bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of new markers for the rapid detection of aneuploidies by quantitative fluorescent PCR (QF–PCR)
Authors: CIRIGLIANO V. , LEWIN P. , SZPIRO‐TAPIES S. , FUSTER C. , ADINOLFI M.
Published: March 2003

Rapid prenatal diagnoses of major chromosome aneuploidies have been achieved successfully using quantitative fluoresent PCR (QF–PCR) assays and small tandem repeat (STR) markers. Here we report the results of evaluating the use of previously untested X‐linked STRs, (DXS6803) and (DXS6809), together with modified amelogenin (AMXY) sequences and the X22 marker that maps in the pseudoautosomal region PAR2 on the long arm of the X and Y chromosomes. These markers will allow prenatal diagnoses of sex chromosome aneuploidies such as 45,X (pure Turner Syndrome), 47,XXY and 47,XYY, while assessing the sex of the fetuses. Data are also presented concerning the difficulties associated with the evaluation of the frequencies of the various types of sub‐populations of cells in amniotic fluid samples collected from fetuses with sex chromosome mosaicism. The results of evaluating the use of new markers for the rapid diagnosis of aneuploidies affecting chromosomes 21,18 and 13 are also presented. Three chromosome 21 specific STRs have been found to produce trisomic triallelic or diallelic patterns from all amniotic samples retrieved from fetuses with Down Syndrome. Since all samples tested were amplified and no false positive or negative results were observed, the present results confirm the diagnostic value of QF–PCR for the prenatal detection of major numerical chromosome disorders.
Linkage analysis of three candidate regions of chromosome 1 in nonsyndromic familial orofacial cleft
Authors: MARTINELLI M. , SCAPOLI L. , PEZZETTI F. , CARINCI F. , FRANCIOSO F. , BACILIERO U. , PADULA E. , CARINCI P. , TOGNON M.
Published: March 2003

Linkage analysis and mouse model knockout studies indicate that loci/genes mapping in different chromosome 1 regions are good candidates for nonsyndromic orofacial cleft (OFC) malformation. On this basis, three different regions of the chromosome 1 have been analysed, by linkage analysis, in 38 families with nonsyndromic OFC. Positive scores were obtained by pairwise analysis and a non‐parametric linkage approach for the 1p36 region, with markers close to the MTHFR locus. Additional results allowed us to exclude the presence of an OFC susceptibility gene in the 1q21 and 1q32‐42·3 regions.
Allelic association discriminates draft orders
Authors: ENNIS S. , COLLINS A. , TAPPER W. , MURRAY A. , MACPHERSON J. N. , MORTON N. E.
Published: March 2003

A year ago there was hope that a finished sequence of the human genome would soon be publicly available and would give a more reliable locus order than an unconstrained radiation hybrid or genetic map. Alas, there are now different draft orders for each region, none of which may be correct because of gaps, uncertain polarity of contigs, and errors in assembly. Shortly before these drafts became available, we analysed allelic association (also called linkage disequilibrium, LD) in the FRAX region in a large sample of haplotypes (Ennis et al. 2000). We demonstrate here that this material discriminates among alternative draft orders. To express support for discrimination between two values of χ2=−2 ln L we use the Akaike criterion AIC = df[χ2/min χ2−1]. Excluding premutations and full mutations at FMR1, all maps have 715 degrees of freedom (df) among 717 pairs of alleles after accepting L = 0 and estimating M, ∈ in the Malecot equation E(ρ) = Me −∈d, where ρ is the association between a pair of alleles at distance d. An AIC in excess of 2 provides evidence against a map with the larger χ2.
Nonsyndromic cleft lip and palate: Complex genetics and environmental effects
Authors: PRESCOTT N. J. , WINTER R. M. , MALCOLM S.
Published: March 2003

Nonsyndromic cleft lip and palate (CL/P) is a common craniofacial malformation with a complex genetic component. Attempts at identifying susceptibility loci via family and case‐control studies have proved inconsistent. It is likely that initial predictions of the complex interactions involved in facial development were underestimated. The candidate gene list for CL/P is getting longer and the need for an impartial, systematic screening technique, to implicate or refute the inclusion of particular loci, is apparent. Large‐scale multi‐centre collaborations will also be necessary if we are to pursue the avenues of gene‐environment interactions, which have opened up over recent years. So we are faced with the question ‘Can this complex trait be too complex?’
Angiotensin converting enzyme insertion allele in relation to high altitude adaptation
Authors: QADAR PASHA M. A. , KHAN A. P. , KUMAR R. , GROVER S. K. , RAM R. B. , NORBOO T. , SRIVASTAVA K. K. , SELVAMURTHY W. , BRAHMACHARI S. K.
Published: March 2003

