analysed in combinations of two or more, or in combination with other polymorphisms indicative of a subject's risk of developing lung cancer inclusive of the remaining polymorphisms listed above.
Expressly contemplated are combinations of the above polymorphisms with polymorphisms as described in PCT International application PCT/NZ02/00106, published as WO 02/099134 (herein incorporated by reference in its entirety).
Assays which involve combinations of polymorphisms, including those amenable to high throughput, such as those utilising microarrays, are preferred.
Statistical analyses, particularly of the combined effects of these polymorphisms, show that the genetic analyses of the present invention can be used to determine the risk quotient of any smoker and in particular to identify smokers at greater risk of developing lung cancer. Such combined analysis can be of combinations of susceptibility polymorphisms only, of protective polymorphisms only, or of combinations of both. Analysis can also be step-wise, with analysis of the presence or absence of protective polymorphisms occurring first and then with analysis of susceptibility polymorphisms proceeding only where no protective polymorphisms are present.
Thus, through systematic analysis of the frequency of these polymorphisms in well defined groups of smokers and non-smokers, as described herein, it is possible to implicate certain proteins in the development of lung cancer and improve the ability to identify which smokers are at increased risk of developing lung cancer-related impaired lung function and lung cancer for predictive purposes.
The present results show for the first time that the minority of smokers who develop lung cancer do so because they have one or more of the susceptibility polymorphisms and few or none of the protective polymorphisms defined herein. It is thought that the presence of one or more suscetptible polymorphisms, together with the damaging irritant and oxidant effects of smoking, combine to make this group of smokers highly susceptible to developing lung cancer. Additional risk factors, such as familial history, age, weight, pack years, etc., will also have an impact on the risk profile of a subject, and can be assessed in combination with the genetic analyses described herein.
The one or more polymorphisms can be detected directly or by detection of one or more polymorphisms which are in linkage disequilibrium with said one or more polymorphisms. As discussed above, linkage disequilibrium is a phenomenon in genetics whereby two or more mutations or polymorphisms are in such close genetic proximity that they are co-inherited. This means that in genotyping, detection of one polymorphism as present implies the presence of the other. (Reich D E et al; Linkage disequilibrium in the human genome, Nature 2001, 411:199-204, herein incorporated by reference in its entirety.)
Examples of polymorphisms described herein that have been reported to be in linkage disequilibrium are presented herein, and include the Interleukin-18 −133 C/G and 105 A/C polymorphisms, and the CYP2E1, 1019 G/C PstI and C/T RsaI polymorphisms, as shown below in Table 1B.












TABLE 1B







rs
Alleles in
LD between
Phenotype in


Gene
SNPs
numbers
LD
alleles
lung cancer







Interleukin-18
IL18 −133 C/G
rs360721
C allele
Strong LD
CC susceptibility



IL18 105 A/C
rs549908
A allele

AA susceptibility


CYP2E1
CYP2E1 1019 G/C PstI
rs3813867
C allele
Strong LD
CG susceptibility



CYP2E1 C/T RsaI
rs2031920
T allele

TC susceptibility









It will be apparent that polymorphsisms in linkage disequilibrium with one or more other polymorphism associated with increased or decreased risk of developing lung cancer will also provide utility as biomarkers for risk of developing lung cancer. The data presented herein shows that the frequency for SNPs in linkage disequilibrium is very similar. Accordingly, these genetically linked SNPs can be utilized in combined polymorphism analyses to derive a level of risk comparable to that calculated from the original SNP.
It will therefore be apparent that one or more polymorphisms in linkage disequilibrium with the polymorphisms specified herein can be identified, for example, using public data bases. Examples of such polymorphisms reported to be in linkage disequilibrium with the polymorphisms specified herein are presented herein in Table 36.
It will also be apparent that frequently a variety of nomenclatures may exist for any given polymorphism. For example, the polymorphism referred to herein as Arg 312 Gln in the gene encoding SOD3 is believed to have been referred to variously as Arg 213 Gly, +760 G/C, and Arg 231 Gly (rs1799895). When referring to a susceptibility or protective polymorphism as herein described, such alternative nomenclatures are also contemplated by the present invention.
The methods of the invention are primarily directed to the detection and identification of the above polymorphisms associated with lung cancer, which are all single nucleotide polymorphisms. In general terms, a single nucleotide polymorphism (SNP) is a single base change or point mutation resulting in genetic variation between individuals. SNPs occur in the human genome approximately once every 100 to 300 bases, and can occur in coding or non-coding regions. Due to the redundancy of the genetic code, a SNP in the coding region may or may not change the amino acid sequence of a protein product. A SNP in a non-coding region can, for example, alter gene expression by, for example, modifying control regions such as promoters, transcription factor binding sites, processing sites, ribosomal binding sites, and affect gene transcription, processing, and translation.
SNPs can facilitate large-scale association genetics studies, and there has recently been great interest in SNP discovery and detection. SNPs show great promise as markers for a number of phenotypic traits (including latent traits), such as for example, disease propensity and severity, wellness propensity, and drug responsiveness including, for example, susceptibility to adverse drug reactions. Knowledge of the association of a particular SNP with a phenotypic trait, coupled with the knowledge of whether an individual has said particular SNP, can enable the targeting of diagnostic, preventative and therapeutic applications to allow better disease management, to enhance understanding of disease states and to ultimately facilitate the discovery of more effective treatments, such as personalised treatment regimens;
Indeed, a number of databases have been constructed of known SNPs, and for some such SNPs, the biological effect associated with a SNP. For example, the NCBI SNP database “dbSNP” is incorporated into NCBI's Entrez system and can be queried using the same approach as the other Entrez databases such as PubMed and GenBank. This database has records for over 1.5 million SNPs mapped onto the human genome sequence. Each dbSNP entry includes the sequence context of the polymorphism (i.e., the surrounding sequence), the occurrence frequency of the polymorphism (by population or individual), and the experimental method(s), protocols, and conditions used to assay the variation, and can include information associating a SNP with a particular phenotypic trait.
At least in part because of the potential impact on health and wellness, there has been and continues to be a great deal of effort to develop methods that reliably and rapidly identify SNPs. This is no trivial task, at least in part because of the complexity of human genomic DNA, with a haploid genome of 3×109 base pairs, and the associated sensitivity and discriminatory requirements.
Genotyping approaches to detect SNPs well-known in the art include DNA sequencing, methods that require allele specific hybridization of primers or probes, allele specific incorporation of nucleotides to primers bound close to or adjacent to the polymorphisms (often referred to as “single base extension”, or “minisequencing”), allele-specific ligation (joining) of oligonucleotides (ligation chain reaction or ligation padlock probes), allele-specific cleavage of oligonucleotides or PCR products by restriction enzymes (restriction fragment length polymorphisms analysis or RFLP) or chemical or other agents, resolution of allele-dependent differences in electrophoretic or chromatographic mobilities, by structure specific enzymes including invasive structure specific enzymes, or mass spectrometry. Analysis of amino acid variation is also possible where the SNP lies in a coding region and results in an amino acid change.
DNA sequencing allows the direct determination and identification of SNPs. The benefits in specificity and accuracy are generally outweighed for screening purposes by the difficulties inherent in whole genome, or even targeted subgenome, sequencing.
Mini-sequencing involves allowing a primer to hybridize to the DNA sequence adjacent to the SNP site on the test sample under investigation. The primer is extended by one nucleotide using all four differentially tagged fluorescent dideoxynucleotides (A,C,G, or T), and a DNA polymerase. Only one of the four nucleotides (homozygous case) or two of the four nucleotides (heterozygous case) is incorporated. The base that is incorporated is complementary to the nucleotide at the SNP position.
A number of methods currently used for SNP detection involve site-specific and/or allele-specific hybridisation (Matsuzaki, H. et al. Genome Res. 14:414-425 (2004); Matsuzaki, H. et al. Nat. Methods 1:109-111 (2004); Sethi, A. A. et al. Clin. Chem. 50(2):443-446 (2004), each of the foregoing which is herein incorporated by reference in its entirety). These methods are largely reliant on the discriminatory binding of oligonucleotides to target sequences containing the SNP of interest. The techniques of Affymetrix (Santa Clara, Calif.) and Nanogen Inc. (San Diego, Calif.) are particularly well-known, and utilize the fact that DNA duplexes containing single base mismatches are much less stable than duplexes that are perfectly base-paired. The presence of a matched duplex is detected by fluorescence.
The majority of methods to detect or identify SNPs by site-specific hybridisation require target amplification by methods such as PCR to increase sensitivity and specificity (see, for example U.S. Pat. No. 5,679,524, PCT publication WO 98/59066, PCT publication WO 95/12607, each of the foregoing which is herein incorporated by reference in its entirety). US Application 20050059030 (herein incorporated by reference in its entirety) describes a method for detecting a single nucleotide polymorphism in total human DNA without prior amplification or complexity reduction to selectively enrich for the target sequence, and without the aid of any enzymatic reaction. The method utilises a single-step hybridization involving two hybridization events: hybridization of a first portion of the target sequence to a capture probe, and hybridization of a second portion of said target sequence to a detection probe. Both hybridization events happen in the same reaction, and the order in which hybridisation occurs is not critical.
US Application 20050042608 (herein incorporated by reference in its entirety) describes a modification of the method of electrochemical detection of nucleic acid hybridization of Thorp et al. (U.S. Pat. No. 5,871,918, herein incorporated by reference in its entirety). Briefly, capture probes are designed, each of which has a different SNP base and a sequence of probe bases on each side of the SNP base. The probe bases are complementary to the corresponding target sequence adjacent to the SNP site. Each capture probe is immobilized on a different electrode having a non-conductive outer layer on a conductive working surface of a substrate. The extent of hybridization between each capture probe and the nucleic acid target is detected by detecting the oxidation-reduction reaction at each electrode, utilizing a transition metal complex. These differences in the oxidation rates at the different electrodes are used to determine whether the selected nucleic acid target has a single nucleotide polymorphism at the selected SNP site.
The technique of Lynx Therapeutics (Hayward, Calif.) using MEGATYPETM technology can genotype very large numbers of SNPs simultaneously from small or large pools of genomic material. This technology uses fluorescently labeled probes and compares the collected genomes of two populations, enabling detection and recovery of DNA fragments spanning SNPs that distinguish the two populations, without requiring prior SNP mapping or knowledge.
A number of other methods for detecting and identifying SNPs exist. These include the use of mass spectrometry, for example, to measure probes that hybridize to the SNP (Ross, P. L. et al. Discrimination of single-nucleotide polymorphisms in human DNA using peptide nucleic acid probes detected by MALDI-TOF mass spectrometry. Anal. Chem. 69, 4197-4202 (1997), herein incorporated by reference in its entirety). This technique varies in how rapidly it can be performed, from a few samples per day to a high throughput of 40,000 SNPs per day, using mass code tags. A preferred example is the use of mass spectrometric determination of a nucleic acid sequence which includes the polymorphisms of the invention, for example, which includes the promoter of the COX2 gene or a complementary sequence. Such mass spectrometric methods are known to those skilled in the art, and the genotyping methods of the invention are amenable to adaptation for the mass spectrometric detection of the polymorphisms of the invention, for example, the COX2 promoter polymorphisms of the invention.
SNPs can also be determined by ligation-bit analysis. This analysis requires two primers that hybridize to a target with a one nucleotide gap between the primers. Each of the four nucleotides is added to a separate reaction mixture containing DNA polymerase, ligase, target DNA and the primers. The polymerase adds a nucleotide to the 3′end of the first primer that is complementary to the SNP, and the ligase then ligates the two adjacent primers together. Upon heating of the sample, if ligation has occurred, the now larger primer will remain hybridized and a signal, for example, fluorescence, can be detected. A further discussion of these methods can be found in U.S. Pat. Nos. 5,919,626; 5,945,283; 5,242,794; and 5,952,174 (each of the foregoing is herein incorporated by reference in its entirety).
U.S. Pat. No. 6,821,733 (herein incorporated by reference in its entirety) describes methods to detect differences in the sequence of two nucleic acid molecules that includes the steps of: contacting two nucleic acids under conditions that allow the formation of a four-way complex and branch migration; contacting the four-way complex with a tracer molecule and a detection molecule under conditions in which the detection molecule is capable of binding the tracer molecule or the four-way complex; and determining binding of the tracer molecule to the detection molecule before and after exposure to the four-way complex. Competition of the four-way complex with the tracer molecule for binding to the detection molecule indicates a difference between the two nucleic acids.
Protein- and proteomics-based approaches are also suitable for polymorphism detection and analysis. Polymorphisms which result in or are associated with variation in expressed proteins can be detected directly by analyzing said proteins. This typically requires separation of the various proteins within a sample, by, for example, gel electrophoresis or HPLC, and identification of said proteins or peptides derived therefrom, for example by NMR or protein sequencing such as chemical sequencing or more prevalently mass spectrometry. Proteomic methodologies are well known in the art, and have great potential for automation. For example, integrated systems, such as the ProteomIQTM system from Proteome Systems, provide high throughput platforms for proteome analysis combining sample preparation, protein separation, image acquisition and analysis, protein processing, mass spectrometry and bioinformatics technologies.
The majority of proteomic methods of protein identification utilise mass spectrometry, including ion trap mass spectrometry, liquid chromatography (LC) and LC/MSn mass spectrometry, gas chromatography (GC) mass spectroscopy,. Fourier transform-ion cyclotron resonance-mass spectrometer (FT-MS), MALDI-TOF mass spectrometry, and ESI mass spectrometry, and their derivatives. Mass spectrometric methods are also useful in the determination of post-translational modification of proteins, such as phosphorylation or glycosylation, and thus have utility in determining polymorphisms that result in or are associated with variation in post-translational modifications of proteins.
Associated technologies are also well known, and include, for example, protein processing devices such as the “Chemical Inkjet Printer” including piezoelectric printing technology that allows in situ enzymatic or chemical digestion of protein samples electroblotted from 2-D PAGE gels to membranes by jetting the enzyme or chemical directly onto the selected protein spots (Sloane, A. J. et al. High throughput peptide mass fingerprinting and protein macroarray analysis using chemical printing strategies. Mol Cell Proteomics 1(7):490-9 (2002), herein incorporated by reference in its entirety). After in-situ digestion and incubation of the proteins, the membrane can be placed directly into the mass spectrometer for peptide analysis.
A large number of methods reliant on the conformational variability of nucleic acids have been developed to detect SNPs.
For example, Single Strand Conformational Polymorphism (SSCP, Orita et al., PNAS 86:2766-2770 (1989), herein incorporated by reference in its entirety) is a method reliant on the ability of single-stranded nucleic acids to form secondary structure in solution under certain conditions. The secondary structure depends on the base composition and can be altered by a single nucleotide substitution, causing differences in electrophoretic mobility under nondenaturing conditions. The various polymorphs are typically detected by autoradiography when radioactively labelled, by silver staining of bands, by hybridisation with detectably labelled probe fragments or the use of fluorescent PCR primers which are subsequently detected, for example by an automated DNA sequencer.
Modifications of SSCP are well known in the art, and include the use of differing gel running conditions, such as for example differing temperature, or the addition of additives, and different gel matrices. Other variations on SSCP are well known to the skilled artisan, including, RNA-SSCP (Gasparini, P. et al. Scanning the first part of the neurofibromatosis type 1 gene by RNA-SSCP: identification of three novel mutations and of two new polymorphisms. Hum Genet. 97(4):492-5 (1996), herein incorporated by reference in its entirety), restriction endonuclease fingerprinting-SSCP (Liu, Q. et al. Restriction endonuclease fingerprinting (REF): a sensitive method for screening mutations in long, contiguous segments of DNA. Biotechniques 18(3):470-7 (1995), herein incorporated by reference in its entirety), dideoxy fingerprinting (a hybrid between dideoxy sequencing and SSCP) (Sarkar, G. et al. Dideoxy fingerprinting (ddF): a rapid and efficient screen for the presence of mutations. Genomics 13:441-443 (1992), herein incorporated by reference in its entirety), bi-directional dideoxy fingerprinting (in which the dideoxy termination reaction is performed simultaneously with two opposing primers) (Liu, Q. et al. Bi-directional dideoxy fingerprinting (Bi-ddF): a rapid method for quantitative detection of mutations in genomic regions of 300-600 bp. Hum Mol Genet. 5(1):107-14 (1996), herein incorporated by reference in its entirety), and Fluorescent PCR-SSCP (in which PCR products are internally labelled with multiple fluorescent dyes, can be digested with restriction enzymes, followed by SSCP, and analysed on an automated DNA sequencer able to detect the fluorescent dyes) (Makino, R. et al. F-SSCP: fluorescence-based polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis. PCR Methods Appl. 2(1):10-13 (1992), herein incorporated by reference in its entirety).
Other methods which utilise the varying mobility of different nucleic acid structures include Denaturing Gradient Gel Electrophoresis (DGGE) (Cariello, N. F. et al. Resolution of a missense mutant in human genomic DNA by denaturing gradient gel electrophoresis and direct sequencing using in vitro DNA amplification: HPRT Munich. Am J Hum Genet. 42(5):726-34 (1988), herein incorporated by reference in its entirety), Temperature Gradient Gel Electrophoresis (TGGE) (Riesner, D. et al. Temperature-gradient gel electrophoresis for the detection of polymorphic DNA and for quantitative polymerase chain reaction. Electrophoresis. 13:632-6 (1992), herein incorporated by reference in its entirety), and Heteroduplex Analysis (HET) (Keen, J. et al. Rapid detection of single base mismatches as heteroduplexes on Hydrolink gels. Trends Genet. 7(1):5 (1991), herein incorporated by reference in its entirety). Here, variation in the dissociation of double stranded DNA (for example, due to base-pair mismatches) results in a change in electrophoretic mobility. These mobility shifts are used to detect nucleotide variations.
Denaturing High Pressure Liquid Chromatography (HPLC) is yet a further method utilised to detect SNPs, using HPLC methods well-known in the art as an alternative to the separation methods described above (such as gel electophoresis) to detect, for example, homoduplexes and heteroduplexes which elute from the HPLC column at different rates, thereby enabling detection of mismatch nucleotides and thus SNPs (Giordano, M. et al. Identification by denaturing high-performance liquid chromatography of numerous polymorphisms in a candidate region for multiple sclerosis susceptibility. Genomics 56(3):247-53 (1999), herein incorporated by reference in its entirety).
Yet further methods to detect SNPs rely on the differing susceptibility of single stranded and double stranded nucleic acids to cleavage by various agents, including chemical cleavage agents and nucleolytic enzymes. For example, cleavage of mismatches within RNA:DNA heteroduplexes by RNase A, of heteroduplexes by, for example bacteriophage T4 endonuclease YII or T7 endonuclease I, of the 5′ end of the hairpin loops at the junction between single stranded and double stranded DNA by cleavase I, and the modification of mispaired nucleotides within heteroduplexes by chemical agents commonly used in Maxam-Gilbert sequencing chemistry, are all well known in the art.
Further examples include the Protein Translation Test (PTT), used to resolve stop codons generated by variations which lead to a premature termination of translation and to protein products of reduced size, and the use of mismatch binding proteins (Moore, W. et al. Mutation detection in the breast cancer gene BRCA1 using the protein truncation test. Mol Biotechnol. 14(2):89-97 (2000), herein incorporated by reference in its entirety). Variations are detected by binding of, for example, the MutS protein, a component of Escherichia coli DNA mismatch repair system, or the human hMSH2 and GTBP proteins, to double stranded DNA heteroduplexes containing mismatched bases. DNA duplexes are then incubated with the mismatch binding protein, and variations are detected by mobility shift assay. For example, a simple assay is based on the fact that the binding of the mismatch binding protein to the heteroduplex protects the heteroduplex from exonuclease degradation.
Those skilled in the art will know that a particular SNP, particularly when it occurs in a regulatory region of a gene such as a promoter, can be associated with altered expression of a gene. Altered expression of a gene can also result when the SNP is located in the coding region of a protein-encoding gene, for example where the SNP is associated with codons of varying usage and thus with tRNAs of differing abundance. Such altered expression can be determined by methods well known in the art, and can thereby be employed to detect such SNPs. Similarly, where a SNP occurs in the coding region of a gene and results in a non-synonomous amino acid substitution, such substitution can result in a change in the function of the gene product. Similarly, in cases where the gene product is an RNA, such SNPs can result in a change of function in the RNA gene product. Any such change in function, for example as assessed in an activity or functionality assay, can be employed to detect such SNPs.
The above methods of detecting and identifying SNPs are amenable to use in the methods of the invention.
Of course, in order to detect and identify SNPs in accordance with the invention, a sample containing material to be tested is obtained from the subject. The sample can be any sample potentially containing the target SNPs (or target polypeptides, as the case may be) and obtained from any bodily fluid (blood, urine, saliva, etc) biopsies or other tissue preparations.
DNA or RNA can be isolated from the sample according to any of a number of methods well known in the art. For example, methods of purification of nucleic acids are described in Tijssen; Laboratory Techniques in Biochemistry and Molecular Biology: Hybridization with nucleic acid probes Part 1: Theory and Nucleic acid preparation, Elsevier, New York, N.Y. 1993, as well as in Maniatis, T., Fritsch, E. F. and Sambrook, J., Molecular Cloning Manual 1989 (each of the foregoing which is herein incorporated by reference in its entirety).
To assist with detecting the presence or absence of polymorphisms/SNPs, nucleic acid probes and/or primers can be provided. Such probes have nucleic acid sequences specific for chromosomal changes evidencing the presence or absence of the polymorphism and are preferably labeled with a substance that emits a detectable signal when combined with the target polymorphism.
The nucleic acid probes can be genomic DNA or cDNA or MRNA, or any RNA-like or DNA-like material, such as peptide nucleic acids, branched DNAs, and the like. The probes can be sense or antisense polynucleotide probes. Where target polynucleotides are double-stranded, the probes can be either sense or antisense strands. Where the target polynucleotides are single-stranded, the probes are complementary single strands.
The probes can be prepared by a variety of synthetic or enzymatic schemes, which are well known in the art. The probes can be synthesized, in whole or in part, using chemical methods well known in the art (Caruthers et al., Nucleic Acids Res., Symp. Ser., 215-233 (1980), herein incorporated by reference in its entirety). Alternatively, the probes can be generated, in whole or in part, enzymatically.
Nucleotide analogs can be incorporated into probes by methods well known in the art. The only requirement is that the incorporated nucleotide analog must serve to base pair with target polynucleotide sequences. For example, certain guanine nucleotides can be substituted with hypoxanthine, which base pairs with cytosine residues. However, these base pairs are less stable than those between guanine and cytosine. Alternatively, adenine nucleotides can be substituted with 2,6-diaminopurine, which can form stronger base pairs than those between adenine and thymidine.
Additionally, the probes can include nucleotides that have been derivatized chemically or enzymatically. Typical chemical modifications include derivatization with acyl, alkyl, aryl or amino groups.
The probes can be immobilized on a substrate. Preferred substrates are any suitable rigid or semi-rigid support including membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles and capillaries. The substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which the polynucleotide probes are bound. Preferably, the substrates are optically transparent.
Furthermore, the probes do not have to be directly bound to the substrate, but rather can be bound to the substrate through a linker group. The linker groups are typically about 6 to 50 atoms long to provide exposure to the attached probe. Preferred linker groups include ethylene glycol oligomers, diamines, diacids and the like. Reactive groups on the substrate surface react with one of the terminal portions of the linker to bind the linker to the substrate. The other terminal portion of the linker is then functionalized for binding the probe.
The probes can be attached to a substrate by dispensing reagents for probe synthesis on the substrate surface or by dispensing preformed DNA fragments or clones on the substrate surface. Typical dispensers include a micropipette delivering solution to the substrate with a robotic system to control the position of the micropipette with respect to the substrate. There can be a multiplicity of dispensers so that reagents can be delivered to the reaction regions simultaneously.
Nucleic acid microarrays are preferred. Such microarrays (including nucleic acid chips) are well known in the art (see, for example U.S. Pat. Nos. 5,578,832; 5,861,242; 6,183,698; 6,287,850; 6,291,183; 6,297,018; 6,306,643; and 6,308,170, each of the foregoing which is herein incorporated by reference in its entirety).
Alternatively, antibody microarrays can be produced. The production of such microarrays is essentially as described in Schweitzer & Kingsmore, “Measuring proteins on microarrays”, Curr Opin Biotechnol 2002; 13(1): 14-9; Avseekno et al., “Immobilization of proteins in immunochemical microarrays fabricated by electrospray deposition”, Anal Chem 2001 15; 73(24): 6047-52; Huang, “Detection of multiple proteins in an antibody-based protein microarray system, Immunol Methods 2001 1; 255 (1-2): 1-13 (each of the foregoing which is herein incorporated by reference in its entirety).
The present invention also contemplates the preparation of kits for use in accordance with the present invention. Suitable kits include various reagents for use in accordance with the present invention in suitable containers and packaging materials, including tubes, vials, and shrink-wrapped and blow-molded packages.
Materials suitable for inclusion in an exemplary kit in accordance with the present invention include one or more of the following: gene specific PCR primer pairs (oligonucleotides) that anneal to DNA or cDNA sequence domains that flank the genetic polymorphisms of interest, reagents capable of amplifying a specific sequence domain in either genomic DNA or cDNA without the requirement of performing PCR; reagents required to discriminate between the various possible alleles in the sequence domains amplified by PCR or non-PCR amplification (e.g., restriction endonucleases, oligonucleotide that anneal preferentially to one allele of the polymorphism, including those modified to contain enzymes or fluorescent chemical groups that amplify the signal from the oligonucleotide and make discrimination of alleles more robust); reagents required to physically separate products derived from the various alleles (e.g. agarose or polyacrylamide and a buffer to be used in electrophoresis, HPLC columns, SSCP gels, formamide gels or a matrix support for MALDI-TOF).
It will be appreciated that the methods of the invention can be performed in conjunction with an analysis of other risk factors known to be associated with lung cancer. Such risk factors include epidemiological risk factors associated with an increased risk of developing lung cancer. Such risk factors include, but are not limited to smoking and/or exposure to tobacco smoke, age, sex and familial history. These risk factors can be used to augment an analysis of one or more polymorphisms as herein described when assessing a subject's risk of developing lung cancer.
The predictive methods of the invention allow a number of therapeutic interventions and/or treatment regimens to be assessed for suitability and implemented for a given subject. The simplest of these can be the provision to the subject of motivation to implement a lifestyle change, for example, where the subject is a current smoker, the methods of the invention can provide motivation to quit smoking.
The manner of therapeutic intervention or treatment will be predicated by the nature of the polymorphism(s) and the biological effect of said polymorphism(s). For example, where a susceptibility polymorphism is associated with a change in the expression of a gene, intervention or treatment is preferably directed to the restoration of normal expression of said gene, by, for example, administration of an agent capable of modulating the expression of said gene. Where a polymorphism is associated with decreased expression of a gene, therapy can involve administration of an agent capable of increasing the expression of said gene, and conversely, where a polymorphism is associated with increased expression of a gene, therapy can involve administration of an agent capable of decreasing the expression of said gene. Methods useful for the modulation of gene expression are well known in the art. For example, in situations where a polymorphism is associated with upregulated expression of a gene, therapy utilising, for example, RNAi or antisense methodologies can be implemented to decrease the abundance of MRNA and so decrease the expression of said gene. Alternatively, therapy can involve methods directed to, for example, modulating the activity of the product of said gene, thereby compensating for the abnormal expression of said gene.
Where a susceptibility polymorphism is associated with decreased gene product function or decreased levels of expression of a gene product, therapeutic intervention or treatment can involve augmenting or replacing of said function, or supplementing the amount of gene product within the subject for example, by administration of said gene product or a functional analogue thereof. For example, where a polymorphism is associated with decreased enzyme function, therapy can involve administration of active enzyme or an enzyme analogue to the subject. Similarly, where a polymorphism is associated with increased gene product function, therapeutic intervention or treatment can involve reduction of said function, for example, by administration of an inhibitor of said gene product or an agent capable of decreasing the level of said gene product in the subject. For example, where a SNP allele or genotype is associated with increased enzyme function, therapy can involve administration of an enzyme inhibitor to the subject.
Likewise, when a protective polymorphism is associated with upregulation of a particular gene or expression of an enzyme or other protein, therapies can be directed to mimic such upregulation or expression in an individual lacking the resistive genotype, and/or delivery of such enzyme or other protein to such individual Further, when a protective polymorphism is associated with downregulation of a particular gene, or with diminished or eliminated expression of an enzyme or other protein, desirable therapies can be directed to mimicking such conditions in an individual that lacks the protective genotype.
The relationship between the various polymorphisms identified above and the susceptibility (or otherwise) of a subject to lung cancer also has application in the design and/or screening of candidate therapeutics. This is particularly the case where the association between a susceptibility or protective polymorphism is manifested by either an upregulation or downregulation of expression of a gene. In such instances, the effect of a candidate therapeutic on such upregulation or downregulation is readily detectable.
For example, in one embodiment existing human lung organ and cell cultures are screened for polymorphisms as set forth above. (For information on human lung organ and cell cultures, see, e.g.: Bohinski et al. (1996) Molecular and Cellular Biology 14:5671-5681; Collettsolberg et al. (1996) Pediatric Research 39:504; Hermanns et al. (2004) Laboratory Investigation 84:736-752; Hume et al. (1996) In Vitro Cellular & Developmental Biology-Animal 32:24-29; Leonardi et al. (1995) 38:352-355; Notingher et al. (2003) Biopolymers (Biospectroscopy) 72:230-240; Ohga et al. (1996) Biochemical and Biophysical Research Communications 228:391-396; each of the foregoing which is herein incorporated by reference in its entirety.) Cultures representing susceptibility and protective genotype groups are selected, together with cultures which are putatively “normal” in terms of the expression of a gene which is either upregulated or downregulated where a protective polymorphism is present.
Samples of such cultures are exposed to a library of candidate therapeutic compounds and screened for any or all of: (a) downregulation of susceptibility genes that are normally upregulated in susceptibility polymorphisms; (b) upregulation of susceptibility genes that are normally downregulated in susceptibility polymorphisms; (c) downregulation of protective genes that are normally downregulated or not expressed (or null forms are expressed) in protective polymorphisms; and (d) upregulation of protective genes that are normally upregulated in protective polymorphisms. Compounds are selected for their ability to alter the regulation and/or action of susceptibility genes and/or protective genes in a culture having a susceptibility polymorphisms.
Similarly, where the polymorphism is one which when present results in a physiologically active concentration of an expressed gene product outside of the normal range for a subject (adjusted for age and sex), and where there is an available prophylactic or therapeutic approach to restoring levels of that expressed gene product to within the normal range, individual subjects can be screened to determine the likelihood of their benefiting from that restorative approach. Such screening involves detecting the presence or absence of the polymorphism in the subject by any of the methods described herein, with those subjects in which the polymorphism is present being identified as individuals likely to benefit from treatment.
EXAMPLES
The invention will now be described in more detail, with reference to non-limiting examples.
Example 1
Case Association Study
Introduction
Case-control association studies allow the careful selection of a control group where matching for important risk factors is critical. In this study, smokers diagnosed with lung cancer and smokers without lung cancer with normal lung function were compared. This unique control group is highly relevant as it is impossible to pre-select smokers with zero risk of lung cancer—i.e., those who although smokers will never develop lung cancer. Smokers with a high pack year history and normal lung function were used as a “low risk” group of smokers, as it is believed that it is not possible with current knowledge to identify a lower risk group of smokers. It is believed, without wishing to be bound by any theory, that this approach allows for a more rigorous comparison of low penetrant, high frequency polymorphisms that can confer an increased risk of developing lung cancer. It is also believed, again without wishing to be bound by any theory, that there can be polymorphisms that confer a degree of protection from lung cancer which may only be evident if a smoking cohort with normal lung function is utilised as a comparator group. Thus smokers with lung cancer would have a lower frequency of these polymorphisms compared to smokers with normal lung function and no diagnosed lung cancer.
Methods
Subject Recruitment
Subjects of European decent who had smoked a minimum of fifteen pack years and diagnosed with lung cancer were recruited. Subjects met the following criteria: diagnosed with lung cancer based on radiological and histological grounds, including primary lung cancers with histological types of small cell lung cancer, squamous cell lung cancer, adenocarinoma of the lung, non-small cell cancer (where histological markers can not distinguish the subtype) and broncho-alveolar carcinoma. Subjects can be of any age and at any stage of treatment after the diagnosis had been confirmed. One hundred and nine subjects were recruited, of these 58% were male, the mean FEV1/FVC (±95% confidence limits) was 51% (49-53), mean FEV1 as a percentage of predicted was 43 (41-45). Mean age, cigarettes per day and pack year history was 65 yrs (64-66), 24 cigarettes/day (22-25) and 50 pack years (41-55), respectively. Two hundred and seventeen European subjects who had smoked a minimum of twenty pack years and who had never suffered breathlessness and had not been diagnosed with an obstructive lung disease or lung cancer in the past were also studied. This control group was recruited through clubs for the elderly and consisted of 63% male, the mean FEV1/FVC (95% CI) was 82% (81-83), mean FEV1 as a percentage of predicted was 96 (95-97). Mean age, cigarettes per day and pack year history was 59 yrs (57-61), 24 cigarettes/day (22-26) and 42 pack years (39-45), respectively. Using a PCR based method (Sandford A J, et al., 1999. Z and S mutations of the al-antitrypsin gene and the risk of chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol. 20; 287-291, herein incorporated by reference in its entirety), all subjects were genotyped for the α1-antitrypsin mutations (S and Z alleles) and those with the ZZ allele were excluded. 190 European blood donors (smoking status unknown) were recruited consecutively through local blood donor services. Sixty-three percent were men and their mean age was 50 years. On regression analysis, the age difference and pack years difference observed between lung cancer sufferers and resistant smokers was found not to determine FEV or lung cancer.
This study shows that polymorphisms found in greater frequency in lung cancer patients compared to resistant smokers can reflect an increased susceptibility to the development of lung cancer. Similarly, polymorphisms found in greater frequency in resistant smokers compared to lung cancer can reflect a protective role. A summary is presented in Table 1C below.







TABLE 1C







Summary of characteristics for the lung cancer


subjects and resistant smokers.










Parameter
Lung Cancer
Resistant smokers



Median (IQR)
N = 109
N = 200
Differences





% male
52%
64%
ns


Age (yrs)
68 (11)
60 (12)
P < 0.05


Pack years
40 (31)
43 (25)
P < 0.05


Cigarettes/day
18 (11)
24 (12)
ns


FEV1 (L)
1.7 (0.6)
2.8 (0.7)
P < 0.05


FEV1 % predict
67 (22)
96% (10)   
P < 0.05


FEV1/FVC
59 (14)
82 (8) 
P < 0.05





Means and 95% confidence limits






Glutathione S-transferase Null Polymorphisms Genotyping

Genomic DNA was extracted using standard phenol and chloroform methods. Cohorts of patients and controls were configured in to 96-well PCR format containing strategic negative controls. The assay primers, PCR conditions and RFLP assays details have been previously described [Cantlay A M. et al. Heterogeneous expression and polymorphic genotype of glutathione S-transferases in human lung. Thorax 49(10):1010-4, (1994), herein incorporated by reference in its entirety]. Genotyping was done using minor modifications of the above protocol optimised for our own laboratory conditions The PCR reactions were amplified in MJ Research thermocyclers in a total volume of 25 μl and contained 80 ng genomic DNA, 100 ng forward and reverse primers, 200 mM dNTPs, 20 mM Tris-HCL (pH 8.4), 50 mM KCl, 2.5 mM MgCl2 and 1.0 unit of Taq polymerase (Qiagen). Forward, internal (GSTM4) and reverse prime sequences were 5′-CTGCCCTACTTGATTGATGG-3′ [SEQ ID NO 143], 5′-ATCTTCTCCTCTTCTGTCTC-3′ [SEQ ID NO 144], and 5′-TTCTGGATTGTAGCAGATCA-3′ [SEQ ID NO 145]. Cycling conditions consisted of 94 C 60 s, 59 C 30 s, 72 C 30 s for 35 cycles with an extended last extension of 3 min. Digested products were separated on 3% agarose gel. The products were visualised by ultraviolet transillumination following ethidium bromide staining and migration compared against a 1 Kb plus ladder standard (Invitrogen). Genotypes were recorded in data spreadsheets and statistical analysis performed.
Cyclooxygenase 2 Polymorphisms Genotyping
Genomic DNA was extracted from whole blood samples (Maniatis, T., Fritsch, E. F. and Sambrook, J., Molecular Cloning Manual. 1989). The Cyclo-oxygenase 2 −765 polymorphism was determined by minor modifications of a previously published method (Papafili A, et al. Common promoter variant in cyclooxygenase-2 represses gene expression. Arterioscler Thromb Vasc Biol. 20: 1631-1635, (2002), herein incorporated by reference in its entirety). The PCR reaction was carried out in a total volume of 25 ul and contained 20 ng genomic DNA, 500 pmol forward and reverse primers, 0.2 mM dNTPs, 10 mM Tris-HCL (pH 8.4), 150 mM KCl, 1.0 mM MgCl2 and 1 unit of polymerase (Life Technologies). Cycling times were incubations for 3 min at 95° C. followed by 33 cycles of 50s at 94° C., 60s at 66° C. and 60s at 72° C. A final elongation of 10 min at 72° C. then followed. 4 ul of PCR products were visualised by ultraviolet trans-illumination of a 3% agarose gel stained with ethidium bromide. An aliquot of 3 ul of amplification product was digested for 1 hr with 4 units of AciI (Roche Diagnostics, New Zealand) at 37° C. Digested products were separated on a 2.5% agarose gel run for 2.0 hours at 80 mV with TBE buffer. The products were visualised against a 123 bp ladder using ultraviolet transillumination after ethidium bromide staining.
Matrix Metalloproteinase 1-1607 1G/2G Polymorphisms Genotyping
Genomic DNA was extracted using standard phenol and chloroform methods. Cohorts of patients and controls were configured in to 96-well PCR format containing strategic negative controls. The assay primers, PCR conditions and RFLP assays details have been previously described [Dunleavey L, et al. Rapid genotype analysis of the matrix metalloproteinase-1 gene 1G/2G polymorphism that is associated with risk of cancer. Matrix Biol. 19(2):175-7 (2000), herein incorporated by reference in its entirety]. Genotyping was done using minor modifications of the above protocol optimised for our own laboratory conditions The PCR reactions were amplified in MJ Research thermocyclers in a total volume of 25 μl and contained 80 ng genomic DNA, 100 ng forward and reverse primers, 200 mM dNTPs, 20 mM Tris-HCL (pH 8.4), 50 mM KCl, 1.5 mM MgCl2 and 1.0 unit of Taq polymerase (Qiagen). Forward and reverse prime sequences were 5′-TCGTGAGAATGTCTTCCCATT-3′ [SEQ ID NO 1] and 5′-TCTTGGATTGATTTGAGATAAGTGAAATC-3′[SEQ ID NO 2]. Cycling conditions consisted of 94° C. 60 s, 55° C. 30s, 72° C. 30 s for 35 cycles with an extended last extension of 3 min. Aliquots of amplification product were digested for 4 hrs with 6 Units of the restriction enzymes XmnI (Roche Diagnostics, New Zealand) at designated temperature conditions. Digested products were separated on 6% polyacrylamide gel. The products were visualised by ultraviolet transillumination following ethidium bromide staining and migration compared against a 1 Kb plus ladder standard (Invitrogen). Genotypes were recorded in data spreadsheets and statistical analysis performed.
Polymorphism Genotyping Using the Sequenom Autoflex Mass Spectrometer
Genomic DNA was extracted from whole blood samples (Maniatis, T., Fritsch, E. F. and Sambrook, J., Molecular Cloning Manual. 1989). Purified genomic DNA was aliquoted (10 ng/ul concentration) into 96 well plates and genotyped on a SequenomTM system (SequenomTM Autoflex Mass Spectrometer and Samsung 24 pin nanodispenser) using the following sequences, amplification conditions and methods.
The following conditions were used for the PCR multiplex reaction: final concentrations were for 10× Buffer 15 mM MgCl2 1.25×, 25 mM MgCl2 1.625 mM, dNTP mix 25 mM 500 uM, primers 4 uM 100 nM, Taq polymerase (Quiagen hot start) 0.15 U/reaction, Genomic DNA 10 ng/ul. Cycling times were 95° C. for 15 min, (5° C. for 15 s, 56° C. 30 s, 72° C. 30 s for 45 cycles with a prolonged extension time of 3 min to finish. We used shrimp alkaline phosphotase (SAP) treatment (2 ul to 5 ul per PCR reaction) incubated at 35° C. for 30 min and extension reaction (add 2 ul to 7 ul after SAP treatment) with the following volumes per reaction of: water, 0.76 ul; hME 10× termination buffer, 0.2 ul; hME primer (10 uM), 1 ul; MassEXTEND enzyme, 0.04 ul.