Angiotensin converting enzyme (ACE) gene I/D polymorphism has been associated with high altitude (HA) disorders as well as physical performance. We, however, envisage that the polymorphism may be associated with adaptation to the hypobaric hypoxia of altitude, thus facilitating physical performance. For this purpose, three unrelated adult male groups, namely (1) the Ladakhis (HLs), who reside at and above a height of 3600 m, (2) lowlanders, who migrated to Ladakh (MLLs), and (3) resident lowlanders (LLs), have been investigated. The HLs had significantly (p < 0.001) greater numbers of the II homozygotes and the ID heterozygotes than the DD homozygotes, the genotype distribution being 0.46, 0.43 and 0.11 for II, ID and DD genotypes respectively. The MLLs comprised 60% II homozygotes, which was higher (p < 0.001) than the HLs (46%). In the LLs, the heterozygotes were greater (p < 0.001) in number than the II and DD homozygotes. The I allele frequency was 0.72 in the MLLs, 0.67 in the HLs and 0.55 in the LLs. Polymorphism study suggested that the II genotype could be associated with altitude adaptation, which might influence physical efficiency.
Gm and Km alleles in two Spanish Pyrenean populations (Andorra and Pallars Sobirà): a review of Gm variation in the Western Mediterranean basin
Authors: GIRALDO M. P. , ESTEBAN E. , ALUJA M. P. , NOGUÉS R. M. , BACKÉS‐DURÓ CH. , DUGOUJON J. M. , MORAL P.
Published: March 2003

Two Spanish eastern Pyrenean populations, Andorra and Pallars Sobirà, have been tested for G1m(1,2,3,17), G2m(23), G3m(5,6,10,11,13,14,15,16,21,24,28) and Km(1) immunoglobulin allotypes. Km allele and Gm haplotype frequencies in both samples fit well into the Western Mediterranean and, more strictly, Pyrenean ranges with some peculiarities: Andorra showed an elevated frequency (14.7%) of the typical Asian and European Gm21,28;1,2,17;.. haplotype, while Pallars Sobirà was characterized by high values (3.7%) of Gm5*;1,17;.., a typical sub‐Saharan Gm haplotype. Gm diversity assessed through genetic distance and variance analyses revealed a significant geographic partition (4.3%) of Mediterraneans among south, north‐east, and north‐west groups. It is interesting to note the relatively low genetic variance (2.1%) found between south and north‐western Mediterraneans that could reflect ancient population relationships. More locally, genetic boundaries and diversity analyses failed to indicate any geographic pattern and/or genetic differentiation related with the political border in the Pyrenees. The present pattern of variation in this area is probably the result of genetic isolation processes, in addition to some specific demographic phenomena, in the Pyrenean valleys.
Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade
Authors: BANDELT H.‐J. , ALVES‐SILVA J. , GUIMARÃES P. E. M. , SANTOS M. S. , BREHM A. , PEREIRA L. , COPPA A. , LARRUGA J. M. , RENGO C. , SCOZZARI R. , TORRONI A. , PRATA M. J. , AMORIM A. , PRADO V. F. , PENA S. D. J.
Published: March 2003

The mtDNA haplogroup L3e, which is identified by the restriction site +2349 MboI within the Afro‐Eurasian superhaplogroup L3 (−3592 HpaI), is omnipresent in Africa but virtually absent in Eurasia (except for neighbouring areas with limited genetic exchange). L3e was hitherto poorly characterised in terms of HVS‐I motifs, as the ancestral HVS‐I type of L3e cannot be distinguished from the putative HVS‐I ancestor of the entire L3 (differing from the CRS by a transition at np 16223). An MboI screening at np 2349 of a large number of Brazilian and Caribbean mtDNAs (encompassing numerous mtDNAs of African ancestry), now reveals that L3e is subdivided into four principal clades, each characterised by a single mutation in HVS‐I, with additional support coming from HVS‐II and partial RFLP analysis. The apparently oldest of these clades (transition at np 16327) occurs mainly in central Africa and was probably carried to southern Africa with the Bantu expansion(s). The most frequent clade (transition at np 16320) testifies to a pronounced expansion event in the mid‐Holocene and seems to be prominent in many Bantu groups from all of Africa. In contrast, one clade (transition at np 16264) is essentially restricted to Atlantic western Africa (including Cabo Verde). We propose a tentative L3e phylogeny that is based on 197 HVS‐I sequences. We conclude that haplogroup L3e originated in central or eastern Africa about 46,000 (±14,000) years ago, and was a hitchhiker of much later dispersal and local expansion events, with the rise of food production and iron smelting. Enforced migration of African slaves to the Americas translocated L3e mitochondria, the descendants of which in Brazil and the Caribbean still reflect their different regional African ancestries.
Power of regression and maximum likelihood methods to map QTL from sib‐pair and DZ twin data
Authors: VISSCHER P. M. , HOPPER J. L.
Published: March 2003