TABLE 1D







Sequenom conditions for the polymorphisms genotyping - 1










TERM
SNP_ID
2nd-PCRP
1st-PCRP














ACT
CYP2E1_1019 G/CPst1
ACGTTGGATGAAACCAGAGGGAAGCAAAGG
ACGTTGGATGTCATTGGTTGTGCTGCACCT





[SEQ ID NO 3]
[SEQ ID NO 4]


 


ACT
XPD-751 G/T
ACGTTGGATGCACCAGGAACCGTTTATGGC
ACGTTGGATGAGCAGCTAGAATCAGAGGAG




[SEQ ID NO 5]
[SEQ ID NO 6]


 


ACT
IL-18 105 A/C
ACGTTGGATGGTCAATGAAGAGAACTTGGTC
ACGTTGGATGAATGTTTATTGTAGAAAACC




[SEQ ID NO 7]
[SEQ ID NO 8]


 


ACT
IL-18-133 G/C
ACGTTGGATGGGGTATTCATAAGCTGAAAC
ACGTTGGATGCCTTCAAGTTCAGTGGTCAG




[SEQ ID NO 9]
[SEQ ID NO 10]


 


ACT
CYP 1A1 Ile 462 Val
ACGTTGGATGGTGATTATCTTTGGCATGGG
ACGTTGGATGGGATAGCCAGGAAGAGAAAG




[SEQ ID NO 11]
[SEQ ID NO 12]


 


ACT
MMP12 Asn 357 Ser A/G
ACGTTGGATGCCCTATTTCTTTGTCTTCAC
ACGTTGGATGCTTGGGATAATTTGGCTCTG




[SEQ ID NO 13]
[SEQ ID NO 14]


 


ACT
OGG1 Ser 326 Cys G/C
ACGTTGGATGGGAACCCTTTCTGCGCTTTG
ACGTTGGATGCCTACAGGTGCTGTTCAGTG




[SEQ ID NO 15]
[SEQ ID NO 16]


 


ACT
NAT2 Arg 197 Gln A/G
ACGTTGGATGCCTGCCAAAGAAGAAACACC
ACGTTGGATGACGTCTGCAGGTATGTATTC




[SEQ ID NO 17]
[SEQ ID NO 18]


 


ACT
CYP2E1_C/T Rsa1
ACGTTGGATGGTTCTTAATTCATAGGTTGC
ACGTTGGATGCTTCATTTCTCATCATATTTTC




[SEQ ID NO 19]
[SEQ ID NO 20]


 


ACG
CCND1 A870G
ACGTTGGATGTAGGTGTCTCCCCCTGTAAG
ACGTTGGATGTCCTCTCCAGAGTGATCAAG




[SEQ ID NO 21]
[SEQ ID NO 22]


 


ACG
ILB1-511 A/G
ACGTTGGATGATTTTCTCCTCAGAGGCTCC
ACGTTGGATGTGTCTGTATTGAGGGTGTGG




[SEQ ID NO 23]
[SEQ ID NO 24]


 


ACG
FAS_A-670G
ACGTTGGATGTTGTGGCTGCAACATGAGAG
ACGTTGGATGCTATGGCGCAACATCTGTAC




[SEQ ID NO 25]
[SEQ ID NO 26]


 


ACG
NOS3-786 T/C
ACGTTGGATGACTGTAGTTTCCCTAGTCCC
ACGTTGGATGAGTCAGCAGAGAGACTAGGG




[SEQ ID NO 27]
[SEQ ID NO 28]


 


ACT
ACT_Ala15Thr
ACGTTGGATGGAGTTGAGAATGGAGAGAATG
ACGTTGGATGTCAAGTGGGCTGTTAGGGTG




[SEQ ID NO 29]
[SEQ ID NO 30]


 


ACT
SOD3 Arg 312 Gln
ACGTTGGATGTGCTGCGTGGTGGGCGTGTG
ACGTTGGATGGGCCTTGCACTCGCTCTCG




[SEQ ID NO 31]
[SEQ ID NO 32]


 


ACT
NOS3 Asp 298 Glu
ACGTTGGATGAAACGGTCGCTTCGACGTGC
ACGTTGGATGACCTCAAGGACCAGCTCGG




[SEQ ID NO 33]
[SEQ ID NO 34]


 


CGT
IL-8-251 A/T
ACGTTGGATGACTGAAGCTCCACAATTTGG
ACGTTGGATGGCCACTCTAGTACTATATCTG




[SEQ ID NO 35]
[SEQ ID NO 36]


 


CGT
IFN gamma 874 A/T
ACGTTGGATGCAGACATTCACAATTGATTT
ACGTTGGATGGATAGTTCCAAACATGTGCG




[SEQ ID NO 37]
[SEQ ID NO 38]


 


ACT
XRCC1 Arg 399 Gln G/A
ACGTTGGATGTAAGGAGTGGGTGCTGGACT
ACGTTGGATGAGGATAAGGAGCAGGGTTGG




[SEQ ID NO 39]
[SEQ ID NO 40]










Sequenom conditions for the polymorphisms genotyping - 2















SNP_ID
AMP_LEN
UP_CONF
MP_CONF
Tm(NN)
PcGC
PWARN
UEP_DIR
UEP_MASS



















CYP2E1_1019G/CPst1
119
95.2
71.3
46.7
47.1

F
5256.4



 


XPD-751 G/T
113
97.6
71.3
49.8
47.4

F
5689.7


 


IL-18 105 A/C
120
65.6
71.3
49.8
36.4

R
6702.4


 


IL-18-133 G/C
112
93.5
81.3
47.1
42.1

F
5811.8


 


CYP 1A1 Ile 462 Val
102
98.2
81.3
55.6
55

F
6222.1


 


MMP12 Asn 357 Ser A/G
95
92.6
81.3
48
30.4

F
7070.6


 


OGG1 Ser 326 Cys G/C
99
96.5
82.2
58.9
70.6

R
5227.4


 


NAT2 Arg 197 Gln A/G
115
97.4
70
48.5
36.4

F
6635.3


 


CYP2E1_C/T Rsa1
105
62.8
77.8
46.4
26.1

R
7018.6


 


CCND1 A870G
106
98.1
83
45.8
47.1

R
5034.3


 


ILB1-511 A/G
111
99.2
83
46
47.1

R
5203.4


 


FAS_A-670G
103
99.2
83
54.4
50

R
6166


 


NOS3-786 T/C
114
97.5
83
61.8
61.9

F
6358.1


 


ACT_Ala15Thr
118
93.4
68.2
45.2
47.1

F
5136.4


 


SOD3 Arg 312 Gln
119
63.2
68.2
55.5
57.9

F
5855.8


 


NOS3 Asp 298 Glu
113
82.2
68.2
65.4
66.7

F
6432.2


 


IL-8-251 A/T
119
92.6
75.8
45.9
28.6

R
6428.2


 


IFN gamma 874 A/T
112
75.3
75.8
46.4
26.1

F
6943.6


 


XRCC1 Arg 399 Gln G/A
109
93.6
93.6
66.8
82.4

F
5099.3










Sequenom conditions for the polymorphisms genotyping - 3















EXT1_
EXT1_

EXT2_



SNP_ID
UEP_SEQ
CALL
MASS
EXT1_SEQ
CALL
















CYP2E1_1019G/CPst1
TTCTTGGTTCAGGAGAG
C
5529.6
TTCTTGGTTCAGGAGAGC
G




[SEQ ID NO 41]


[SEQ ID NO 421


 


XPD-751 G/T
GCAATCTGCTCTATCCTCT
T
5977.9
GCAATCTGCTCTATCCTCTT
G



[SEQ ID NO 43]


[SEQ ID NO 44]


 


IL-18 105 A/C
ATTCAAGCTTGCCAAAGTAATC
A
6990.6
ATTCAAGCTTGCCAAAGTAATCT
C



[SEQ ID NO 45]


[SEQ ID NO 46]


 


IL-18-133 G/C
CATAAGCTGAAACTTCTGG
C
6085
CATAAGCTGAAACTTCTGGC
G



[SEQ ID NO 47]


[SEQ ID NO 48]


 


CYP 1A1 Ile 462 Val
GGAAGTGTATCGGTGAGACC
A
6519.3
GGAAGTGTATCGGTGAGACCA
G



[SEQ ID NO 49]


[SEQ ID NO 50]


 


MMP12 Asn 357 Ser A/G
TGACAAATACTGGTTAATTAGCA
A
7367.8
TGACAAATATCGGTTAATTAGCAA
G



[SEQ ID NO 51]


[SEQ ID NO 52]


 


OGG1 Ser 326 Cys G/C
GCTCCTGAGCATGGCGG
G
5500.6
GCTCCTGAGCATGGCGGC
C



[SEQ ID NO 53]


[SEQ ID NO 54]


 


NAT2 Arg 197 Gln A/G
TACTTATTTACGCTTGAACCTC
A
6932.5
TACTTATTTACGCTTGAACCTCA
G



[SEQ ID NO 55]


[SEQ ID NO 56]


 


CYP2E1_C/T Rsa1
CTTAATTCATAGGTTGCAATTTT
T
7315.8
CTTAATTCATAGGTTGCAATTTTA
C



[SEQ ID NO 57]


[SEQ ID NO 58]


 


CCND1 A870G
ACATCACCCTCACTTAC
G
5307.5
ACATCACCCTCACTTACC
A



[SEQ ID NO 59]


[SEQ ID NO 60]


 


ILB1-511 A/G
AATTGACAGAGAGCTCC
G
5476.6
AATTGACAGAGAGCTCCC
A



[SEQ ID NO 61]


[SEQ ID NO 62]


 


FAS_A-670G
ATGAGAGGCTCACAGACGTT
G
6439.2
ATGAGAGGCTCACAGACGTTC
A



[SEQ ID NO 63]


[SEQ ID NO 64]


 


NOS3-786 T/C
GGCATCAAGCTCTTCCCTGGC
C
6631.3
GGCATCAAGCTCTTCCCTGGCC
T



[SEQ ID NO 65]


[SEQ ID NO 66]


 


ACT_Ala15Thr
GAATGTTACCTCTCCTG
A
5433.6
GAATGTTACCTCTCCTGA
G



[SEQ ID NO 67]


[SEQ ID NO 68]


 


SOD3 Arg 312 Gln
GCACTCAGAGCGCAAGAAG
C
6129
GCACTCAGAGCGCAAGAAGC
G



[SEQ ID NO 69]


[SEQ ID NO 70]


 


NOS3 Asp 298 Glu
GCTGCTGCAGGCCCCAGATGA
T
6720.4
GCTGCTGCAGGCCCCAGATGAT
G



[SEQ ID NO 71]


[SEQ ID NO 72]


 


IL-8-251 A/T
CACAATTTGGTGAATTATCAA
A
6716.4
CACAATTTGGTGAATTATCAAT
T



[SEQ ID NO 73]


[SEQ ID NO 74]


 


IFN gamma 874 A/T
TTCTTACAACACAAAATCAAATC
T
7231.8
TTCTTACAACACAAAATCAAATCT
A



[SEQ ID NO 75]


[SEQ ID NO 76]


 


XRCC1 Arg 399 Gln G/A
TCGGCGGCTGCCCTCCC
A
5396.5
TCGGCGGCTGCCCTCCCA
G



[SEQ ID NO 77]


[SEQ ID NO 78]










Sequenom conditions for the polymorphisms genotyping - 4










SNP_ID
EXT2_MASS
EXT2_SEQ
1stPAUSE















CYP2E1_1019G/CPst1
5873.8
TTCTTGGTTCAGGAGAGGT
[SEQ ID NO 79]
5585.6



 


XPD-751 G/T
6292.1
GCAATCTGCTCTATCCTCTGC
[SEQ ID NO 80]
6018.9


 


IL-18 105 A/C
7658
ATTCAAGCTTGCCAAAGTAATCGGA
[SEQ ID NO 81]
7031.6


 


IL-18-133 G/C
6438.2
CATAAGCTGAAACTTCTGGGA
[SEQ ID NO 82]
6141


 


GYP 1A1 Ile 462 Val
6839.5
GGAAGTGTATCGGTGAGACCGT
[SEQ ID NO 83]
6551.3


 


MMP12 Asn 357 Ser A/G
7688
TGACAAATACTGGTTAATTAGCAGT
[SEQ ID NO 84]
7399.8


 


OGG1 Ser 326 Cys G/C
5853.8
GCTCCTGAGCATGGCGGGA
[SEQ ID NO 85]
5556.6


 


NAT2 Arg 197 Gln A/G
7261.8
TACTTATTTACGCTTGAACCTCGA
[SEQ ID NO 86]
6964.5


 


CYP2E1_C/T Rsa1
7636
CTTAATTCATAGGTTGCAATTTTGT
[SEQ ID NO 871
7347.8


 


CCND1 A870G
5651.7
ACATCACCCTCACTTACTG
[SEQ ID NO 88]
5338.5


 


ILB1-511 A/G
5820.8
AATTGACAGAGAGCTCCTG
[SEQ ID NO 89]
5507.6


 


FAS_A-670G
6743.4
ATGAGAGGCTCACAGACGTTTC
[SEQ ID NO 90]
6470.2


 


NOS3-786 T/C
6975.5
GGCATCAAGCTCTTCCCTGGCTG
[SEQ ID NO 91]
6662.3


 


ACT_Ala15Thr
5738.7
GAATGTTACCTCTCCTGGC
[SEQ ID NO 92]
5465.6


 


SOD3 Arg 312 Gln
7116.6
GCACTCAGAGCGCAAGAAGGGGC
[SEQ ID NO 93]
6185


 


NOS3 Asp 298 Glu
7034.6
GCTGCTGCAGGCCCCAGATGAGC
[SEQ ID NO 94]
6761.4


 


IL-8-251 A/T
7029.6
CACAATTTGGTGAATTATCAAAT
[SEQ ID NO 95]
6741.4


 


IFN gamma 874 A/T
7530
TTCTTACAACACAAAATCAAATCAC
[SEQ ID NO 96]
7256.8


 


XRCC1 Arg 399 G/n G/A
6054.9
TCGGCGGCTGCCCTCCCGGA
[SEQ ID NO 97]
5428.5










Sequenom conditions for the polymorphisms genotyping - 5










TERM
SNP_ID
2nd-PCRP
1st-PCRP














ACT
CTGF-447G/C
ACGTTGGATGAGGTAGCTGAAGAGGCAAAC
ACGTTGGATGGCCTATAGCCTCTAAAACGC





[SEQ ID NO 98]
[SEQ ID NO 99]


 


ACT
NBS1 Gln185Glu G/C
ACGTTGGATGCTTTCAATTTGTGGAGGCTG
ACGTTGGATGTGTGCACTCATTTGTGGACG




[SEQ ID NO 100]
[SEQ ID NO 101]


 


ACT
MBL2 161 G/A
ACGTTGGATGGTAGCTCTCCAGGCATCAAC
ACGTTGGATGGTACCTGGTTCCCCCTTTTC




[SEQ ID NO 102]
[SEQ ID NO 103]


 


ACT
IGF2R Leu252Val C/G
ACGTTGGATGACACCAGGCGTTTGATGTTG
ACGTTGGATGAAAAACGCCAACAGCATCGG




[SEQ ID NO 104]
[SEQ ID NO 105]


 


ACT
MUC5AC-221 C/T
ACGTTGGATGAGGCGGAGATGGGTGTGTC
ACGTTGGATGAGTCTAGGGTGGGGTATGTG




[SEQ ID NO 106]
[SEQ ID NO 107]


 


ACT
Arg1 intron1 C/T
ACGTTGGATGATGTGTGGATTCACAGCTCG
ACGTTGGATGGGGTTGGCAACTCTAAAAGG




[SEQ ID NO 108]
[SEQ ID NO 109]


 


ACT
REV1 Phe257Ser C/T
ACGTTGGATGCTCTGAAATCAGTGCTGCTC
ACGTTGGATGATGGTCAACAGTGTTGCCAG




[SEQ ID NO 110]
[SEQ ID NO 111]


 


ACT
Apex1 Asp148Glu G/T
ACGTTGGATGCACCTCTTGATTGCTTTCCC
ACGTTGGATGACCCGGCCTTCCTGATCATG




[SEQ ID NO 112]
[SEQ ID NO 113]


 


ACG
IL-10-1082 A/G
ACGTTGGATGATTCCATGGAGGCTGGATAG
ACGTTGGATGGACAACACTACTAAGGCTTC




[SEQ ID NO 114]
[SEQ ID NO 115]










Sequenom conditions for the polymorphisms genotyping - 6















SNP_ID
AMP_LEN
UP_CONF
MP_CONF
Tm(NN)
PcGC
PWARN
UEP_DIR
UEP_MASS



















CTGF-447G/C
119
98.2
65
52
52.9

R
5090.3



 


NBS1 Gln185Glu G/C
118
97
65
51
52.9

R
5192.4


 


MBL2 161 G/A
99
96.8
65
50.3
52.9

F
5299.5


 


IGF2R Leu252Val C/G
114
98.5
67.8
68.6
82.4

F
5206.4


 


MUC5AC-221 C/T
119
81.8
67.8
56.9
64.7 g

R
5273.4


 


Arg1 intron1 C/T
102
99.6
67.8
53.3
52.6

R
5932.9


 


REV1 Phe257Ser C/T
105
99.6
67.8
57.5
55

R
6003.9


 


Apex1 Asp148Glu G/T
114
92.9
67.8
46.8
35

F
6113


 


IL-10-1082A/G
107
98
68.8
51.2
58.8

R
4977.2










Sequenom conditions for the polymorphisms genotyping - 7














EXT1_
EXT1_




SNP_ID
UEP_SEQ
CALL
MASS
EXT1_SEQ















CTGF-447 G/C
AAAAGGTTTCTCCCCCC
G
5363.5
AAAAGGTTTCTCCCCCCC




[SEQ ID NO 116]


[SEQ ID NO 117]


 


NBS1 Gln185Glu G/C
AGGCTGCTTCTTGGACT
G
5465.6
AGGCTGCTTCTTGGACTC



[SEQ ID NO 118]


[SEQ ID NO 119]


 


MBL2 161 G/A
CAAAGATGGGCGTGATG
A
5596.7
CAAAGATGGGCGTGATGA



[SEQ ID NO 120]


[SEQ ID NO 121]


 


IGF2R Leu252Val C/G
GCCAGCCCCGGGACGGA
C
5479.6
GCCAGCCCCGGGACGGAC



[SEQ ID NO 122]


[SEQ ID NO 123]


 


MUC5AC-221 C/T
ATGGGTGTGTCTGCCGG
T
5570.6
ATGGGTGTGTCTGCCGGA



[SEQ ID NO 124]


[SEQ ID NO 125]


 


Arg1 intron1 C/T
GGCTGTAAGGAAATCTGGG
T
6230.1
GGCTGTAAGGAAATCTGGGA



[SEQ ID NO 126]


[SEQ ID NO 127]


 


REV1 Phe257Ser C/T
CCTTATCCTCCTCCTGGGAA
T
6301.1
CCTTATCCTCCTCCTGGGAAA



[SEQ ID NO 128]


[SEQ ID NO 129]


 


Apex1 Asp148Glu G/T
TGTTTCATTTCTATAGGCGA
T
6401.2
TGTTTCATTTCTATAGGCGAT



[SEQ ID NO 130]


[SEQ ID NO 131]


 


IL-10-1082 A/G
CCTATCCCTACTTCCCC
G
5250.4
CCTATCCCTACTTCCCCC



[SEQ ID NO 132]


[SEQ ID NO 133]










Sequenom conditions for the polymorphisms genotyping - 8











SNP_ID
EXT2_CALL
EXT2_MASS
EXT2_SEQ
1stPAUSE
















CTGF-447G/C
C
5716.7
AAAAGGTTTCTCCCCCCGA
[SEQ ID NO 134]
5419.5



 


NBS1 Gln185Glu G/C
C
5818.8
AGGCTGCTTCTTGGACTGA
[SEQ ID NO 135]
5521.6


 


MBL2 161 G/A
G
5901.9
CAAAGATGGGCGTGATGGC
[SEQ ID NO 136]
5628.7


 


IGF2R Leu252Val C/G
G
5823.8
GCCAGCCCCGGGACGGAGT
[SEQ ID NO 137]
5535.6


 


MUC5AC -221 C/T
C
5890.8
ATGGGTGTGTCTGCCGGGT
[SEQ ID NO 138]
5602.6


 


Arg1 intron1 C/T
C
6879.5
GGCTGTAAGGAAATCTGGGGGT
[SEQ ID NO 139]
6262.1


 


REV1 Phe257Ser C/T
C
6630.3
CCTTATCCTCCTCCTGGGAAGA
[SEQ ID NO 140]
6333.1


 


Apex1 Asp148Glu G/T
G
7068.6
TGTTTCATTTCTATAGGCGAGGA
[SEQ ID NO 141]
6442.2


 


IL-10 -1082 A/G
A
5858.8
CCTATCCCTACTTCCCCTTC
[SEQ ID NO 142]
5281.4









Results

Example 2
Nitric Oxide Synthase 3 Asp 298 Glu (T/G) Polymorphism Allele and Genotype Frequencies in the Lung Cancer Patients, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients, resistant smokers, and controls. The frequencies are shown in the following table.