A common study design to map quantitative trait loci (QTL) is to compare the phenotypes and marker genotypes of two or more siblings in a sample of unrelated sib groups, and to test for linkage between chromosome location and quantitative trait values. The simplest case is sib pairs only, in particular dizygotic twin pairs, and a simple and elegant regression method was proposed by Haseman & Elston in 1972 to test for linkage. Since then, several other methods have been proposed to test for linkage. In this study, we derived the statistical power of linear regression and maximum likelihood methods to map QTL from sib pair data analytically, and determined which methods are superior under which set of population parameters. In particular, we considered four regression‐based and three maximum likelihood‐based approaches, and derived asymptotic approximations of the mean test statistic and statistical power for each method. It was found, both analytically and by computer simulation, that the revisited or new Haseman–Elston method (based upon the mean‐corrected crossproduct of the observations on sib‐pairs) is less powerful than a full maximum likelihood approach and is also inferior to the Haseman–Elston method under a realistic range of values for the population parameters. We found that a simple regression method, based upon both the squared difference and the mean‐corrected squared sum of the observations on sib‐pairs, is as powerful as a full maximum likelihood approach. Our derivations of statistical power for regression and maximum likelihood methods provide a simple way to compare alternative methods and obviate the need to perform elaborate computer simulations. DZ twin pairs are likely to be more powerful for linkage analysis than ordinary siblings because they may share more common environmental effects, thereby increasing the proportion of within‐family variance that is explained by a QTL.
Robust TDT‐type candidate‐gene association tests
Authors: ZHENG G. , FREIDLIN B. , GASTWIRTH J. L.
Published: March 2003

In studies of association between genetic markers and a disease, the transmission disequilibrium test (TDT) has become a standard procedure. It was introduced originally as a test for linkage in the presence of association and can be used as a test for association under appropriate assumptions. The power of the TDT test for association between a candidate gene and disease depends on the underlying genetic model and the TDT is the optimal test if the additive model holds. Related methods have been obtained for a given mode of inheritance (e.g. dominant or recessive). Quite often, however, the true model is unknown and selection of a single method of analysis is problematic, since use of a test optimal for one genetic model usually leads to a substantial loss of power if another genetic model is the true one. The general approach of efficiency robustness has suggested two types of robust procedures, which we apply to TDT‐type association tests. When the plausible range of alternative models is wide (e.g. dominant through recessive) our results indicate that the maximum (MAX) of several test statistics, each of which is optimal for quite different models, has good power under all genetic models. In situations where the set of possible models can be narrowed (e.g. dominant through additive) a simple linear combination also performs well. In general, the MAX has better power properties than the TDT for the study of candidate genes when the mode of inheritance is unknown.
Genetic and environmental determinants of plasma high density lipoprotein cholesterol and apolipoprotein AI concentrations in healthy middle‐aged men
Authors: TALMUD P. J. , HAWE E. , ROBERTSON K. , MILLER G. J. , MILLER N. E. , HUMPHRIES S. E.
Published: March 2003

The effects of common variants of cholesteryl ester transfer protein (CETP) (TaqIB), hepatic lipase (HL) (−514C>T), lipoprotein lipase (LPL) (S447X) and lecithin cholesterol acyl transferase (LCAT) (S208T) on the determination of high density lipoprotein cholesterol (HDL‐C) and apolipoprotein AI (apoAI) levels were examined in 2773 healthy middle‐aged men participating in the second Northwick Park Heart Study. The extent of gene:gene, gene:smoking and gene:alcohol interactions were determined. For HDL‐C levels, only CETP genotype was associated with significant effects (p<0·0001), with the B2 allele being associated with higher levels in both smokers and non‐smokers. This interaction was significant at the lowest tertile of TG, suggesting that TG levels were rate limiting. As previously reported, CETP, LPL and HL genotypes were all associated with significant effects on apoAI levels (all p<0·01), with carriers of the rare alleles having higher levels and with no evidence of heterogeneity of effects in smokers and non‐smokers. LCAT genotype was not associated with significant effects on either trait. There was no significant interaction between any of the genotypes and alcohol consumption on either HDL‐C or apoAI levels. All genotypic effects were additive for HDL‐C and apoAI. Environmental and TG levels explained more than 20% and 5·5% of the variance in HDL‐C and apoAI, respectively. The novel aspect of this finding is that genetic variation at these loci explained in total only 2·5% of the variance in HDL‐C and 1·89% of the variance in apoAI levels. Thus despite the key roles played by these enzymes in HDL metabolism, variation at these loci, at least as detected by these common genotypes, contributes minimally to the variance in HDL‐C and apoAI levels in healthy men, highlighting the polygenic and multifactorial control of HDL‐C.
Extension of conditional model‐free likelihood‐based linkage analysis to additive and other models
Authors: CURTIS D. , NORTH B. V. , SHAM P. C.
Published: March 2003