TABLE 1E







Nitric oxide synthase 3 Asp 298 Glu (T/G) polymorphism


allele and genotype frequencies in the lung cancer patients,


resistant smokers and controls.










Allele*
Genotype












Frequency
T
G
TT
TG
GG





Controls n = 183 (%)
108 (30%)
258 (70%)
13 (7%) 
82 (45%)
88 (48%)


Lung Cancer n = 107 (%)
 71 (33%)
143 (67%)
9 (8%)
53 (50%)
45 (42%)


Resistant n = 198 (%)
135 (34%)
261 (66%)
281,2 (14%)  
79 (40%)
91 (46%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. TT vs TG/GG for resistant vs lung cancer, Odds ratio (OR)=1.8, 95% confidence limits 0.8-4.3, χ2 (Yates uncorrected)=2.14, p=0.14, TT genotype=protective for lung cancer; and
        2. Genotype. TT vs TG/GG for resistant vs controls, Odds ratio (OR)=2.2, 95% confidence limits 1.0-4.6, χ2 (Yates corrected)=4.2, p=0.04, TT genotype=protective for lung cancer.

Thus, for the Asp 298 Glu (T/G) polymorphism of the Nitric oxide synthase 3 gene, the TT genotype was found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.8, P=0.14) consistent with a protective role. This greater frequency compared to the blood donor cohort also suggests that the TT genotype is over represented in the resistant group (see Table 1E)

    
    


Example 3
Nitric Oxide Synthase 3 −786 T/C Polymorphism Allele and Genotype Frequencies in the Lung Cancer Patients, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients, resistant smokers, and controls. The frequencies are shown in the following table.







TABLE 1F







Nitric oxide synthase 3 −786 T/C polymorphism allele and genotype


frequencies in the lung cancer patients, resistant smokers and controls.










Allele*
Genotype












Frequency
C
T
CC
CT
TT





Controls n = 183 (%)







Lung Cancer n = 107 (%)
 82 (38%)
132 (62%)
16 (15%)
 50 (47%)
411 (38%) 


Resistant n = 198 (%)
166 (42%)
228 (58%)
31 (16%)
104 (53%)
62 (31%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. TT vs CC/CT for Lung cancer vs resistant, Odds ratio (OR)=1.4, 95% confidence limits 0.8-2.3, χ2 (Yates uncorrected)=1.45, p=0.23, TT genotype=susceptibility to lung cancer.

Thus, for the −786 T/C polymorphism of the Nitric oxide synthase 3 gene, the TT genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.4, P=0.23) consistent with a susceptibility role (see Table 1F).

    
    


Example 4
Super Oxide Dismutase 3 Arg 312 Gln C/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients, resistant smokers, and controls. The frequencies are shown in the following table.







TABLE 2







Super Oxide Dismutase 3 Arg 312 Gln C/G Polymorphism Allele


And Genotype Frequencies In The Lung Cancer, Resistant Smokers And Controls.










Allele*
Genotype












Frequency
C
G
CC
CG
GG





Controls n = 190 (%)
371 (98%) 
9 (2%)
183 (96%) 
5 (3%)
2 (1%)


Lung Cancer n = 104 (%)
208 (100%)
0 (0%)
104 (100%)
0 (0%)
0 (0%)


Resistant n = 182 (%)
390 (98%) 
10 (3%) 
191 (95%) 
81 (4%) 
11 (1%) 





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype CG/GG vs CC for resistant vs lung cancer, Yates uncorrected=3.38, P=0.07 and Fisher's Two tailed test, P=0.03. CG/GG=protective for lung cancer.

Thus, for the analysis of the Arg 312 Gln polymorphism of the Superoxide dismutase 3 gene, the CG and GG genotypes were found to be significantly greater in the smoking resistant cohort compared to the lung cancer cohort (P=0.03) consistent with each having a protective role (Table 2).

    
    


Example 5
XRCC1 Arg 399 Gln A/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients, resistant smokers, and controls. The frequencies are shown in the following table.







TABLE 3







XRCC1 Arg 399 Gln A/G Polymorphism Allele And Genotype Frequencies


In The Lung Cancer, Resistant Smokers And Controls.










Allele*
Genotype












Frequency
A
G
AA
AG
GG





Controls n = 190 (%)







Lung Cancer n = 103
68 (33%)
138 (67%)
 4 (4%)
60 (58%)
39 (38%)


(%)


Resistant n = 193 (%)
132 (34%) 
254 (66%)
181 (9%) 
96 (50%)
79 (41%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. AA vs AG/GG for resistant vs lung cancer, Odds ratio (OR)=2.6, 95% confidence limits 0.8-9.2, χ2 (Yates uncorrected)=2.89, p=0.09. AA genotype=protective for lung cancer.

Thus, for the analysis of the Arg 399 Gln A/G polymorphism of the XRCC1 gene, the AA genotype was found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=2.6, P=0.09) consistent with a protective role (Table 3).

    
    


Example 6
Interleukin 8 −251 A/T Polymorphism Allele and Genotype Frequencies in the Lung Cancer, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients, resistant smokers, and controls. The frequencies are shown in the following table.







TABLE 4







Interleukin 8 −251 A/T Polymorphism Allele And Genotype Frequencies In The


Lung Cancer, Resistant Smokers And Controls.










Allele*
Genotype












Frequency
A
T
AA
AT
TT





Controls n = 188 (%)
175 (47%)
201 (53%)
39 (21%)
97 (52%)
52 (28%)


Lung Cancer n = 90
 68 (38%)
112 (62%)
6 (7%)
56 (52%)
28 (31%)


Resistant n = 199 (%)
1922 (48%) 
206 (52%)
451 (23%) 
102 (51%) 
52 (26%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. AA vs AT/TT for resistant vs lung cancer, Odds ratio (OR)=4.1, 95% confidence limits=1.6=11.2, χ2 (Yates corrected)=9.8, p=0.002, AA=protective for lung cancer; and
        2. Allele. A vs T for resistant smokers vs lung cancer, Odds ratio (OR)=1.5, 95% confidence limits 1.0-2.2, χ2 (Yates corrected)=5.07, p=0.02 A=protective for lung cancer.

Thus, for the analysis of the −251 A/T polymorphism of Interleukin-8 gene, the AA genotype was found to be significantly greater in the smoking resistant cohort compared to the lung cancer cohort (OR=4.1, P=0.002) consistent with a protective role (Table 4). The A allele was also found to be significantly greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.5, P=0.02) consistent with a protective role (Table 4).

    
    


Example 7
Anti-Chymotrypsin Ala −15 Thr Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 5







Anti-chymotrypsin Ala-15 Thr polymorphism allele and genotype


frequencies in the lung cancer subjects, resistant smokers and controls.










Allele*
Genotype












Frequency
A
G
AA
AG
GG





Lung Cancer n = 108
 99 (46%)
1172 (54%) 
24 (22%)
 51 (47%)
331 (31%) 


Resistant n = 196
207 (53%)
185 (47%)
52 (27%)
103 (53%)
41 (21%)


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs AA/AG for Lung cancer vs resistant, Odds ratio (OR)=1.7, 95% confidence limits=0.9-2.9, χ2 (Yates uncorrected)=3.51, p=0.06, GG=susceptibile to lung cancer; and
        2. Allele. G vs A for lung cancer vs resistant smokers, Odds ratio (OR)=1.3, 95% confidence limits 0.9-1.9, χ2 (Yates uncorrected)=2.71, p=0.10, G=susceptibility to lung cancer.

Thus, for the analysis of the Ala 15 Thr polymorphism of Anti-chymotrypsin gene, the GG genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.7, P=0.06) consistent with a susceptibility role (see Table 5). The G allele was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.3, P=0.1) consistent with a susceptibility role (see Table 5).

    
    


Example 8
Cyclin D1 (CCND1) A 870 G Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 6







Cyclin D1 (CCND1) A 870 G Polymorphism Allele And Genotype


Frequencies In The Lung Cancer Subjects And Resistant Smokers.










Allele*
Genotype












Frequency
A
G
AA
AG
GG





Lung Cancer
109 (51%)
105 (49%)
252 (23%) 
59 (55%)
23 (21%)


n = 107


Resistant n = 199 (%)
188 (47%)
210 (53%)
45 (23%)
98 (49%)
561 (28%) 





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs AG/AA for Resistant vs lung cancer, Odds ratio (OR)=1.4, 95% confidence limits=0.8-2.6, χ2 (Yates uncorrected)=1.6, p=0.20, GG=protective for lung cancer; and
        2. Genotype. AG/AA vs GG for Lung cancer vs resistant, Odds ratio (OR)=1.4, 95% confidence limits=0.8-2.6, χ2 (Yates uncorrected)=1.6, p=0.20, AA=susceptibility to lung cancer.

Thus, for the analysis of the A 870 G polymorphism of the Cyclin D1 gene, the GG genotype was found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.4, P=0.20) consistent with a protective role (see Table 6). In contrast, the AA genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.4, P=0.2) consistent with a susceptibility role (see Table 6).

    
    


Example 9
Interleukin 1B (IL-1b) −511 A/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 7







Interleukin 1B (IL-1b) −511 A/G Polymorphism Allele And Genotype


Frequencies In The Lung Cancer Subjects, Resistant Smokers And Controls.










Allele*
Genotype












Frequency
A
G
AA
AG
GG





Lung Cancer n = 107
 64 (30%)
150 (70%)
12 (11%)
40 (37%)
551 (51%) 


Resistant n = 198 (%)
143 (36%)
253 (64%)
23 (12%)
97 (49%)
78 (39%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs AA/AG for Lung cancer vs resistant, Odds ratio (OR)=1.6, 95% confidence limits=1-2.7, χ2 (Yates uncorrected)=4.07, p=0.04, GG=susceptibility to lung cancer.

Thus, for the analysis of the −511 A/G polymorphism of the Interleukin 1B gene, the GG genotype was found to be significantly greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.6, P=0.04) consistent with a susceptibility role (see Table 7).

    
    


Example 10
FAS (Apo-1/CD 95) A −670 G Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 8







FAS (Apo-1/CD 95) A −670 G Polymorphism Allele And Genotype


Frequencies In The Lung Cancer Subjects, Resistant Smokers And Controls.










Allele*
Genotype












Frequency
A
G
AA
AG
GG





Lung Cancer
1212 (57%) 
 91 (43%)
321 (30%) 
 57 (54%)
17 (16%)


n = 106


Resistant n = 198 (%)
202 (51%)
194 (49%)
45 (23%)
112 (57%)
41 (21%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. AA vs AG/GG for Lung cancer vs resistant, Odds ratio (OR)=1.5, 95% confidence limits=0.8-2.6, χ2 (Yates uncorrected)=2.03, p=0.15, AA=susceptibility to lung cancer; and
        2. Allele. A vs G for Lung cancer vs resistant, Odds ratio (OR)=1.3, 95% confidence limits 0.9-1.8, χ2 (Yates uncorrected)=2.04, p=0.15, A=susceptibility to lung cancer.

Thus, for the analysis of the A −670 G polymorphism of the FAS (Apo-1/CD95) gene, the AA genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.5, P=0.15) consistent with a susceptibility role (see Table 8). The A allele was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.3, P=0.15) consistent with a susceptibility role (see Table 8).

    
    


Example 11
XPD 751 T/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 9







XPD 751 T/G Polymorphism Allele And Genotype Frequencies


In The Lung Cancer Subjects And Resistant Smokers.









Frequency










Allele*
Genotype













G
T
GG
TG
TT
















Lung
 72 (33%)
144 (66%)
11 (10%)
50 (46%)
47 (44%)


Cancer


n = 108


Resistant
147 (37%)
247 (63%)
311 (16%) 
85 (43%)
81 (41%)


n = 197


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs TG/TT for Resistant vs lung cancer, Odds ratio (OR)=1.7, 95% confidence limits=0.8-3.7, χ2 (Yates uncorrected)=1.81, p=0.18, GG=protective for lung cancer.

Thus, for the analysis of the 751 T/G polymorphism of the XPD gene, the GG genotype was found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.7, P=0.18) consistent with a protective role (Table 9).

    
    


Example 12
Cytochrome P450 1A1 Ile 462 Val G/A Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 10







Cytochrome P450 1A1 Ile 462 Val G/A Polymorphism Allele And Genotype


Frequencies In The Lung Cancer Subjects, Resistant Smokers And Controls.









Frequency










Allele*
Genotype













G
A
GG
AG
AA
















Lung Cancer
5 (2%)
213 (98%)
0 (0%)
5 (5%)
1041 (95%) 


n = 109


Resistant n = 199 (%)
20 (5%) 
378 (95%)
131 (1%)  
181 (9%)  
180 (90%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. AG/GG vs AA for Resistant vs lung cancer, Odds ratio (OR)=2.2, 95% confidence limits=0.7-6.9, χ2 (Yates uncorrected)=2.41, p=0.12, GG/AG=protective for lung cancer, AA=susceptibility to lung cancer.

Thus, for the analysis of the Ile 462 Val G/A polymorphism of the CYP 450 1A1 gene, the AG and GG genotypes were found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=2.2, P=0.12) consistent with each having a protective role (see Table 10). In contrast, the AA genotype was found to be consistent with a susceptibility role (see Table 10).

    
    


Example 13
MMP12 Asn 357 Ser Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 11







MMP12 Asn 357 Ser Polymorphism Allele And Genotype


Frequencies In The Lung Cancer Subjects And Resistant Smokers.









Frequency










Allele*
Genotype













G
A
GG
AG
AA
















Lung
8 (4%)
210 (96%)
1 (1%)
6 (5%)
102 (94%)


Cancer


n = 109


Resistant
21 (5%) 
377 (95%)
01 (0%) 
211 (11%) 
178 (89%)


n = 199


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG/AG vs AA for Resistant vs lung cancer, Odds ratio (OR)=1.7, 95% confidence limits=0.7-4.6, χ2 (Yates uncorrected)=1.45, p=0.23, GG/AG=protective for lung cancer.

Thus, for the analysis of the Asn 357 Ser polymorphism of the Matrix metalloproteinase 12 gene, the GG and AG genotypes were found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.7, P=0.23) consistent with each having a protective role (Table 11).

    
    


Example 14
8-Oxoguanine DNA Glycosylase (OGG1) Ser 326 Cys C/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 12







8-Oxoguanine DNA Glycosylase (OGG1) Ser 326 Cys C/G


Polymorphism Allele And Genotype Frequencies In The Lung Cancer


Subjects And Resistant Smokers.









Frequency










Allele*
Genotype













G
C
GG
CG
CC
















Lung
 40 (18%)
178 (82%)
2 (2%)
36 (33%)
 71 (65%)


Cancer


n = 109


Resistant
100 (25%)
298 (75%)
141 (7%)  
72 (36%)
113 (57%)


n = 199


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs CG/CC for Resistant vs lung cancer, Odds ratio (OR)=4.0, 95% confidence limits=0.9-26.3, χ2 (Yates uncorrected)=3.87, p=0.05, GG=protective for lung cancer.

Thus, for the analysis of the Ser 326 Cys (C/G) polymorphism of the OGGI gene, the GG genotype was found to be significantly greater in the smoking resistant cohort compared to the lung cancer cohort (OR=4.0, P=0.05) consistent with a protective role (Table 12).

    
    


Example 15
N-Acetyltransferase 2 Arg 197 Gln G/A Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 13







N-Acetyltransferase 2 Arg 197 Gln G/A Polymorphism Allele And


Genotype Frequencies In The Lung Cancer Subjects


And Resistant Smokers.









Frequency










Allele*
Genotype













A
G
AA
AG
GG
















Lung Cancer
55 (26%)
157 (74%)
 9 (8%)
37 (35%)
601 (57%) 


n = 106


Resistant
122 (31%)
268 (69%)
17 (9%)
88 (45%)
90 (46%)


n = 195


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs AG/AA for Lung cancer vs resistant, Odds ratio (OR)=1.5, 95% confidence limits=0.9-2.5, χ2 (Yates uncorrected)=3.0, p=0.08, GG=susceptibility to lung cancer.

Thus, for the analysis of the Arg 197 Gln G/A polymorphism of the N-Acetyltransferase 2 gene, the GG genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.5, P=0.08) consistent with a susceptibility role (see Table 13).

    
    


Example 16
Cytochrome P450 2E1 1019 G/C Pst1 Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 14a







Cytochrome P450 2E1 1019 G/C Pst1 Polymorphism Allele And


Genotype Frequencies In The Lung Cancer Subjects


And Resistant Smokers.









Frequency










Allele*
Genotype













C
G
CC
CG
GG
















Lung Cancer
10 (5%)
208 (95%)
0 (0%)
101 (9%) 
 99 (91%)


n = 109


Resistant n = 197
11 (3%)
383 (97%)
0 (0%)
11 (6%)
186 (94%)


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. CG vs GG for Lung cancer and resistant, Odds ratio (OR)=1.7, 95% confidence limits=0.7-4.5, χ2 (Yates uncorrected)=1.42, p=0.23, CG=susceptibility to lung cancer.

Thus, for the analysis of the 1019 G/C Pst 1 polymorphism of the CYP 2E1 gene, the CG genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.7, P=0.23) consistent with a susceptibility role (see Table 14a).

    
    


Example 17
Cytochrome P450 2E1 C/T Rsa I Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 14b







Cytochrome P450 2E1 C/T Rsa I Polymorphism Allele And Genotype


Frequencies In The Lung Cancer Subjects And Resistant Smokers.









Frequency










Allele*
Genotype













T
C
TT
TC
CC
















Lung Cancer
11 (5%)
205 (95%)
0 (0%)
111 (10%)
 97 (90%)


n = 108


Resistant
11 (3%)
385 (97%)
0 (0%)
11 (6%) 
187 (94%)


n = 198 (%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. TC vs CC for Lung cancer and resistant, Odds ratio (OR)=1.9, 95% confidence limits=0.8-5.0, χ2 (Yates uncorrected)=2.24, p=0.13, TC=susceptibility to lung cancer.

Thus, for the analysis of the C/T Rsa 1 polymorphism of the CYP 2E1 gene, the TC genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.9, P=0.13) consistent with a susceptibility role (see Table 14b).

    
    


Example 18
Interleukin 18 105 A/C Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 15a







Interleukin 18 105 A/C Polymorphism Allele And Genotype|


Frequencies In The Lung Cancer Subjects And Resistant Smokers.









Frequency










Allele*
Genotype













C
A
CC
AC
AA
















Lung
 50 (23%)
164 (77%)
  8 (8%)
 34 (33%)
651 (61%)


Cancer


n = 107


Resistant
116 (29%)
284 (71%)
171 (9%)
821 (41%)
101 (50%) 


n = 200


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. AA vs AC/CC for Lung cancer and resistant, Odds ratio (OR)=1.6, 95% confidence limits=1.0-2.6, χ2 (Yates uncorrected)=3.51, p=0.06, AA=susceptibility to lung cancer, AC/CC=protective for lung cancer

Thus, for the analysis of the 105 A/C polymorphism of the Interleukin-18 gene, the AA genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.6, P=0.06) consistent with a susceptibility role (see Table 15a). In contrast, the AC and CC genotypes were each consistent with a protective role (see Table 15).

    
    


Example 19
Interleukin 18−133 C/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 15b







Interleukin 18 −133 C/G Polymorphism Allele And Genotype


Frequencies In The Lung Cancer Subjects And Resistant Smokers.









Frequency










Allele*
Genotype













G
C
GG
CG
CC
















Lung Cancer
 52 (24%)
166 (76%)
  8 (7%)
 36 (33%)
651 (60%)


n = 109


Resistant
117 (30%)
279 (70%)
171 (9%)
831 (42%)
 98 (49%)


n = 198


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. CC vs CG/GG for Lung cancer and resistant, Odds ratio (OR)=1.5, 95% confidence limits=0.9-2.5, χ2 (Yates uncorrected)=2.90, p=0.09, CC=susceptibility to lung cancer, CG/GG=protective for lung cancer.

Thus, for the analysis of the −1.33 C/G polymorphism of the Interleukin-18 gene, the CC genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.5, P=0.09) consistent with a susceptibility role (see Table 15b). In contrast, the CG and GG genotypes were each consistent with a protective role (see Table 15b).

    
    


Example 20
Glutathione S-Transferase M Null Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects, Controls, and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 16







Glutathione S-Transferase M Null Polymorphism Allele


And Genotype Frequencies In The Lung Cancer Subjects,


Controls, And Resistant Smokers.










Allele*












Frequency
Null
Wild






Controls n = 178
75 (42%)
103 (58%) 



Lung Cancer n = 107
671 (58%) 
48 (42%)



Resistant n = 182
100 (55%) 
82 (45%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. Null vs wild for Lung cancer and controls, Odds ratio (OR)=1.92, 95% confidence limits=1.2-3.2, χ2 (Yates corrected)=6.64, p=0.01, Null=susceptibility to lung cancer.

Thus, for the analysis of the null polymorphism of the Glutathione S Transferase gene, the null genotype was found to be greater in the lung cancer cohort compared to the blood donor cohort (OR=1.92, P=0.01) consistent with a susceptibility role (see Table 16).

    
    


Example 21
Interferon-Gamma 874 A/T Polymorphism Allele and Genotype Frequencies in the Lung Cancer Subjects, Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 17







Interferon-Gamma 874 A/T Polymorphism Allele And Genotype


Frequencies In The Lung Cancer Subjects, Resistant Smokers And Controls.









Frequency










Allele*
Genotype













A
T
AA
AT
TT
















Controls n = 186 (%)
183 (49%)
189 (51%)
37 (20%)
109 (58%)
40 (22%)


Lung cancer n = 106
116 (55%)
 96 (45%)
341,2 (32%)  
 48 (45%)
24 (23%)


(%)


Resistant n = 196
209 (53%)
183 (47%)
50 (26%)
109 (56%)
37 (19%)


(%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. AA vs AT/TT for lung cancer vs resistant, Odds ratio (OR)=1.4, 95% confidence limits 0.8-2.4, χ2 (Yates uncorrected)=1.48, p=0.22, AA genotype=susceptibile to lung cancer; and
        2. Genotype. AA vs AT/TT for lung cancer vs controls, Odds ratio (OR)=1.9, 95% confidence limits 1.1-3.4, χ2 (Yates corrected)=5.45, p=0.02, AA genotype=susceptibile to lung cancer.

Thus, for the analysis of the 874 A/T polymorphism of the Interferon gamma gene, the AA genotype was found to be greater in the lung cancer cohort compared to the blood donor cohort (OR=1.9, P=0.02) and compared to the smoking resistant cohort (OR=1.4, P=0.22) consistent with a susceptibility role (see Table 17).

    
    


Example 22
Cyclo-Oxygenase 2 Polymorphism Allele and Genotype Frequency in the Lung Cancer Patients, Exposed Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 18







Cyclo-Oxygenase 2 Polymorphism Allele And Genotype Frequency In


The Lung Cancer Patients, Exposed Resistant Smokers And Controls.










Allele*
Genotype












Frequency
C
G
CC
CG
GG





Controls
27 (14%)
161
3 (3%)
21 (22%)
70


n = 95 (%)

(86%)


(75%)


Lung Cancer
34 (16%)
184
5 (5%)
24 (22%)
80


n = 109 (%)

(84%)


(73%)


Resistant n = 158
75 (24%)
241
11 (7%) 
53 (34%)
94


(%)

(76%)


(59%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. CC/CG vs GG for Lung cancer vs resistant, Odds ratio (OR)=0.53, 95% confidence limits=0.3-0.9, χ2 (Yates corrected)=4.9, p=0.03 CC/CG=protective;
        2. Allele. C vs G for Lung cancer vs resistant, Odds ratio (OR)=0.59, 95% confidence limits 0.4-0.9, χ2 (Yates corrected)=4.8, p=0.03, C=protective;
        3. Genotype. GG vs CG/CC for Lung cancer vs resistant, Odds ratio (OR)=1.88, 95% confidence limits=1.1-3.3, χ2 (Yates corrected)=4.9, p=0.03 GG=susceptibility; and
        4. Allele. G vs C for Lung cancer vs resistant, Odds ratio (OR)=1.7, 95% confidence limits 1.1-2.7, χ2 (Yates corrected)=4.8, p=0.03, G=susceptibility.

Thus, for the analysis of the −765 C/G promoter polymorphisms of the cyclo-oxygenase 2 gene, the C allele, and CC and CG genotypes were found to be significantly greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.59, P=0.03 and OR=0.53, P=0.03, respectively), consistent with a protective role. This greater frequency compared to the blood donor cohort also suggests that the C allele (CC genotype) is over-represented in the resistant group (see Table 18). In contrast, the G allele and GG genotype were found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.7, P=0.03 and OR=1.88, P=0.03, respectively), consistent with a susceptibility role (see Table 18).

    
    


Example 23
Matrix Metalloproteinase 1 (MMP1) −1607 1G/2G Polymorphism Allele and Genotype Frequencies in Lung Cancer Patients, Exposed Resistant Smokers and Controls
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 19







Matrix Metalloproteinase 1 (MMP1) −1607 1G/2G Polymorphism


Allele And Genotype Frequencies In Lung Cancer Patients,


Exposed Resistant Smokers And Controls.










Allele*
Genotype












Frequency
1G
2G
1G1G
1G2G
2G2G





Controls n = 174
214
134
68 (39%)
78 (45%)
28 (16%)


(%)
(61%)
(39%)


Lung Cancer
 58
 76
13 (19%)
32 (48%)
22 (33%)


n = 67 (%)
(43%)
(57%)


Resistant n = 171
167
175
41 (24%)
85 (50%)
45 (26%)


(%)
(49%)
(51%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. 2G2G vs 1G1G/1G2G for Lung cancer vs controls, Odds ratio (OR)=2.58, 95% confidence limits 1.3-5.2, χ2 (Yates uncorrected)=7.5, p=0.006 2G2G genotype=susceptibility; and
        2. Allele. 2G vs 1G for Lung cancer vs controls, Odds ratio (OR)=2.1, 95% confidence limits 1.4-3.2, χ2 (Yates corrected)=12.3, p=0.0004, 2G=susceptibility.

Thus, for the analysis of the −1607 1G/2G polymorphisms of the Matrix metalloproteteinase 1 gene, the 2G2G genotype was found to be significantly greater in the lung cancer cohort compared to the blood donor cohort (OR=2.58, P=0.006), consistent with a susceptibility role (see Table 19). The 2G allele was found to be significantly greater than the lung cancer cohort compared to the blood donor cohort (OR=2.1, P=0.0004), consistent with a susceptibility role (see Table 19).

    
    


Example 24
Connective Tissue Growth Factor (CTGF) −447 G/C Polymorphism Allele and Genotype Frequencies in the Lung Cancer And Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 20







Connective Tissue Growth Factor (CTGF) −447 G/C Polymorphism Allele


And Genotype Frequencies In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
G
C
GG
GC
CC





Lung cancer
201 (92%)
17
 92 (84%)
17 (16%)
0 (0%)


n = 109 (%)

(8%)


Resistant n = 200
379 (95%)
21
179 (90%)
21 (10%)
0 (0%)


(%)

(5%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GC/CC vs GG for lung cancer vs resistant, Odds ratio (OR)=1.6, 95% confidence limits 0.8-3.3, χ2 (Yates uncorrected)=1.70, p=0.19, GC/CC genotype=susceptibility (trend).

Thus, for the analysis of the −447 G/C polymorphism of the connective tissue growth factor gene, the CC and GC genotypes were found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.6, P=0.19) consistent with a susceptibility role (see Table 20).

    
    


Example 25
Mucin SAC (Muc5AC) −221 C/T Polymorphism Allele and Genotype Frequencies in the Lung Cancer and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 21







Mucin 5AC (Muc5AC) −221 C/T Polymorphism Allele And


Genotype Frequencies In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
C
T
CC
CT
TT





Lung cancer
177 (81%)
41 (19%)
 73 (67%)
31
 5


n = 109 (%)



(28%)
(5%)


Resistant n = 195
296 (76%)
94 (24%)
119 (61%)
58
18


(%)



(30%)
(9%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. TT vs CC/CT for lung cancer vs resistant, Odds ratio (OR)=0.47, 95% confidence limits 0.2-1.4, χ2 (Yates uncorrected)=2.16, p=0.14, TT genotype=protective (trend).

Thus, for the analysis of the −221 C/T polymorphism in the Mucin 5AC gene the TT genotype was found to be greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.47, P=0.14) consistent with a protective role (see Table 21).

    
    


Example 26
Mannose Binding Lectin (MBL2) 161 G/A Polymorphism Allele and Genotype Frequencies in the Lung Cancer and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 22







Mannose Binding Lectin (MBL2) 161 G/A Polymorphism Allele And


Genotype Frequencies In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
G
A
GG
AG
AA





Lung cancer
173 (82%)
37 (18%)
 71 (67%)
31
3


n = 105 (%)



(30%)
(3%)


Resistant n = 197
338 (86%)
56 (14%)
147 (75%)
44
6


(%)



(22%)
(3%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. AG/AA vs GG for lung cancer vs resistant, Odds ratio (OR)=1.4, 95% confidence limits 0.8-2.4, χ2 (Yates uncorrected)=1.67, p=0.20, AG/AA genotype=susceptibility (trend).

Thus, for the analysis of the 161 G/A polymorphism of the Mannose binding lectin (MBL2) gene, the AA and AG genotypes were found to be greater in the lung cancer cohort compared to the resistant smoker cohort (OR=1.4, P=0.20) consistent with each having a susceptibility role (see Table 22).

    
    


Example 27
Nibrin (NBS1) Gln185Glu G/C Polymorphism Allele and Genotype Frequencies in the Lung Cancer and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 23







Nibrin (NBS1) Gln185Glu G/C Polymorphism Allele And Genotype


Frequencies In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
G
C
GG
GC
CC





Lung
150 (69%)
 68 (31%)
 54
42
13


cancer n = 109 (%)


(50%)
(39%)
(12%)


Resistant n = 199
295 (74%)
103 (26%)
107
81
11


(%)


(54%)
(41%)
 (6%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. CC vs CG/GG for lung cancer vs resistant, Odds ratio (OR)=2.3, 95% confidence limits 0.9-5.8, χ2 (Yates uncorrected)=4.01, p=0.05, CC genotype=susceptibility.

Thus, for the analysis of the Gln 185 Glu G/C polymorphism of the Nibrin gene, the CC genotype was found to be significantly greater in the lung cancer cohort compared to the resistant smoker cohort (OR=2.3, P=0.05), consistent with a susceptibility role (see Table 23).

    
    


Example 28
Arginase 1 (Arg1) Intron 1 C/T Polymorphism Allele and Genotype Frequencies in the Lung Cancer and Resistant Smokers
The genotype frequency for, the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 24







Arginase 1 (Arg1) Intron 1 C/T Polymorphism Allele And Genotype


Frequencies In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
C
T
CC
CT
TT





Lung cancer n = 105
137
 73 (35%)
45
47
13


(%)
(65%)

(43%)
(45%)
(12%)


Resistant n = 180
203
157 (44%)
65
73
42


(%)
(56%)

(36%)
(41%)
(23%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. TT vs CC/CT for lung cancer vs resistant, Odds ratio (OR)=0.46, 95% confidence limits 0.2-0.95, χ2 (Yates uncorrected)=5.11, p=0.02, TT genotype=protective; and
        2. Allele. T vs C for lung cancer vs resistant, Odds ratio (OR)=0.69, 95% confidence limits 0.5-1.0, χ2 (Yates corrected)=3.96, p=0.05, T allele=protective.

Thus, for the analysis of the intron 1 C/T polymorphism of the Arginase 1 gene, the TT genotype was found to be significantly greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.46, P=0.02) consistent with a protective role (see Table 24). The T allele was found to be significantly greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.69, P=0.05) consistent with a protective role (see Table 24).

    
    


Example 29
REV1 Phe257Ser C/T Polymorphism Allele and Genotype Frequencies in the Lung Cancer and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 25







REV1 Phe257Ser C/T Polymorphism Allele And Genotype


Frequencies In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
C
T
CC
CT
TT





Lung cancer n = 109
129 (59%)
 89
39
51
19


(%)

(41%)
(36%)
(47%)
(17%)


Resistant n = 192
242 (63%)
142
83
76
33


(%)

(37%)
(43%)
(40%)
(17%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. CC vs CT/TT for lung cancer vs resistant, Odds ratio (OR)=0.73, 95% confidence limits 0.4-1.2, χ2 (Yates uncorrected)=1.6, p=0.20, CC genotype=protective (trend).

Thus, for the analysis of the Phe 257 Ser C/T polymorphism of the REV1 gene, the CC genotype was found to be greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.73, P=0.20), consistent with a protective role (see Table 25).

    
    


Example 30
Insulin-Like Growth Factor II Receptor (IGF2R) Leu252Val C/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 26







Insulin-Like Growth Factor II Receptor (IGF2R)


Leu252Val C/G Polymorphism Allele And Genotype Frequencies


In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
C
G
CC
CG
GG





Lung cancer n = 109
190
28 (13%)
 82 (75%)
26
1


(%)
(87%)


(24%)
(1%)


Resistant n = 198
342
54 (14%)
150 (76%)
42
6


(%)
(86%)


(21%)
(3%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs CC/CG for lung cancer vs resistant, Odds ratio (OR)=0.30, 95% confidence limits 0.01-2.5, χ2 (Yates uncorrected)=1.41, p=0.22 (1-tailed t-test), GG genotype=protective (trend).

Thus, for the analysis of the Leu 252 Val C/G polymorphism of the Insulin-like growth factor II receptor gene the GG genotype was found to be greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.30, P=0.22) consistent with a protective role (see Table 26).

    
    


Example 31
Apex Nuclease (APE1) Asp148Glu T/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 27







Apex Nuclease (APE1) Asp148Glu T/G Polymorphism Allele And


Genotype Frequencies In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
T
G
TT
TG
GG





Lung
124
 94 (43%)
39 (36%)
46
24


cancer n = 109 (%)
(57%)


(42%)
(22%)


Resistant n = 192
229
155 (40%)
69 (36%)
91
32


(%)
(60%)


(47%)
(17%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs TT/TG for lung cancer vs resistant, Odds ratio (OR)=1.4, 95% confidence limits 0.8-2.7, χ2 (Yates uncorrected)=1.3, p=0.25, GG genotype=susceptibility (trend).

Thus, for the analysis of the Asp 148 Glu T/G polymorphism of the Apex nuclease gene, the GG genotype was found to be greater in the lung cancer cohort compared to the resistant smoker cohort (OR=1.4, P=0.25), consistent with a susceptibility role (see Table 27).

    
    


Example 32
Interleukin 10 (IL-10) −1082 A/G Polymorphism Allele and Genotype Frequencies in the Lung Cancer and Resistant Smokers
The genotype frequency for the above allele was determined in lung cancer patients and resistant smokers. The frequencies are shown in the following table.







TABLE 28







Interleukin 10 (IL-10) −1082 A/G Polymorphism Allele


And Genotype Frequencies In The Lung Cancer And Resistant Smokers.










Allele*
Genotype












Frequency
G
C
GG
GC
CC





Lung cancer
 91 (46%)
105 (54%)
16 (16%)
59 (60%)
23 (24%)


n = 98 (%)


Resistant
174 (44%)
218 (56%)
40 (20%)
94 (48%)
62 (32%)


n = 196 (%)





*number of chromosomes (2n)






A mathematical analysis of the data in the table indicated that:

    
    
        1. Genotype. GG vs GC/CC for lung cancer vs resistant, Odds ratio (OR)=0.66, 95% confidence limits 0.4-1.2, χ2 (Yates uncorrected)=2.12, p=0.15, GG genotype=protective (trend).

Thus, for the analysis of the −108 2A/G polymorphism of the Interleukin-10 gene the GG genotype was found to be greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.66, P=0.15), consistent with a protective role (see Table 28).

    
    


Table 29 presents a summary of the above results.







TABLE 29







Summary Of Protective And Susceptibility Polymorphisms In


Lung Cancer Patients Relative To Resistant Smokers


(With Normal Lung Function)









Gene
Polymorphism
Role





Nitric Oxide synthase 3 (NOS3)
NOS3 Asp 298 Glu
TT protective


Nitric Oxide synthase 3 (NOS3)
NOS3 −786 T/C
TT susceptibility


Superoxide dismutase 3 (SOD3)
SOD3 Arg 312 Gln
CG/GG protective


XRCC1
XRCC1 Arg 399 Gln G/A
AA protective


Interleukin-8 (IL-8)
IL-8 −251 A/T
AA protective


Anti-chymotrypsin (ACT)
ACT Ala 15 Thr
GG susceptibility


Cyclin D (CCND1)
CCND1 A870G
GG protective AA




susceptibility


Interleukin 1B (IL-1B)
IL-1B −511 A/G
GG susceptibility


FAS (Apo-1/CD95)
FAS A-670G
AA susceptibility


XPD
XPD −751 G/T
GG protective


CYP 1A1
CYP 1A1 Ile 462 Val
GG/AG protective



A/G
AA susceptibility


Matrix metalloproteinase 12
MMP12 Asn 357 Ser
GG/AG protective


(MMP12)
A/G



8-Oxoguanine DNA glycolase
OGG1 Ser 326 Cys G/C
GG protective


(OGG1)




N-acetyltransferase 2 (NAT2)
NAT2 Arg 197 Gln A/G
GG susceptibility


CYP2E1
CYP2E1 1019 G/C Pst I
CC/CG




susceptibility


CYP2E1
CYP2E1 C/T Rsa I
TT/TC




susceptibility


Interleukin-18 (IL-18)
IL-18 105 A/C
AC/CC protective




AA susceptibility


Interleukin-18 (IL-18)
IL-18 −133 G/C
CG/GG protective




CC susceptibility


Glutathione S-transferase M
GSTM null
Null




susceptibility


Interferon gamma (IFNγ)
IFNγ 874 A/T
AA susceptibility


Cyclo-oxygenase 2 (COX2)
COX2 −765 G/C
CC/CG protective




GG susceptibility


Matrix metalloproteinase 1 (MMP1)
MMP −1607 1G/2G
2G2G




susceptibility


Connective tissue growth factor
CTGF −447 G/C
GC/CC


(CTGF)

susceptibility


Mucin 5AC (MUC5AC)
MUC5AC −221 C/T
TT protective


Mannose binding lectin 2 (MBL2)
MBL2 +161 G/A
AG/AA




susceptibility


Nibrin (NBS1)
NBS1 Gln185Glu G/C
CC susceptibility


Arginase 1 (Arg1)
Arg1 intron 1 C/T
TT protective


REV1
REV1 Phe257Ser C/T
CC protective


Insulin-like growth factor II receptor
IGF2R Leu252Val C/G
GG protective


(IGF2R)




Apex nuclease (Apex or APE1))
Apex Asp148Glu G/T
GG susceptibility


Interleukin 10 (IL-10)
IL-10 −1082 A/G
GG protective









Example 33
In addition to examining the individual frequencies, the combined frequencies of the presence or absence of protective genotypes was also examined. The results are shown in Tables 31-35 and are discussed below.