We have previously described extending our method of ‘model‐free’ linkage analysis, implemented in the MFLINK program, in order to deal with liability classes. This allows a new form of conditional two‐locus linkage analysis, meaning that the genotypes of a known risk locus can be used to define liability classes so that their effects can be incorporated in tests for linkage at additional loci. In this method, relationships between transmission models for different liability classes were constrained so that there was a constant multiplicative effect on penetrance values. Here we present further extensions to the method to allow for different relationships. In particular, rather than only having a multiplicative effect on risk of affection we now allow specification of a multiplicative effect on risk of non‐affection, or a combination of both relationships, across liability classes. We now also allow specification of an additive effect on penetrance. By way of example, we apply these methods to genome scan data for Alzheimer's disease using apolipoprotein E genotype to define liability classes. We show that, although in general the different methods produce results which tend to be quite highly correlated, certain markers can produce quite different results according to the method applied and that these could well lead to differences of interpretation. Without knowing a priori which relationship is likely to be most appropriate to describe the overall combined effect of the two loci one might be obliged to apply a number of different methods. This in turn may lead to the familiar difficulties associated with multiple testing. Nevertheless, the new method allows researchers greater flexibility in analysing linkage data for diseases in which one or more risk polymorphisms have already been identified.
Integrating sibship data for mapping quantitative trait loci
Authors: GHOSH S. , REICH T.
Published: March 2003

Sibship methods have been shown to be more powerful than traditional sib‐pair methods in mapping quantative trait loci. We propose a statistical procedure which integrates data on sibships into a so‐called ‘contrast function’, a natural extension of the classical squared sib‐pair trait difference proposed by Haseman & Elston (1972). We also develop a combined mean and contrast function which provides more information on linkage compared to the contrast function. Our method is extended to multiple, epistatically interacting trait loci. Monte‐Carlo simulations are included to compare the efficiencies of the proposed procedures with some currently used methods. An application of our proposed method is presented using data on alcohol dependence.
Sampling distribution of summary linkage disequilibrium measures
Authors: TEARE M. D. , DUNNING A. M. , DUROCHER F. , RENNART G. , 3EASTON D. F.
Published: March 2003

The design of association studies is critically dependent upon the extent of linkage disequilibrium (LD) across different genomic regions, often summarised in terms of the mean absolute value of summary linkage disequilibrium measures. The two most commonly used measures are D′ for estimating the magnitude or extent of LD, and Δ which is directly proportional to the power of LD mapping.

We studied the sampling distribution of the mean of ∣D^′∣ and ∣Δ^∣ statistics for varying sample size and major allele frequencies. When the sample size is small or one allele frequency is extreme, estimates of the magnitude of association based on the mean of ∣D^′∣ can be substantially inflated. This inflation is more marked when the haplotype frequencies have been inferred from genotype counts. The net effect of this means that smaller studies will tend to show higher levels of LD. The magnitude of this inflation can be reduced by use of a bootstrap correction, and by avoiding using markers with extreme allele frequencies. In contrast, the ∣Δ^∣ statistic is much less affected by sample size and high major allele frequencies. These effects are illustrated with real data on 36 SNPs typed in an Ashkenasi Jewish population.
Mapping quantitative effects of oligogenes by allelic association
Authors: ZHANG W. , COLLINS A. , ABECASIS G. R. , CARDON L. R. , MORTON N. E.
Published: March 2003

Regression analysis of a quantitative trait as a function of a single diallelic polymorphism has been extended to allelic association by composite likelihood under the Malecot model for multiple markers. We applied the method to 10 single nucleotide polymorphisms (SNPs) spanning 27 kb of the angiotensin‐I converting enzyme (ACE) gene in British families, localising a causal SNP between G2530A and 4656(CT)3/2 in the 3′ region, at a distance of 21.6±0.9 kb from the most proximal SNP T‐5491C. Neither they nor the I/D polymorphism is causal. To clarify genetic parameters we applied combined segregation, linkage and association analysis. Stronger evidence for the 3′ region was obtained, with significant evidence of a lesser 5′ effect as reported in French and Nigerian families. However, rigorous confirmation requires that the causal SNPs be identified. Both Malecot and parametric analysis appear to have high power by comparison with alternative methods for localizing oligogenes and their causal polymorphisms.
The expected power of genome‐wide linkage disequilibrium testing using single nucleotide polymorphism markers for detecting a low‐frequency disease variant
Authors: OHASHI J. , TOKUNAGA K.
Published: March 2003

The expected power of genome‐wide linkage disequilibrium (LD) testing for a low‐frequency disease variant was examined using a simple genetic model in which the degree of LD between the disease variant and the adjacent single nucleotide polymorphism (SNP) marker decreases in proportion to the number of generations since the LD‐generating event. In this study, the frequency of the SNP marker being in complete LD with a low‐frequency disease variant at the LD‐generating event was regarded as the random variable having the probability distribution expected from the neutral infinite sites model, which enables us to derive the formula for calculating the expected power of genome‐wide LD testing without determining the allele frequency of the associated SNP marker. Such a treatment is essential for the evaluation of the power of LD testing, because the frequency of the associated marker allele is always unknown. The main results obtained are as follows: (1) genome‐wide LD testing with a case‐control design could identify a disease variant with a high penetrance, while a low‐frequency disease variant showing a low penetrance is difficult to detect; (2) although the degree of LD increases as the number of markers increases, the power of LD testing does not necessarily increase after the significance level is adjusted by the Šidák correction or the Bonferroni correction based on the number of testings; (3) the use of SNP markers with only high‐frequency minor alleles is more powerful for detecting LD even with a low‐frequency disease variant than the use of SNP markers with both high‐ and low‐frequency minor alleles. Thus, the study design of LD testing must be evaluated prior to the investigation. The present study will provide a guideline for determining the number of SNP markers and the range of SNP allele frequencies suitable for genome‐wide LD testing.
Interaction between smoking and the stromelysin‐1 (MMP3) gene 5A/6A promoter polymorphism and risk of coronary heart disease in healthy men
Authors: HUMPHRIES S. E. , MARTIN S. , COOPER J. , MILLER G.
Published: March 2003

Smoking is a major risk factor for coronary heart disease (CHD), but this risk may be modified by an individual's genotype. A common functional 5A/6A polymorphism in the promoter of the stromelysin‐1 (matrix metalloproteinase 3, MMP3) gene has been identified. The 6A allele has been consistently associated with faster progression of angiographically determined CHD, while the 5A allele has recently been associated with risk of acute myocardial infarction (MI) in patients with unstable angina. To date there has been no prospective study of the relationship of this genotype to CHD risk in smokers and non‐smokers.

DNA was available from 2743 middle‐aged men, free of CHD at baseline, recruited through nine general practices in the UK for prospective surveillance. To date there have been almost 24000 person‐years of follow‐up with 125 CHD events (fatal and non‐fatal MI, sudden coronary death, need for coronary artery surgery or new major ECG Q‐wave abnormality). Men with events were each matched for age, practice and cholesterol level with three healthy men. Smoking habit was determined by questionnaire. 5A/6A genotype was determined using a heteroduplex generator method. Associations between genotype and disease outcome, according to smoking status, were assessed using conditional logistic regression. Overall, current smoking was associated with a relative risk (RR) of 1.99 (95% CI 1.30–3.06) as compared with never‐smokers and ex‐smokers combined (p<0.002). In non‐smoking men, and after adjustment for conventional risk factors, compared with the 5A5A group, the RR was 1.37 (0.64–2.94) in those with the genotype 5A6A and 3.02 (1.38–6.61) in those with the genotype 6A6A. Smoking increased risk 1.4 fold in the 5A6A group to 1.91 (1.84–4.36), by 1.3 fold in the 6A6A group to 4.01 (1.57–10.24), but by 3.81 fold (1.54–9.40) in the 5A5A group (smoking–genotype interaction p = 0.01). The data indicate a key role for stromelysin in the atherosclerotic process. Men with the stromelysin genotype 5A5A represent 29% of the general population, and their high risk, if smokers, provides a further strong argument for smoking avoidance.
Haplotype analysis and phylogeny of ornithine transcarbamylase polymorphisms
Authors: AZEVEDO L. , CALAFELL F. , VILARINHO L. , AMORIM A.
Published: March 2003