TABLE 30





Combined Frequencies Of The Presence Or Absence Of


Protective Genotypes (CYP1A1 GG/AG, OGG1 GG, CCND1 GG,


NOS3 298 TT, IL-8 AA, XRCC1 AA) In The Exposed Smoking Subjects


(Lung Cancer Subjects And Resistant Smokers).


















Number of protective polymorphisms












Cohorts
0
1
≧2
Total





Lung Cancer
66 (61%)
37 (34%)
6 (6%)
109


Resistant
71 (36%)
86 (43%)
42 (21%)
199


smokers






% of
66/137 (48%)   
37/123 (30%)   
6/42 (14%)  



smokers with






Lung cancer





Comparison
Odd's ratio
95% CI
χ2
P value





0 vs 1 vs 2+, Resist 
—
—
22.3
<0.0001


vs Lung cancer






2+ vs 0-1, Resist vs
4.6
 1.8-12.5
11.87
0.0005


Lung cancer






0 vs 2+, Lung cancer 
2.8
1.7-4.6
16.7
<0.0001


vs Resist









When the frequencies of resistant smokers and smokers with lung cancer were compared according to the presence of 0, 1 and 2+ protective genotypes selected from a subset of six of the protective genotypes (CYP1A1GG/AG, OGG1 GG, CCND1 GG, NOS3 298 TT, IL-8 AA, XRCC1 AA), significant differences were found (overall γ2=22.3, P<0.0001) (see Table 30). This analysis suggests smokers with 2+ protective genotypes had 4-5 times more likelihood of being resistant (OR=4.6, P=0.0005), while those with no protective genotypes were nearly three times as likely to have lung cancer (OR=2.8, P<0.0001). Examined another way, the chance of having lung cancer diminished from 48%, to 30%, to 14%, in smokers with 0, 1, or 2+ protective genotypes, respectively. Analyses of larger groups of protective polymorphisms resulted in similar findings (see Tables 32 and 34).
From the analyses of the individual polymorphisms, 19 possible susceptibility genotypes were identified and analysed for their frequencies in the smoker cohort consisting of resistant smokers and those with lung cancer. When the frequencies of resistant smokers and smokers with lung cancer were compared according to the presence of 0, 1 and 2+ susceptibility genotypes selected from a subset of six of the susceptibility genotypes (CYP2E1 1019 CC/CG, FAS AA, IL-1B GG, ACT 15 GG genotypes) significant differences were found (overall γ2=10.2, P=0.006) (see Table 31). This analysis suggests that smokers with 2+ susceptibility genotypes had nearly two times more likelihood of having lung cancer (OR=1.8, P=0.04), while those with no susceptibility genotypes were two fold as likely to be resistant (OR=2.3, P=0.004). Examined another way, the chances of having lung cancer increased from 23%, to 38%, to 45% in smokers with 0, 1 or 2+ susceptibility genotypes, respectively. Analyses of larger groups of susceptibility polymorphisms resulted in similar findings (see Tables 33 and 35).







TABLE 31





Combined Frequencies Of The Presence Or Absence Of


Susceptibility Genotypes (CYP2E1 1019 CC/CG, FAS AA,


IL-1B GG, ACT 15 GG) In The Exposed Smoking Subjects


(Lung Cancer Subjects And Resistant Smokers).


















Number of susceptibility polymorphisms












Cohorts
0
1
≧2
Total





Lung Cancer
21 (19%)
52 (48%)
35 (33%)
108


Resistant
71 (36%)
85 (43%)
42 (21%)
198


smokers






% of
21/92 (23%)  
52/137 (38%)   
35/77 (45%)  



smokers with






lung cancer






Odd's





Comparison
ratio
95% CI
χ2
P value





0 vs 1 vs 2+, Lung
—
—
10.2
0.006


cancer vs Resist






2+ vs 0-1, Lung 
1.8
1.0-3.1
4.1
0.04


cancer vs Resist






0+ vs 1-2+, Resist 
2.3
1.3-4.2
8.2
0.004


vs Lung cancer
















TABLE 32





Combined Frequencies Of The Presence Or Absence Of Protective


Genotypes (CYP1A1 GG/AG, OGG1 GG, CCND1 GG, NOS3 298 TT,


SOD3 CG/GG, XPD GG, MMP12 GG/AG, XRCC1 AA, N = 8) In The


Exposed Smoking Subjects (Lung Cancer Subjects


And Resistant Smokers).


















Number of protective polymorphisms n = 8












Cohorts
0
1
≧2
Total





Lung Cancer
54 (50%)
50 (46%)
5 (4%)
109


Resistant
67 (34%)
83 (42%)
50 (25%)
199


smokers






% of
54/121 (45%)   
50/133 (38%)   
5/55 (9%)  



smokers with






Lung cancer






Odd's





Comparison
ratio
95% CI
χ2
P value





0 vs 1 vs 2+, Resist 
—
—
21.5
<0.0001


vs Lungcancer






2+ vs 0-1, Resist 
6.9
 2.5-20.5
18.7
<0.0001


vs Lung cancer






0 vs 2+, Lung 
2.0
1.2-3.2
6.96
0.008


cancer vs Resist
















TABLE 33





Combined Frequencies Of The Presence Or Absence Of


Susceptibility Genotypes (CYP2E1 1019 CC/CG, FAS AA, IL-1B GG,


ACT 15 GG, NAT2 GG, IL-18 105 AA, Ifnγ AA, N = 7) In The


Exposed Smoking Subjects (Lung Cancer Subjects


And Resistant Smokers).


















Number of susceptibility polymorphisms n = 7












Cohorts
1
2
≧3
Total





Lung
16 (15%)
35 (32%)
58 (53%)
109


Cancer






Resistant
65 (33%)
66 (33%)
69 (34%)
200


smokers






% of
16/81 (20%)  
35/101 (35%)   
58/127 (46%)   



smokers






with Lung






cancer






Odd's





Comparison
ratio
95% CI
χ2
P value





0 vs 1 vs 2+, Lung 
—
—
14.6
0.0007


cancer vs Resist






3+ vs 1-2, Lung 
2.2
1.3-5.6
9.4
0.002


cancer vs Resist






1 vs 2-3+, Resist 
2.8
1.5-5.4
10.7
0.001


vs Lung cancer
















TABLE 34





Combined Frequencies Of The Presence Or Absence


Of Protective Genotypes (CYP1A1 GG/AG, OGG1 GG, CCND1 GG,


NOS3 298 TT, IL-8 AA, XRCC1 AA, Cox 2 −765 CC/CG) In


The Exposed Smoking Subjects (Lung Cancer Subjects


And Resistant Smokers).


















Number of protective polymorphisms












Cohorts
0
1
≧2
Total





Lung Cancer
45 (40%)
50 (43%)
19 (17%)
114


Resistant
47 (23%)
79 (40%)
74 (37%)
200


smokers






% of
45/47 (49%)  
50/129 (39%)   
19/93 (20%)  



smokers with






Lung cancer






Odd's





Comparison
ratio
95% CI
χ2
P value





0 vs 1 vs 2+, Resist 
—
—
16.8
0.0002


vs Lung cancer






2+ vs 0-1, Resist 
2.94
1.6-5.4
13.44
0.0002


vs Lung cancer






0 vs 2+, Lung 
2.12
1.3-3.6
8.2
0.004


cancer vs Resist
















TABLE 35





Combined Frequencies Of The Presence Or Absence Of


Susceptibility Genotypes (CYP2E1 1019 CC/CG, FAS AA, IL-B1 GG,


ACT 15 GG, MMP1 2G2G) In The Exposed Smoking Subjects (Lung


Cancer Subjects And Resistant Smokers).


















Number of suceptibility polymorphisms












Cohorts
0-1
2-3
4-6
Total





Lung Cancer
13 (12%)
66 (61%)
30 (28%)
109


Resistant
54 (27%)
113 (56%) 
33 (17%)
200


smokers






% of
13/67 (19%)  
66/179 (37%)   
30/63 (48%)  



smokers with






Lung cancer






Odd's





Comparison
ratio
95% CI
χ2
P value





0 vs 1 vs 2+, Lung 
—
—
11.8
0.003


cancer vs Resist






2+ vs 0-1, Lung 
1.9
1.0-3.5
4.6
0.03


cancer vs Resist






0+ vs 1-2+, Resist 
2.7
1.4-5.6
8.6
0.003


vs Lung cancer









The above results show that several polymorphisms were associated with either increased or decreased risk of developing lung cancer. Additionally, while the associations of individual polymorphisms did provide discriminatory value, such predictions did not necessarily provide the most accurate prediction of disease possible. For example, when examined in combination, these polymorphisms distinguish susceptible subjects from those who are resistant (for example, between the smokers who develop lung cancer and those with the least risk with comparable smoking exposure). The polymorphisms represent both promoter polymorphisms, thought to modify gene expression and hence protein synthesis, and exonic polymorphisms known to alter amino-acid sequence (and likely expression and/or function) in a number of genes involved in processes known to underlie lung remodelling and lung cancer. The polymorphisms identified here are found in genes encoding proteins central to these processes which include inflammation, matrix remodelling, oxidant stress, DNA repair, cell replication and apoptosis.
In the comparison of smokers with lung cancer and matched smokers with near normal lung function (lowest risk for lung cancer despite smoking), several polymorphisms were identified as being found in significantly greater or lesser frequency than in the comparator groups (sometimes including the blood donor cohort). Due to the small cohort of lung cancer patients, polymorphisms where there are only trends towards differences (P=0.06-0.25) were included in the analyses, although in the combined analyses only those polymorphisms with the most significant differences were utilised.

    
    
        In the analysis of the Asp 298 Glu (T/G) polymorphism of the Nitric oxide synthase 3 gene, the TT genotype was found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.8, P=0.14) consistent with a protective role. This greater frequency compared to the blood donor cohort also suggests that the TT genotype is over represented in the resistant group (see Table 1E).
        In the analysis of the −786 T/C polymorphism of the Nitric oxide synthase 3 gene, the TT genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.4, P=0.23) consistent with a susceptibility role (see Table 1F).
        In the analysis of the Arg 312 Gln polymorphism of the Superoxide dismutase 3 gene, the CG and GG genotypes were found to be significantly greater in the smoking resistant cohort compared to the lung cancer cohort (P=0.03) consistent with each having a protective role (Table 2).
        In the analysis of the Arg 399 Gln A/G polymorphism of the XRCC1 gene, the AA genotype was found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=2.6, P=0.09) consistent with a protective role (Table 3).
        In the analysis of the −251 A/T polymorphism of Interleukin-8 gene, the AA genotype was found to be significantly greater in the smoking resistant cohort compared to the lung cancer cohort (OR=4.1, P=0.002) consistent with a protective role (Table 4). The A allele was also found to be significantly greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.5, P=0.02) consistent with a protective role (Table 4).
        In the analysis of the Ala 15 Thr polymorphism of Anti-chymotrypsin gene, the GG genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.7, P=0.06) consistent with a susceptibility role (see Table 5). The G allele was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.3, P=0.1) consistent with a susceptibility role (see Table 5).
        In the analysis of the A 870 G polymorphism of the Cyclin D1 gene, the GG genotype was found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.4, P=0.20) consistent with a protective role (see Table 6). In contrast, the AA genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.4, P=0.2) consistent with a susceptibility role (see Table 6).
        In the analysis of the −511 A/G polymorphism of the Interleukin 1B gene, the GG genotype was found to be significantly greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.6, P=0.04) consistent with a susceptibility role (see Table 7).
        In the analysis of the A −670 G polymorphism of the FAS (Apo-1/CD95) gene, the AA genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.5, P=0.15) consistent with a susceptibility role (see Table 8). The A allele was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.3, P=0.15) consistent with a susceptibility role (see Table 8).
        In the analysis of the 751 T/G polymorphism of the XPD gene, the GG genotype was found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.7, P=0.18) consistent with a protective role (Table 9).
        In the analysis of the Ile 462 Val G/A polymorphism of the CYP 450 1A1 gene, the AG and GG genotypes were found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=2.2, P=0.12) consistent with each having a protective role (see Table 10). In contrast, the AA genotype was found to be consistent with a susceptibility role (see Table 10).
        In the analysis of the Asn 357 Ser polymorphism of the Matrix metalloproteinase 12 gene, the GG and AG genotypes were found to be greater in the smoking resistant cohort compared to the lung cancer cohort (OR=1.7, P=0.23) consistent with each having a protective role (Table 11).
        In the analysis of the Ser 326 Cys (C/G) polymorphism of the OGG1 gene, the GG genotype was found to be significantly greater in the smoking resistant cohort compared to the lung cancer cohort (OR=4.0, P=0.05) consistent with a protective role (Table 12).
        In the analysis of the Arg 197 Gln G/A polymorphism of the N-Acetyltransferase 2 gene, the GG genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.5, P=0.08) consistent with a susceptibility role (see Table 13).
        In the analysis of the 1019 G/C Pst 1 polymorphism of the CYP 2E1 gene, the CG genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.7, P=0.23) consistent with a susceptibility role (see Table 14a).
        In the analysis of the C/T Rsa 1 polymorphism of the CYP 2E1 gene, the TC genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.9, P=0.13) consistent with a susceptibility role (see Table 14b).
        In the analysis of the 105 A/C polymorphism of the Interleukin-18 gene, the AA genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.6, P=0.06) consistent with a susceptibility role (see Table 15a). In contrast, the AC and CC genotypes were each consistent with a protective role (see Table 15).
        In the analysis of the −133 C/G polymorphism of the Interleukin-18 gene, the CC genotype was found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.5, P=0.09) consistent with a susceptibility role (see Table 15b). In contrast, the CG and GG genotypes were each consistent with a protective role (see Table 15b).
        In the analysis of the null polymorphism of the Glutathione S Transferase gene, the null genotype was found to be greater in the lung cancer cohort compared to the blood donor cohort (OR=1.92, P=0.01) consistent with a susceptibility role (see Table 16).
        In the analysis of the 874 A/T polymorphism of the Interferon gamma gene, the AA genotype was found to be greater in the lung cancer cohort compared to the blood donor cohort (OR=1.9, P=0.02) and compared to the smoking resistant cohort (OR=1.4, P=0.22) consistent with a susceptibility role (see Table 17).
        In the analysis of the −765 C/G promoter polymorphisms of the cyclo-oxygenase 2 gene, the C allele, and CC and CG genotypes were found to be significantly greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.59, P=0.03 and OR=0.53, P=0.03, respectively), consistent with a protective role. This greater frequency compared to the blood donor cohort also suggests that the C allele (CC genotype) is over-represented in the resistant group (see Table 18). In contrast, the G allele and GG genotype were found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.7, P=0.03 and OR=1.88, P=0.03, respectively), consistent with a susceptibility role (see Table 18).
        In the analysis of the −1607 1G/2G polymorphisms of the Matrix metalloproteteinase 1 gene, the 2G2G genotype was found to be significantly greater in the lung cancer cohort compared to the blood donor cohort (OR=2.58, P=0.006), consistent with a susceptibility role (see Table 19). The 2G allele was found to be significantly greater than the lung cancer cohort compared to the blood donor cohort (OR=2.1, P=0.0004), consistent with a susceptibility role (see Table 19).
        In the analysis of the −447 G/C polymorphism of the connective tissue growth factor gene, the CC and GC genotypes were found to be greater in the lung cancer cohort compared to the smoking resistant cohort (OR=1.6, P=0.19) consistent with a susceptibility role (see Table 20).
        In the analysis of the −221 C/T polymorphism in the Mucin 5AC gene the TT genotype was found to be greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.47, P=0.14) consistent with a protective role (see Table 21).
        In the analysis of the 161 G/A polymorphism of the Mannose binding lectin (MBL2) gene, the AA and AG genotypes were found to be greater in the lung cancer cohort compared to the resistant smoker cohort (OR=1.4, P=0.20) consistent with each having a susceptibility role (see Table 22).
        In the analysis of the Gln 185 Glu G/C polymorphism of the Nibrin gene, the CC genotype was found to be significantly greater in the lung cancer cohort compared to the resistant smoker cohort (OR=2.3, P=0.05), consistent with a susceptibility role (see Table 23).
        In the analysis of the intron 1 C/T polymorphism of the Arginase 1 gene, the TT genotype was found to be significantly greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.46, P=0.02) consistent with a protective role (see Table 24). The T allele was found to be significantly greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.69, P=0.05) consistent with a protective role (see Table 24).
        In the analysis of the Phe 257 Ser C/T polymorphism of the REV1 gene, the CC genotype was found to be greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.73, P=0.20), consistent with a protective role (see Table 25).
        In the analysis of the Leu 252 Val C/G polymorphism of the Insulin-like growth factor II receptor gene the GG genotype was found to be greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.30, P=0.22) consistent with a protective role (see Table 26).
        In the analysis of the Asp 148 Glu T/G polymorphism of the Apex nuclease gene, the GG genotype was found to be greater in the lung cancer cohort compared to the resistant smoker cohort (OR=1.4, P=0.25), consistent with a susceptibility role (see Table 27).
        In the analysis of the −108 2A/G polymorphism of the Interleukin-10 gene the GG genotype was found to be greater in the resistant smoker cohort compared to the lung cancer cohort (OR=0.66, P=0.15), consistent with a protective role (see Table 28).
    