Ornithine transcarbamylase (OTC, EC 2.1.3.3) deficiency, the most common inborn error of urea cycle, is caused by a vast number of point mutations, deletions and insertions in the respective gene. Furthermore, 12 single nucleotide polymorphisms (SNPs) have been described in the OTC gene, four of them causing an amino acid change. We have studied the frequency of these markers in two populations: Portuguese and Mozambican. No significant differences were observed between populations, except for Lys→Arg in codon 46. Allelic associations between polymorphisms were used to define haplotypic patterns. The three common haplotypes (H1, H2 and H3) show a combined frequency of 95% in Portugal and 87% in Mozambique. One haplotype was found only in Portugal and three are only present in Mozambique, resulting in a higher haplotype diversity. The combined information from the SNPs and the DXS1068 (CA)n repeat was used to outline OTC haplotype phylogeny, which, in conjunction with the population data, allowed us to sketch possible evolutionary pathways, although some haplotypes could have arisen by either repeated mutation or recombination.
Association analysis for quantitative traits by data mining: QHPM
Authors: ONKAMO P. , OLLIKAINEN V. , SEVON P. , TOIVONEN H. T. T. , MANNILA H. , KERE J.
Published: March 2003

Previously, we have presented a data mining‐based algorithmic approach to genetic association analysis, Haplotype Pattern Mining. We have now extended the approach with the possibility of analysing quantitative traits and utilising covariates. This is accomplished by using a linear model for measuring association. We present results with the extended version, QHPM, with simulated quantitative trait data. One data set was simulated with the population simulator package Populus, and another was obtained from GAW12. In the former, there were 2–3 underlying susceptibility genes for a trait, each with several ancestral disease mutations, and 1 or 2 environmental components. We show that QHPM is capable of finding the susceptibility loci, even when there is strong allelic heterogeneity and environmental effects in the disease models. The power of finding quantitative trait loci is dependent on the ascertainment scheme of the data: collecting the study subjects from both ends of the quantitative trait distribution is more effective than using unselected individuals or individuals ascertained based on disease status, but QHPM has good power to localize the genes even with unselected individuals. Comparison with quantitative trait TDT (QTDT) showed that QHPM has better localization accuracy when the gene effect is weak.
Haplotype Structure of TP53 Locus in Indian Population and Possible Association with Head and Neck Cancer
Authors: Mitra S. , Chatterjee S , Panda C. K. , Chaudhuri K. , Ray K. , Bhattacharyya N. P. , Sengupta A. , Roychoudhury S.
Published: March 2003

It has been proposed that a constellation of three TP53 polymorphisms (intron 3 16 bp duplication, codon 72 BstUI, and intron 6 Nci I RFLP at nt 13494) constitute a haplotype predictive of increased cancer risk. We have estimated the allele frequency of these polymorphisms in three endogamous Indian ethnic populations from three different geographic locations (viz. Iyer from south India, Brahmin from central India and Mahishya from eastern India), as well as in head and neck squamous cell carcinoma (HNSCC) patients, and in ethnically matched normal individuals from the eastern region of India. The genotype distributions and allele frequencies of the three polymorphisms in all but one population, as well as in patients, showed a good fit to Hardy‐Weinberg equilibrium. Strong linkage disequilibria were observed between all loci in every population examined, except for the 16bp‐Nci I haplotype in the Mahishya population. The Mahishya population differed significantly from the other two populations with respect to differences in allele frequency and haplotype frequency. Although there were no significant differences in genotypic frequency at any of the loci between HNSCC patients and the matched control population, the minor allele frequency of codon 72 and intron 3 16 bp polymorphisms showed significant variation. Variation in overall haplotype frequency between patients and normal individuals was significant (p = 0.036) when two rare haplotypes 2‐1‐2 and 1‐2‐1 were combined. The rare haplotype 2‐1‐2 was found to be modestly over represented in HNSCC patients as compared to normal individuals.
CARD15/NOD2 Risk Alleles in the Development of Crohn's Disease in the Australian Population
Authors: Cavanaugh J. A. , Adams K. E. , Quak E. J. , Bryce M. E. , O'Callaghan N. J. , Rodgers H. J. , Magarry G. R. , Butler W. J. , Eaden J. A. , Roberts‐Thomson I. C. , Pavli P. , Wilson S. R. , Callen D. F.
Published: March 2003

We have previously reported strong evidence for linkage between IBD1 and Crohn's disease (CD) in Australian Crohn's disease families. Three risk alleles for Crohn's disease, (Arg702Trp (C/T), Gly908Arg (G/C) and 980fs981 (‐/C), were recently identified in the CARD15/NOD2 gene on chromosome 16, implicating this as the IBD1 locus. Using a novel diagnostic PCR‐RFLP, we have examined the frequency of these alleles in 205 multiplex IBD families, 107 sporadic Crohn's disease cases and 409 normal individuals. We demonstrate that the three risk alleles are more frequent in Crohn's disease, than in controls, with allelic frequencies of 0.11, 0.02 and 0.07 respectively. Heterozygosity for individual variants conferred a three‐fold increase in risk for Crohn's disease while substantially higher risks were associated with being homozygous or compound heterozygous. Despite a significantly lower population allele frequency for the frameshift mutation than reported by other groups, we see a similar contribution by this allele to the risk of developing Crohn's disease. While the three risk alleles influence susceptibility to Crohn's disease in Australia, we show that these alleles do not fully explain the linkage evidence and suggest that there are very likely additional IBD1 susceptibility alleles yet to be described in Australian CD at the NOD2 locus. We also show a second linkage peak in Australian CD that provides some support for a second disease susceptibility locus on chromosome 16.
The Study ofAPOA1,APOC3andAPOA4Variability in Healthy Ageing People Reveals Another Paradox   in the Oldest Old Subjects
Authors: Garasto S. , Rose G. , Derango F. , Berardelli M. , Corsonello A. , Feraco E. , Mari V. , Maletta R. , Bruni A. , Franceschi C. , Carotenuto L. , De Benedictis G.
Published: March 2003

The genes coding for apolipoprotein A1 (APOA1), apolipoprotein C3 (APOC3) and apolipoprotein A4 (APOA4) are tandemly organised within a short region on chromosome 11q23‐q24. Polymorphisms of these genes have been extensively investigated in lipoprotein disorders and cardiovascular diseases, but poorly investigated in healthy ageing. The aim of this study was to describe possible modifications of theAPOA1,APOC3, andAPOA4gene pool by cross‐sectional studies carried out in a healthy ageing population whose ages ranged from 18 to 109 years (800 subjects, 327 males and 473 females, free of clinically manifested disease, and with emato‐chemical parameters in the norm).APOA1‐MspI‐RFLP (−75 nt from the transcription starting site),APOC3‐SstI‐RFLP (3′UTR, 3238 nt), andAPOA4‐HincII‐RFLP (Asp127/Ser127) were analysed according to age and sex. A significant age‐related variation of theAPOA1gene pool was observed in males. An analysis of the allele average effect exerted byAPOA1‐MspI‐RFLP A/P alleles (Absence/Presence of the restriction site) on lipidemic parameters in 46–80 year old males showed that allele A decreased, while allele P significantly increased, serum LDL‐cholesterol. Unexpectedly, the P allele was over‐represented in the group of the oldest old subjects, thus giving evidence of another “genetic paradox of centenarians”.
A Predominant European Ancestry of Paternal Lineages from Canary Islanders
Authors: Flores C. , Maca‐Meyer N. , Pérez J. A. , González A. M. , Larruga J. M. , Cabrera V. M.
Published: March 2003

We genotyped 24 biallelic sites and 5 microsatellites from the non‐recombining portion of the Y chromosome in 652 males from the Canary Islands. The results indicate that, contrary to mtDNA data, paternal lineages of the current population are overwhelmingly (>90%) of European origin, arguing for a highly asymmetric pattern of mating after European occupation. However, the presence of lineages of indisputable African assignation demonstrates that an aboriginal background still persists (<10%). On the basis of distribution and dating of some of these lineages we derived a genetic perspective of settlement processes of the archipelago in two stages, congruent with anthropological, archaeological and linguistic findings.
Family History is a Coronary Heart Disease Risk Factor in the Second Northwick Park Heart Study
Authors: Hawe E. , Talmud P. J. , Miller G. J. , Humphries S. E.
Published: March 2003

We have estimated the risk of coronary heart disease (CHD) from family history of CHD (FHCHD) in 2827 healthy European middle‐aged men, and explored the extent to which this can be explained by classical and genetic risk factors. Men with FHCHD (obtained by questionnaire) had a hazard ratio of CHD of 1.73 (95% confidence interval: 1.30, 2.31) compared to those without FHCHD; after adjusting for classical risk factors this did not change substantially. Those with FHCHD had 2.3% lower Factor VIIc (p = 0.03) and 1.14% higher systolic and 1.21% higher diastolic blood pressure (p = 0.04 and p = 0.02), with evidence of interaction between blood pressure and FHCHD status on risk (p = 0.01). The risk for those with a positive family history who were also current smokers was 3.01 compared to non‐smokers without FHCHD, which is greater than the risk posed by smoking or FHCHD alone (1.96 and 2.05 respectively compared to non‐smokers without FHCHD), but not significantly different from a multiplicative model (p‐value for interaction 0.33). Allele frequencies for 13 candidate gene variants were not significantly different between those with and without FHCHD. In those with FHCHD, current smokers who carried the APOE4 allele (e4+) had a hazard ratio of 5.66 compared to non‐smokers who had no FHCHD and were not APOE4+, with a significant interaction between smoking and APOE4 in those with FHCHD p = 0.001. These data demonstrate the complex interaction between genetic and environmental factors in determining CHD risk, and suggest that the causes of the familial clustering of CHD remain largely unexplained.
Estimation of Multilocus Haplotype Effects Using Weighted Penalised Log‐Likelihood: Analysis of Five Sequence Variations at the Cholesteryl Ester Transfer Protein Gene Locus
Authors: Tanck M. W. T. , Klerkx A. H. E. M. , Jukema J. W. , Knijff P. De , Kastelein J. J. P. , Zwinderman A. H.
Published: March 2003