    


It is accepted that the disposition to lung cancer is the result of the combined effects of the individual's genetic makeup and other factors, including their lifetime exposure to various aero-pollutants including tobacco smoke. Similarly it is accepted that lung cancer encompasses several obstructive lung diseases and characterised by impaired expiratory flow rates (eg FEV1). The data herein reveal that several genes can contribute to the development of lung cancer. A number of genetic mutations working in combination either promoting or protecting the lungs from damage are likely to be involved in elevated resistance or susceptibility to lung cancer.
From the analyses of the individual polymorphisms, 17 protective genotypes were identified and analysed for their frequencies in the smoker cohort consisting of low risk smokers, i.e., resistant smokers (near normal lung function) and those with lung cancer. When the frequencies of resistant smokers and smokers with lung cancer were compared according to the presence of 0, 1 and 2+ protective genotypes selected from a subset of six of the protective genotypes (CYP1A1 GG/AG, OGG1 GG, CCND1 GG, NOS3 298 TT, IL-8 AA, XRCC1 AA), significant differences were found (overall γ2=22.3, P<0.0001) (see Table 30). This analysis suggests smokers with 2+ protective genotypes had 4-5 times more likelihood of being resistant (OR=4.6, P=0.0005), while those with no protective genotypes were nearly three times as likely to have lung cancer (OR=2.8, P<0.0001). Examined another way, the chance of having lung cancer diminished from 48%, to 30%, to 14%, in smokers with 0, 1, or 2+ protective genotypes, respectively. Analyses of larger groups of protective polymorphisms resulted in similar findings (see Tables 32 and 34).
From the analyses of the individual polymorphisms, 19 possible susceptibility genotypes were identified and analysed for their frequencies in the smoker cohort consisting of resistant smokers and those with lung cancer. When the frequencies of resistant smokers and smokers with lung cancer were compared according to the presence of 0, 1 and 2+ susceptibility genotypes selected from a subset of six of the susceptibility genotypes (CYP2E1 1019 CC/CG, FAS AA, IL-1B GG, ACT 15 GG genotypes) significant differences were found (overall γ2=10.2, P=0.006) (see Table 31). This analysis suggests that smokers with 2+ susceptibility genotypes had nearly two times more likelihood of having lung cancer (OR=1.8, P=0.04), while those with no susceptibility genotypes were two fold as likely to be resistant (OR=2.3, P=0.004). Examined another way, the chances of having lung cancer increased from 23%, to 38%, to 45% in smokers with 0, 1 or 2+ susceptibility genotypes, respectively. Analyses of larger groups of susceptibility polymorphisms resulted in similar findings (see Tables 33 and 35).
These findings indicate that the methods of the present invention can be predictive of lung cancer in an individual well before symptoms present.
These findings therefore also present opportunities for therapeutic interventions and/or treatment regimens, as discussed herein. Briefly, such interventions or regimens can include the provision to the subject of motivation to implement a lifestyle change, or therapeutic methods directed at normalising aberrant gene expression or gene product function. For example, the −765 G allele in the promoter of the gene encoding COX2 is associated with increased expression of the gene relative to that observed with the C allele. As shown herein, the C allele is protective with respect to risk of developing lung cancer, whereby a suitable therapy in subjects known to possess the −765 G allele can be the administration of an agent capable of reducing expression of the gene encoding COX2. An alternative suitable therapy can be the administration to such a subject of a COX2 inhibitor, and/or additional therapeutic approaches such as gene therapy or RNAi.
Example 34
A subject with the −765 G allele in the promoter of the gene encoding COX2 is identified. An agent that reduces the expression of the gene encoding COX2 is administered to the subject. An alternative suitable therapy can be the administration to such a subject of a COX2 inhibitor such as additional therapeutic approaches, gene therapy, RNAi. Thus, the risk that the subject will develop lung cancer will be reduced.
In another example, as shown herein the −133 C allele in the promoter of the gene encoding IL-18 is associated with susceptibility to lung cancer. The -133 G allele in the promoter of the gene encoding IL-18 is associated with increased IL-18 levels, whereby a suitable therapy in subjects known to possess the −133 C allele can be the administration of an agent capable of increasing expression of the gene encoding IL-18. An alternative therapy can be to administer IL-18 or an functional analogue thereof to a subject or to otherwise augment IL-18 levels in the subject.
Example 35
A subject with the −133C allele in the promoter of the gene encoding IL18 will be identified. An agent capable of increasing IL18 will be provided to the subject (for example, additional IL18). Repeated doses will be administered as needed. Thus, the risk that the subject will develop lung cancer will be reduced.
In a further example, as shown herein the −1607 2G/2G genotype in the promoter of the gene encoding MMP1 is associated with susceptibility to lung cancer. A number of inhibitors of matrix metalloproteinases are known, for example those discussed in U.S. Pat. No. 6,600,057 (incorporated herein in its entirety), such as tissue inhibitors of metalloproteinases (TIMPs) including TIMP1, TIMP2, TIMP3, and TIMP4, which form inactive complexes with MMPs, more general proteinase regulators which prevent MMP action, regulators of MMP gene expression including membrane bound MMPs (MT-MMP) that activate the excreted proenzyme form of MMPs, and compounds such as 4,5-dihydroxyanthaquinone-2-carboxylic acid (AQCA) and derivatives thereof. A suitable therapy in subjects known to possess the −1607 2G/2G genotype can be the administration of an agent capable of reducing expression of the gene encoding MMP1, or administration of an agent capable of reducing the activity of MMP1, for example by administration of an agent capable of increasing expression of or the activity of one or more TIMPs, or administration of an agent capable of reducing expression of or the activity of one or more membrane bound MMPs or other activators of MMP1. For example, a suitable therapy can be the administration to such a subject of a MMP1 inhibitor such as 4,5-dihydroxyanthaquinone-2-carboxylic acid (AQCA), anthraquinyl-mercaptoethyamine, anthraquinyl-alanine hydroxamate, or derivatives thereof. In another example, a given susceptibility genotype is associated with increased expression of a gene relative to that observed with the protective genotype. A suitable therapy in subjects known to possess the susceptibility genotype is the administration of an agent capable of reducing expression of the gene, for example using antisense or RNAi methods. An alternative suitable therapy can be the administration to such a subject of an inhibitor of the gene product. In still another example, a susceptibility genotype present in the promoter of a gene is associated with increased binding of a repressor protein and decreased transcription of the gene. A suitable therapy is the administration of an agent capable of decreasing the level of repressor and/or preventing binding of the repressor, thereby alleviating its downregulatory effect on transcription. An alternative therapy can include gene therapy, for example the introduction of at least one additional copy of the gene having a reduced affinity for repressor binding (for example, a gene copy having a protective genotype).
Example 36
A subject with the −1607 2G/2G genotype in the promoter of the gene encoding MMP1 is identified. The subject is administered an inhibitor of matrix metalloproteinases, such as tissue inhibitors of metalloproteinases (TIMPs) including TIMP1. Repeated administrations can be applied, thereby reducing the risk that the subject will develop lung cancer.
Suitable methods and agents for use in such therapy are well known in the art, and are discussed herein.
The identification of both susceptibility and protective polymorphisms as described herein also provides the opportunity to screen candidate compounds to assess their efficacy in methods of prophylactic and/or therapeutic treatment. Such screening methods involve identifying which of a range of candidate compounds have the ability to reverse or counteract a genotypic or phenotypic effect of a susceptibility polymorphism, or the ability to mimic or replicate a genotypic or phenotypic effect of a protective polymorphism.
Example 37
The present example provides one example for how one can screen for compounds that modulate the expression of a gene whose expression is upregulated or downregulated when associated with a susceptibility or protective polymorphism.
One first obtains a cell that includes a particular gene of interest. The expression of the gene of interest is upregulated or downregulated when associated with a susceptibility or a protective polymorphism. The polymorphism (and gene) can be selected from the following: the Asp 298 Glu TT genotype in the gene encoding NOS3; the Arg 312 Gln CG or GG genotype in the gene encoding SOD3; the Asn 357 Ser AG or GG genotype in the gene encoding MMP12; the 105 AC or CC genotype in the gene encoding IL-1 8; the −133 CG or GG genotype in the gene encoding IL-18; the −765 CC or CG genotype in the promoter of the gene encoding COX2; the −221 TT genotype in the gene encoding MUC5AC; the intron 1 C/T TT genotype in the gene encoding Arg1; the Leu252Val GG genotype in the gene encoding IGF2R; the −1082 GG genotype in the gene encoding IL-10; the −786 TT genotype in the promoter of the gene encoding NOS3; the Ala 15 Thr GG genotype in the gene encoding ACT; the 105 AA genotype in the gene encoding IL-18; the −133 CC genotype in the promoter of the gene encoding IL-18; the 874 AA genotype in the gene encoding IFNγ; the −765 GG genotype in the promoter of the gene encoding COX2; the −447 CC or GC genotype in the gene encoding CTGF; the +161 AA or AG genotype in the gene encoding MBL2; and some combination thereof.
In the cell, the expression of the gene is neither upregulated nor downregulated except as noted below. One then contacts the cell expressing the gene of interest with the candidate compound. Next, one determines the level of expression of the gene following contact of the cell with the candidate compound. A change in the level of expression after the contacting step as compared to before the contacting step is indicative of the ability of the compound to modulate an expression, activity, or expression and activity of the gene. As will be appreciated by on of skill in the art, the above method can allow one to identify compounds that can be useful in the treatment of lung cancer or in reducing the risk that one will develop lung cancer.
Still further, methods for assessing the likely responsiveness of a subject to an available prophylactic or therapeutic approach are provided. Such methods have particular application where the available treatment approach involves restoring the physiologically active concentration of a product of an expressed gene from either an excess or deficit to be within a range which is normal for the age and sex of the subject. In such cases, the can method include the detection of the presence or absence of a susceptibility polymorphism which when present either upregulates or downregulates expression of the gene such that a state of such excess or deficit is the outcome, with those subjects in which the polymorphism is present being likely responders to treatment.
Example 38
This example demonstrates one method of estimating the potential responsiveness of a subject to a prophylactic or therapeutic treatment for lung cancer. The treatment involves restoring the physiologically active concentration of a product of gene expression to within a range that is normal for the age and sex of a subject without lung cancer.
A subject at risk of developing or already having lung cancer is first identified. Next, one detects the presence or absence of a susceptibility polymorphism in the subject. The susceptibility polymorphism can be selected from the group consisting of: the −786 TT genotype in the promoter of the gene encoding NOS3; the Ala 15 Thr GG genotype in the gene encoding ACT; the 105 AA genotype in the gene encoding IL-18; the −133 CC genotype in the promoter of the gene encoding IL-18; the 874 AA genotype in the gene encoding IFNγ; the −765 GG genotype in the promoter of the gene encoding COX2; the −447 CC or GC genotype in the gene encoding CTGF; the +161 AA or AG genotype in the gene encoding MBL2; and some combination thereof. The presence of the polymorphism in the subject indicates that the subject will respond to treatment with an agent that appropriately alters the expression or activity of the particular gene that is altered by the polymorphism.
Example 39
Table 36 below presents representative examples of polymorphisms in linkage disequilibrium with the polymorphisms specified herein. Examples of such polymorphisms can be located using public databases, such as that available at world wide web “dot” hapmap “dot” org. Specified polymorphisms are indicated in parentheses. The rs numbers provided are identifiers unique to each polymorphism.







TABLE 36





Polymorphism Reported To Be In LD With


Polymorphisms Specified Herein.







NOS3











rs2373962
rs3918225
rs3918169
rs2373961
rs3918160


rs3918170
rs6951150
rs1800779
rs3793342
rs13238512


rs2243311
rs3793341
rs10247107
rs3918161
rs1549758


rs10276930
rs10952298
rs1007311
rs10277237
rs2070744 (−786






T/C)


rs9282803
rs12703107
rs9282804
rs6946340
rs3918226


rs1799983 (Asp 298
rs6946091
rs3918162
rs6946415
rs3918163


Glu)


rs10952296
rs3918164
rs13309715
rs3918165
rs10952297


rs1800781
rs7784943
rs13310854
rs11771443
rs13310763


rs2243310
rs2853797
rs1800783
rs13311166
rs3918155


rs13310774
rs3918156
rs2853798
rs2566519
rs11974098


rs3918157
rs3918166
rs3918158
rs3730001
rs3918159


rs3918167
rs2566516
rs3918168







XRCC1











rs1799782
rs2307175
rs2307173
rs2307192
rs2307176


rs25492
rs6413430
rs3213363
rs25493
rs909008


rs3213365
rs25485
rs1799780
rs25488
rs3213367


rs3213360
rs25489
rs25486
rs3213361
rs2307188


rs2271980
rs915927
rs3213366
rs25487 (Arg 399 Gln)
rs3192714


rs25490
rs10407677
rs25491







IL8











rs4694635
rs2227527
rs2227543
rs11730560
rs11730284


rs1957663
rs7682639
rs12420
rs13106097
rs11944402


rs4694636
rs2227529
rs16849942
rs4694178
rs7658422


rs16849925
rs2227530
rs3181685
rs4694637
rs11940656


rs16849928
rs2227531
rs11733933
rs11729759
rs1951700


rs11730667
rs2227532
rs2227544
rs10938093
rs1951699


rs16849934
rs2227534
rs2227545
rs13109377
rs1957662


rs4073 (−251 A/T)
rs2227550
rs1951236
rs16849938
rs2227546


rs1951237
rs6831816
rs2227535
rs1126647
rs6446955


rs2227517
rs2227536
rs11545234
rs6446956
rs2227518


rs2227537
rs2227548
rs6446957
rs2227519
rs2227538


rs10938092
rs16849945
rs2227520
rs1803205
rs13112910


rs1951239
rs2227521
rs2227539
rs13142454
rs1951240


rs2227522
rs3756069
rs11937527
rs1957661
rs2227523


rs2227307
rs12647924
rs7674884
rs2227524
rs2227549


rs13152254
rs16849958
rs2227525
rs2227540
rs13138765


rs17202249
rs2227526
rs2227306
rs13139170
rs1951242







Anti-chymotrypsin, ACT











rs4900239
rs6575448
rs9323909
rs4905225
rs4362321


rs2896288
rs10131646
rs1884082
rs11160196
rs10131818


rs7492561
rs10131754
rs10133663
rs11845108
rs12886656


rs1004761
rs12886657
rs9671421
rs7493944
rs7151480


rs7493955
rs9671431
rs4934 (ACT Ala 15 Thr)
rs12433006
rs9671948


rs1800463
rs10135321
rs17826465
rs10150184
rs11538071


rs10150491
rs11538070







CCND1











rs3862792
rs11557712
rs11604847
rs12049899
rs603965 (A 870 G)


rs678653
rs1051357
rs12288719
rs3212893
rs1803191


rs12283700
rs3918298
rs2510607
rs1803190
rs948886


rs3918299
rs3212894
rs3212910
rs948887
rs3918301


rs3212895
rs3212911
rs3212880
rs3212896
rs3212912


rs3212881
rs3212897
rs3212913
rs3212882
rs3212898


rs3212915
rs3212883
rs11557584
rs3212916
rs3212884


rs2062445
rs3212917
rs3781611
rs3212899
rs3212918


rs649392
rs3212900
rs3212919
rs3212885
rs3212901


rs12805391
rs3212886
rs3212902
rs3212920
rs3212887


rs3212903
rs3212921
rs3918302
rs3212904
rs3212922


rs7944853
rs1051062
rs11603541
rs3212888
rs3212905


rs7116781
rs3212889
rs3212906
rs7121246
rs3212890


rs3212907
rs7124951
rs3212891
rs3212908
rs12281701


rs2510467
rs3212909
rs12288567
rs3212892
rs3802782


rs1192925
rs7177
rs7178
rs1192926







Interleukin 1B, IL1B











rs10169916
rs6743326
rs13009179
rs6743322
rs4849127


rs6761220
rs4849126
rs6761218
rs7558108
rs5021469


rs13032029
rs6710598
rs13013349
rs1143623
rs12623093


rs1143624
rs3087255
rs2708920
rs3087256
rs1143625


rs6721954
rs2853545
rs12621220
rs2708921
rs7596849


rs1143626
rs4848306
rs3087258
rs3087257
rs16944 (C −511 T)


rs7556811
rs7556903
rs3917346
rs6743438
rs4986962


rs6743427
rs1143627
rs6761336
rs6761335
rs6743338


rs6761245
rs6761237
rs6743330







FAS, TNFRSF6











rs3758483
rs6586166
rs9658718
rs3218618
rs2234767


rs6586167
rs1926193
rs12720435
rs9658674
rs9658691


rs1926192
rs7910435
rs9658675
rs9658692
rs1926191


rs17114661
rs2234768
rs9658693
rs4244983
rs3218614


rs1800682 (A −670 G)
rs9658694
rs9658719
rs9658754
rs9658695


rs9658721
rs12720436
rs9658676
rs4345878
rs9658722


rs7911226
rs5030765
rs9658696
rs9658723
rs1926190


rs7474952
rs9658697
rs11202924
rs9658755
rs9658677


rs9658698
rs9658724
rs9658756
rs12251390
rs9658699


rs9658725
rs9658757
rs2274355
rs9658700
rs9658726


rs3781202
rs5030766
rs9658702
rs2296604
rs9658759


rs12775501
rs7094676
rs9658727
rs9658761
rs7079111


rs9658703
rs9658728
rs982764
rs3740286
rs9658704


rs9658729
rs9658763
rs4064
rs9658705
rs7069750


rs3218620
rs1324551
rs9658706
rs9658730
rs2296600


rs10509561
rs9658707
rs9658731
rs6586163
rs1571011


rs3218619
rs6586164
rs9658708
rs9333296
rs3824730


rs1571012
rs3218621
rs3781204
rs1571013
rs3218613


rs12571917
rs9658710
rs9658732
rs3824729
rs9658711


rs2296603
rs10887877
rs7911752
rs9658733
rs11596616


rs11591675
rs9658734
rs7076197
rs11591676
rs9658735


rs12359362
rs12766185
rs9658736
rs7097467
rs11591677


rs9658738
rs7097572
rs9658712
rs9658739
rs9658679


rs9658713
rs9658740
rs9658680
rs2147421
rs9658741


rs1926196
rs2147420
rs7896789
rs1926195
rs9658714


rs9658742
rs9658681
rs1159120
rs9658744
rs9325603


rs4406737
rs9658745
rs2031610
rs2148287
rs9658748


rs7897395
rs9658715
rs9658749
rs7909414
rs9658716


rs7901656
rs9658682
rs2147419
rs9658750
rs7069061


rs2148286
rs9658751
rs7072828
rs2147418
rs2031613


rs6586165
rs9658717
rs2031612
rs9658683
rs4406738


rs9658753
rs9658684
rs7916814
rs2296602
rs9658685


rs2182408
rs2031611
rs7913007
rs7920305
rs3218612


rs9658687
rs1926194
rs2296601







XPD, ERCC2











rs1799793
rs238409
rs3916858
rs3916876
rs7257638


rs3916838
rs106433
rs238417
rs3916816
rs50871


rs3916860
rs3916878
rs3916817
rs50872
rs3916861


rs3916879
rs3916818
rs3916839
rs3916862
rs1799787


rs3916819
rs3916840
rs3916863
rs1799788
rs3916820


rs3916841
rs238412
rs1799789
rs238404
rs3916842


rs3916864
rs16979773
rs3916821
rs3916843
rs11668936


rs1052555
rs3916822
rs3916844
rs3916866
rs3916881


rs238403
rs7251321
rs2070831
rs3916882
rs171140


rs3916845
rs3916868
rs3916883
rs3895625
rs3916846


rs238413
rs238418
rs3916824
rs3916847
rs238414


rs3916885
rs3916825
rs3916848
rs3916870
rs3916886


rs3916826
rs238410
rs3916871
rs1799790
rs3916827


rs238411
rs3916872
rs13181 (751 G/T)
rs3916830
rs3916849


rs238415
rs3916831
rs3916850
rs3916873
rs3916832


rs3916851
rs3932979
rs3916833
rs3916853
rs238416


rs3916834
rs3916854
rs3916874
rs3916835
rs3916855


rs11667568
rs3916836
rs3916856
rs3916875
rs3916837


rs3916857
rs11666730







CYP1A1











rs11631784
rs4646418
rs2515900
rs7496395
rs2856844


rs4646903
rs7496533
rs2606345
rs2472309
rs4886605


rs8031941
rs2472308
rs12441817
rs4646420
rs12915975


rs2470891
rs4646421
rs6495121
rs2470892
rs4986885


rs1456432
rs7182554
rs2606344
rs2198843
rs936225


rs4646422
rs11072499
rs7180012
rs2229150
rs8039800


rs4986879
rs7179952
rs4987133
rs7181062
rs2856833


rs7179590
rs1799814
rs7180066
rs1048943 (Ile 462 Val)
rs7495708


rs2470893
rs2278970
rs3809585
rs2606346
rs2445619


rs4986880
rs2472296
rs4986881
rs4646417
rs4986882


rs2856831
rs1800031
rs2856832
rs4986883
rs3826042


rs4986884
rs3826041
rs2472307







MMP12











rs652438 (Asn 357 Ser)
rs641519
rs585007
rs640735
rs672745


rs651159
rs644008
rs672743
rs644552
rs1291647


rs12794039
rs476185
rs1291646
rs12796315
rs476391


rs1295870
rs505770
rs1291645
rs1042509
rs597518


rs626729
rs626407
rs686375
rs626393
rs12808148


rs1291643
rs484171
rs1296235
rs660727
rs1291642


rs7102181
rs1296234
rs674546
rs1794204
rs7128711


rs580266
rs660599
rs615932
rs511081
rs737693


rs654600
rs686439
rs645763
rs518509
rs561849


rs586701
rs641957
rs11821430
rs1296237
rs1299505


rs641920
rs673217
rs644885
rs673163







OGG1











rs159154
rs11548133
rs3219007
rs2471902
rs17291491


rs3219001
rs3219008
rs2308329
rs12498111
rs17050550


rs3219009
rs2072668
rs454071
rs1801127
rs159150


rs3219012
rs11928210
rs2472031
rs1805373
rs2471903


rs17050542
rs3219002
rs2472038
rs2472042
rs17775374


rs2471894
rs3219010
rs3219013
rs17050543
rs2472032


rs2472039
rs1801128
rs17050545
rs4986999
rs2472040


rs3219014
rs1042294
rs2472033
rs2472041
rs9824261


rs2269112
rs2472034
rs4686370
rs1052133 (Ser 326 Cys)
rs17050547


rs3219003
rs2471899
rs11632
rs2472035
rs9818365


rs3895085
rs2619496
rs2075747
rs159153
rs415153


rs1091453
rs3218993
rs3219004
rs2471900
rs3218994


rs2471895
rs809256
rs3218995
rs2471896
rs812536


rs125701
rs2472036
rs2471901
rs3218996
rs2471897


rs786514
rs3218997
rs3219005
rs809784
rs3218999


rs159151
rs3219011
rs1801129
rs6787046
rs786513


rs1801126
rs2472037
rs786512
rs11548134
rs3219006


rs810862







NAT2











rs11780272
rs1495744
rs2101857
rs7832071
rs13363820


rs1805158
rs6984200
rs1801279
rs13277605
rs1041983


rs9987109
rs1801280
rs7820330
rs4986996
rs7460995


rs12720065
rs2087852
rs4986997
rs2101684
rs1799929


rs7011792
rs1799930 (Arg 197 Gln)
rs1390358
rs923796
rs1208


rs4546703
rs1799931
rs4634684
rs2552
rs2410556


rs4646247
rs11996129
rs971473
rs4621844
rs721398


rs11785247
rs1115783
rs11157841
rs1961456
rs1112005


rs11782802
rs973874







CYP2E1











rs7091961
rs12776213
rs1329148
rs10857736
rs12262150


rs6537611
rs10857732
rs10857737
rs9418989
rs6537612


rs10857733
rs12776473
rs10776686
rs10466129
rs1101801


rs10466130
rs4838767
rs11101810
rs9419081
rs9418990


rs9419082
rs10857738
rs11101803
rs11101811
rs10776687


rs3813865
rs4838688
rs3813866
rs11101805
rs11575869


rs2031918
rs8192766
rs2031919
rs11575870
rs11101806


rs6413423
rs4838689
rs3813867 (1019 G/C
rs10857734
rs4838768




Pst1)


rs6413422
rs11101807
rs2031920 (Rsa1 C/T)
rs11101808
rs11101809


rs10857735







IL18











rs187238
rs5744238
rs5744255
rs5744228
rs5744239


rs5744256
rs360718
rs7932965
rs5744257
rs360717


rs11214103
rs360720
rs5744229
rs5744241
rs5744258


rs100000353
rs5744242
rs5744259
rs5744231
rs5744243


rs5744260
rs5744232
rs5744244
rs5744261
rs7106524


rs360722
rs549908 (105 A/C)
rs189667
rs5023207
rs12290658


rs5744246
rs12271175
rs5744247
rs11606049
rs360721 (−133 C/G)


rs360716
rs360715
rs4988359
rs360714
rs12721559


rs2043055
rs5744248
rs5744233
rs5744249
rs795467


rs5744250
rs12270240
rs5744251
rs100000354
rs100000356


rs4937113
rs1834481
rs100000355
rs17215057
rs360723


rs5744253
rs5744237
rs5744254







GSTM1








(Null genotype)
Not in



LD







MMP1











rs529381
rs685265
rs1144396
rs7107224
rs504875


rs1155764
rs526215
rs534191
rs12280880
rs509332


rs542603
rs12283759
rs574939
rs2105581
rs573764


rs470206
rs7102189
rs533621
rs575727
rs1799750 (−1607 G/GG)


rs552306
rs634607
rs470211
rs12286876
rs470146


rs12285331
rs2075847
rs519806
rs473509
rs12283571


rs498186
rs2839969
rs2000609
rs7125865
rs570662


rs11225427
rs484915
rs470307
rs2408490
rs12279710







COX2











rs7527769
rs689465
rs4648270
rs7550380
rs12027712


rs12759220
rs2206594
rs689466
rs20430
rs6687495


rs2745558
rs4648271
rs6681231
rs3918304
rs11567825


rs13376484
rs20415
rs4648273
rs12064238
rs20416


rs16825748
rs10911911
rs4648254
rs4648274
rs12743673


rs11567815
rs16825745
rs10911910
rs20417 (−765G > C)
rs20432


rs12743516
rs20433
rs10911909
rs4648256
rs3218622


rs1119066
rs20419
rs2066826
rs1119065
rs2734779


rs5278
rs1119064
rs20420
rs4648276
rs10798053


rs20422
rs20434
rs12409744
rs20423
rs3218623


rs10911908
rs5270
rs3218624
rs10911907
rs20424


rs5279
rs7416022
rs5271
rs4648278
rs2745561


rs4648257
rs13306034
rs10911906
rs11567819
rs2853803


rs2734776
rs3134591
rs4648279
rs2734777
rs3134592


rs4648281
rs12084433
rs20426
rs4648282
rs2734778


rs4648258
rs11567826
rs2745560
rs11567820
rs4648283


rs2223627
rs2745557
rs4648284
rs2383517
rs11567821


rs4648285
rs4295848
rs4648259
rs11567827
rs4428839


rs4648260
rs4648286
rs4609389
rs4648261
rs4648287


rs4428838
rs4648262
rs5272
rs12131210
rs11567822


rs4648288
rs2179555
rs11567823
rs5273
rs2143417


rs2066824
rs5274
rs2143416
rs20427
rs3218625


rs11583191
rs5277
rs4648289
rs2383516
rs2066823


rs4648290
rs2383515
rs4648263
rs1051896
rs10911905


rs4987012
rs5275
rs10911904
rs20428
rs6684912


rs20429
rs2745559
rs4648264
rs12042763
rs4648265


rs4648250
rs4648266
rs4648251
rs4648267
rs2223626


rs11567824
rs689462
rs4648268
rs4648253
rs4648269







IFNG











rs2069707
rs2069720
rs3814242
rs1042274
rs2069709


rs2069721
rs2069710
rs2069734
rs2069711
rs2069722


rs2069712
rs2234687
rs2430561 (874 A/T)
rs7957366
rs2069723


rs2069713
rs2069724
rs1861494
rs2069725
rs2234685


rs4394909
rs1861493
rs2069726
rs2069714
rs2069727


rs2069715
rs2069716
rs2069717
rs2069718
rs3087272


rs2069719
rs9282708







CTGF








(−447 G/C), no rs
Region of


number
recombination







MUC5AC








(−221 C/T, no rs number
No LD data







MBL2











rs7899547
rs12264958
rs12255312
rs10824797
rs11003126


rs11003122
rs11003131
rs1031101
rs1982267
rs930506


rs10824795
rs1982266
rs930505
rs10824794
rs4935047


rs11003130
rs920725
rs4935046
rs2384044
rs7916582


rs10824793
rs2384045
rs920724
rs1838066
rs5027257


rs16933335
rs1838065
rs2384046
rs11003125
rs930509


rs12263867
rs7100749
rs930508
rs11003129
rs11003124


rs930507
rs12221393
rs7084554
rs2165811
rs7096206


rs12782244
rs11003123
rs11003128
rs11575988
rs17664818


rs11575989
rs7475766
rs7095891
rs10824796
rs4647963


rs16933417
rs8179079
rs2165810
rs5030737
rs11003127


rs1800450 (161 G/A)
rs3925313
rs7094151
rs1800451
rs7071882


rs12246310







SOD3








rs1799895 (Arg 231 Gly)
Region of low



LD







APEX1








rs3136820 (Asp 148
Recombination


Glu)
region







NBS1











rs1805800
rs1805793
rs1805824
rs1805788
rs3026273


rs13312874
rs13312891
rs1805787
rs1805847
rs7463645


rs1805823
rs1805816
rs13312847
rs13312877
rs6990969


rs3026269
rs1805846
rs3026272
rs13312893
rs1805815


rs1805845
rs1805833
rs13312894
rs13312922
rs1805844


rs1805832
rs741777
rs1805786
rs13312849
rs7818138


rs13312895
rs709816
rs1805799
rs9792335
rs6985934


rs13312850
rs2339025
rs867185
rs13312851
rs3358


rs4596696
rs13312852
rs13277858
rs1805822
rs13312853


rs1805831
rs1805790
rs2073635
rs1805830
rs1569162


rs1063045
rs2293775
rs1805821
rs13312854
rs13259550


rs1805820
rs13312855
rs741778
rs1235369
rs1805798


rs1805829
rs3026270
rs1805797
rs1805828
rs1805789


rs2308961
rs769416
rs9694776
rs13312858
rs2272581


rs2293774
rs13312859
rs13312879
rs7008218
rs1805796


rs3026271
rs11998021
rs1805843
rs1805827
rs13312896


rs769417
rs13312880
rs13312897
rs769414
rs769418


rs12550313
rs1805842
rs769420
rs13312898
rs1805841


rs13312881
rs13312900
rs13312860
rs2308960
rs13312901


rs1805840
rs1805826
rs16786
rs13312861
rs10092465


rs13312902
rs1805839
rs13312883
rs1805819
rs1805838


rs1805792
rs2234744
rs13312862
rs13312884
rs13312903


rs13312863
rs13312885
rs1805818
rs1805837
rs13312886


rs7818042
rs13312864
rs13312887
rs13312904
rs13312865


rs1805791
rs7818989
rs13312866
rs1805825
rs13312905


rs13312867
rs13278453
rs13312906
rs11995115
rs13275276


rs13312907
rs1805836
rs10282890
rs9650096
rs1805795


rs16902052
rs9649958
rs7832009
rs7006322
rs7010210


rs1805835
rs7006318
rs13312913
rs13312871
rs6987873


rs2516635
rs13312872
rs9650098
rs13312916
rs1805794 (Gln 185 Glu)


rs13312888
rs11784904
rs13312889
rs13312921
rs1805834


rs13312890
rs1805817







ARG1











rs2781659
rs2781660
rs2781661
rs2781662
rs2781663


rs2608898
rs2781664
rs3756780
rs2781665
rs2608897


rs2781666
rs17788484
rs9493029
rs2781667 (Intron1 C/T)







REV1, REV1L











rs6714244
rs10172068
rs1000409
rs7597141
rs3208832


rs1839666
rs10180138
rs5013068
rs6714650
rs1801874


rs7560795
rs12465846
rs1451245
rs17022663
rs14534


rs10179697
rs9308821
rs3792141
rs17763586
rs2305353


rs4143760
rs10183488
rs3792142
rs13402784
rs2305352


rs10173883
rs7580448
rs3792143
rs7574943
rs12474305


rs10176205
rs7426356
rs3792144
rs4851205
rs13423815


rs12470050
rs13395100
rs2309585
rs7571793
rs17022639


rs7571186
rs11889026
rs7573502
rs3792152
rs7579403


rs13384316
rs13395095
rs10179435
rs10177775
rs12053237


rs6542882
rs11889025
rs7423755
rs3087394
rs12233126


rs13430962
rs2053917
rs1451244
rs3087398
rs11123786


rs13427780
rs13392042
rs3087386 (Phe 257 Ser)
rs2242037
rs11123785


rs6737560
rs13429806
rs11675410
rs3197957
rs1011633


rs10173466
rs3087391
rs17022653
rs2242036
rs6707685


rs10170425
rs3087399
rs12104881
rs17022634
rs13420087


rs10172752
rs10175852
rs12104509
rs3205290
rs6713792


rs10169151
rs12105223
rs12105686
rs7593274
rs7564587


rs4851206
rs7582085
rs12104601
rs13389623
rs11676988


rs7567674
rs6542880
rs13420293
rs11695517
rs7594838


rs11695422
rs3087383
rs2309604
rs13432046
rs7582133


rs3087385
rs6542881
rs10210346
rs13419448
rs3749087


rs896249
rs10210257
rs3087402
rs7560996
rs737094


rs13385501
rs3792146
rs7601730
rs11893335
rs2122748


rs3792147
rs13428419
rs13405400
rs13427424
rs3792148


rs3828316
rs13405256
rs10188633
rs13409359
rs717454


rs9308823
rs1451246
rs10496337
rs13394927
rs1973011


rs1839667
rs6542879
rs3087396
rs13398476
rs9973846


rs3792149
rs1053544
rs9308822
rs11899745
rs4341989


rs2290261
rs10191001
rs10865031
rs12479064
rs2290260


rs6746320
rs7572779
rs13429185
rs3087401
rs6728175


rs7563462
rs6717515
rs6711073
rs13415713
rs7563455


rs6727483
rs12465153
rs11902376
rs12986447
rs11887109


rs3087389
rs17022732
rs2053916
rs12619546
rs3087388


rs6748200
rs3792135
rs10182492
rs3209289
rs3792134


rs3792136
rs3792150
rs1046340
rs3087382
rs3792137


rs3792151
rs3087393
rs3087384
rs13416265
rs6723062


rs2305354
rs896248
rs3792138
rs1451243
rs3087392


rs959929
rs13387148
rs13426758
rs3087400
rs769105


rs1901283
rs9941566
rs3087387
rs7421436
rs10207435


rs7602535
rs3792153
rs13400661
rs7598629
rs3087395


rs2290259
rs7585019
rs3087403
rs17763718
rs2290258


rs13394688
rs3087390
rs4535093
rs9308819
rs10207981


rs10186223
rs10206944
rs2290257







IGF2R











rs3798189
rs8191748
rs1570070
rs8191771
rs3798188


rs8191750
rs8191764
rs8191772
rs3798187
rs8191751


rs8191765
rs8191773
rs9365122
rs3798186
rs408889


rs13198308
rs9347380
rs6455680
rs8191766
rs8191774


rs6904531
rs8191752
rs8191767
rs8191775
rs2342868


rs11751626
rs8191768
rs2297358
rs12174439
rs8191753


rs2297357
rs3777413
rs12173776
rs8191754 (Leu 252 Val)
rs8191769


rs3798185
rs9347382
rs8191770
rs435612
rs9365124


rs2297356
rs448116
rs8191776
rs9457809
rs8191755


rs399919
rs6413489
rs12179343
rs8191756
rs1867348


rs894817
rs449276
rs8191757
rs7762627
rs9456496


rs9295121
rs7763887
rs9456497
rs9365125
rs11758686


rs9457811
rs8191758
rs681401
rs9457812
rs8191759


rs9456499
rs9295120
rs8191760
rs12662414
rs9456498


rs8191761
rs4709391
rs2277071
rs4709390
rs13218689


rs11759563
rs8191762
rs13220128
rs8191746
rs8191763


rs1036951
rs2277070
rs12374637
rs4709392
rs8191747


rs12374638
rs3777414







IL10











rs1800896 (−1082 A/G)
rs3021098
rs5743626
rs3024509
rs2222202


rs1554286
rs5743627
rs1800894
rs3024490
rs2352792


rs3024495
rs1800871
rs3790622
rs3024492
rs5743628


rs1800895
rs3021093
rs3024507
rs3024496
rs1800872


rs3024491
rs3024493
rs3024497
rs3024488
rs3021094


rs1878672
rs3024510
rs3024489
rs1518110
rs3024508


rs3024498
rs5743625
rs3024506
rs9282740
rs3001099


rs1518111
rs3024494









INDUSTRIAL APPLICATION
The present invention is directed to methods for assessing a subject's risk of developing lung cancer. The methods include the analysis of polymorphisms herein shown to be associated with increased or decreased risk of developing lung cancer, or the analysis of results obtained from such an analysis. The use of polymorphisms herein shown to be associated with increased or decreased risk of developing lung cancer in the assessment of a subject's risk are also provided, as are nucleotide probes and primers, kits, and microarrays suitable for such assessment. Methods of treating subjects having the polymorphisms herein described are also provided. Methods for screening for compounds able to modulate the expression of genes associated with the polymorphisms herein described are also provided.
Additional information regarding the above methods and compositions can be found in U.S. patent application Ser. No. 10/479,525, filed Jun. 16, 2004; and PCT Application No. PCT/NZ02/00106, filed Jun. 5, 2002, which further designates New Zealand Application No. 512169, filed Jun. 5, 2001; New Zealand Application No. 513016, filed Jul. 17, 2001, and New Zealand Application No. 514275, filed Sep. 18, 2001, all of which are incorporated by reference in their entireties. Additional information can also be found in PCT application Nos. PCT/NZ2006/000103 and PCT/NZ2006/000104, filed May 10, 2006, entitled “Methods and Compsitions for Assessment of Pulmonary Function and Disorders” and “Methods of Analysis of Polymorphisms and Uses Thereof”, both of which are incorporated in their entireties by reference. PCT Application No. PCT/NZ 2006/000103 claims priority to: NZ application No. 539934, filed May 10, 2005; NZ application No. 541935, filed Aug. 19, 2005; and JP application No. 2005-360523, filed Dec. 14, 2005, all of which are incorporated by reference in their entireties. PCT Application No. PCT/NZ2006/000104 claims priority to: NZ application No. 540249, filed May 20, 2005; and NZ application No. 541842, filed Aug. 15, 2005, all of which are incorporated in their entirties by reference. Additional information can also be found in U.S. patent application Ser. No. 11/432,770, filed May 10, 2006, entitled “Methods of Analysis of Polymorphisms and Uses Thereof,”incorporated in its entirety.
PUBLICATIONS


    1. Alberg A J, Samet J M. Epidemiology of lung cancer. Chest 2003, 123, 21s-49s.
    2. Anthonisen N R. Prognosis in COPD: results from multi-center clinical trials. Am Rev Respir Dis 1989, 140, s95-s99.
    3. Cantlay A M, Smith C A, Wallace W A, Yap P L, Lamb D, Harrison D J. Heterogeneous expression and polymorphic genotype of glutathione S-transferases in human lung. Thorax. 1994, 49(10):1010-4.
    4. Kuller L H, et al. Relation of forced expiratory volume in one second to lung cancer mortality in the MRFIT. Am J Epidmiol 1190, 132, 265-274.
    5. Mayne S T, et al. Previous lung disease and risk of lung cancer among men and women nonsmokers. Am J Epidemiol 1999, 149, 13-20.
    6. Nomura a, et al. Prospective study of pulmonary function and lung cancer. Am Rev Respir Dis 1991, 144, 307-311.
    7. Schwartz A G. Genetic predisposition to lung cancer. Chest 2004, 125, 86s-89s.
    8. Skillrud D M, et al. Higher risk of lung cancer in COPD: a prospective matched controlled study. Ann Int Med 1986, 105, 503-507.
    9. Tockman M S, et al. Airways obstruction and the risk for lung cancer. Ann Int Med 1987, 106, 512-518.
    10. Wu X, Zhao H, Suk R, Christiani D C. Genetic susceptibility to tobacco-related cancer. Oncogene 2004, 23, 6500-6523.


***
All patents, publications, scientific articles, and other documents and materials referenced or mentioned herein are indicative of the levels of skill of those skilled in the art to which the invention pertains, and each such referenced document and material is hereby incorporated by reference to the same extent as if it had been incorporated by reference in its entirety individually or set forth herein in its entirety. Any and all materials and information from the above patents, publications, scientific articles, web sites, electronically available information, and other referenced materials or documents can be physically incorporated into this specification.
The specific methods and compositions described herein are representative. of various embodiments or preferred embodiments and are exemplary only and not intended as limitations on the scope of the invention. Other objects, aspects, examples and embodiments will occur to those skilled in the art upon consideration of this specification, and are encompassed within the spirit of the invention as defined by the scope of the claims. It will be readily apparent to one skilled in the art that varying substitutions and modifications can be made to the invention disclosed herein without departing from the scope and spirit of the invention. The invention illustratively described herein suitably can be practiced in the absence of any element or elements, or limitation or limitations, which is not specifically disclosed herein as essential. Thus, for example, in each instance herein, in embodiments or examples of the present invention, any of the terms “comprising”, “consisting essentially of”, and “consisting of” can be replaced with either of the other two terms in the specification, thus indicating additional examples, having different scope, of various alternative embodiments of the invention. Also, the terms “comprising”, “including”, containing”, etc. are to be read expansively and without limitation. The methods and processes illustratively described herein suitably can be practiced in differing orders of steps, and that they are not necessarily restricted to the orders of steps indicated herein or in the claims. It is also that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a host cell” includes a plurality (for example, a culture or population) of such host cells, and so forth. Under no circumstances may the patent be interpreted to be limited to the specific examples or embodiments or methods specifically disclosed herein. Under no circumstances may the patent be interpreted to be limited by any statement made by any Examiner or any other official or employee of the Patent and Trademark Office unless such statement is specifically and without qualification or reservation expressly adopted in a responsive writing during the prosecution of the application.
The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intent in the use of such terms and expressions to exclude any equivalent of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention as claimed. Thus, it will be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the concepts herein disclosed can be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims.

## Claims

1. A method of determining a human subject's increased risk of developing lung cancer when exposed to at least fifteen pack years of tobacco smoking, comprising:
obtaining a sample from said subject and detecting a genotype of CC at position -133 in the promoter of the gene encoding Interleukin-18 and a genotype of AT or TT at position -251 in the gene encoding Interleukin-8 (IL-8);

wherein the presence of the genotype indicates an increased risk for developing lung cancer when exposed to at least fifteen pack years of tobacco smoking.

2. The method according to claim 1, wherein said method further comprises the analysis of one or more epidemiological risk factors.