Direct analyses of haplotype effects can be used to identify those specific combinations of alleles that are associated with a specific phenotype. We introduce a method for direct haplotype analysis that solves two problems that arise when haplotypes are analysed in populations of unrelated subjects. Instead of assigning a single, most likely, haplotype pair to multiple heterozygous subjects, all haplotype pairs compatible with their genotype were determined and the posterior probabilities of these pairs were calculated using Bayes’ theorem and estimated haplotype frequencies. For the individual patients, all possible haplotype pairs were included in the statistical analysis using the posterior probabilities as weights, which were re‐estimated in an iterative process together with the haplotype effects. The second problem of unstable haplotype effect estimates, due to the numerous haplotypes and the low frequency at which some occur, was solved by assuming that haplotypes sharing the same alleles show a similar effect and that the extent of this similarity relates to the number of alleles shared. These assumptions were incorporated in a weighted log‐likelihood model by introducing a penalty, where differences in effects of similar haplotypes were penalised. UsingCETPgene haplotypes, consisting of five closely linked polymorphisms, and baseline CETP and HDL‐C concentrations from the REGRESS population, we demonstrated that the model resulted in more stable effects than estimates based on unambiguous patients only.
Cladistic Analysis of Human Apolipoprotein A4 Polymorphisms in Relation to Quantitative Plasma Lipid Risk Factors of Coronary Heart Disease
Authors: Wang G. Q. , DiPietro M. , Roeder K. , Heng C.‐K. , Bunker C. H. , Hamman R. F. , Kamboh M. I.
Published: March 2003

Genetic variation in several genes involved in lipid metabolism is known to affect population variation in quantitative lipid risk factor profiles for coronary heart disease (CHD). The apolipoprotein A‐IV gene (APOA4) is one such candidate gene. We genotyped five polymorphisms in theAPOA4gene (codon 127, codon 130, codon347, codon 360 and 3’ VNTR) and investigated their impact on plasma lipid trait levels in three populations comprising 604 U.S. non‐Hispanic Whites (NHWs), 408 U.S. Hispanics and 708 Nigerian Blacks. Cladistic analysis was carried out to identify 5‐site haplotypes that were associated with significant phenotypic differences in each population. The distribution ofAPOA4genotypes was significantly different between ethnic groups. The Africans were monomorphic for two of the five sites (codons 130 and 360), but possess a unique 12 bp insertion that was not observed in NHWs and Hispanics. Due to linkage disequilibrium between the sites, only 6 haplotypes were observed in NHWs and Hispanics, and 4 in Africans. Several gender‐and ethnic‐specific associations between genotypes and plasma lipid traits were observed when single sites were used. Several haplotypes were identified by cladistic analysis that may carry functional mutations that affect plasma lipid trait levels.
Maternal and Paternal Lineages of the Samaritan Isolate: Mutation Rates and Time to Most Recent Common Male Ancestor
Authors: Bonné‐Tamir B. , Korostishevsky M. , Redd A. J. , Pel‐Or Y. , Kaplan M. E. , Hammer M. F.
Published: March 2003

The Samaritan community is a small, isolated, and highly endogamous group numbering some 650 members who have maintained extensive genealogical records for the past 13–15 generations. We performed mutation detection experiments on mitochondrial DNAs and Y chromosomes from confirmed maternal and paternal lineages to estimate mutation rates in these two haploid compartments of the genome. One hundred and twenty four DNA samples from different pedigrees (representing 200 generation links) were analyzed for the mtDNA hypervariable I and II regions, and 74 male samples (comprising 139 links) were typed for 12 Y‐STRs mapping to the non‐recombining portion of the Y chromosome (NRY). Excluding two somatic heteroplasmic substitutions and several length variants in the homopolymeric C run in the HVII region, no mutations were found in the Samaritans' maternal lineages. Based on mutations found in Samaritan paternal lineages, an estimate of a mutation rate of 0.42% (95% confidence interval of 0.22%–0.71%) across 12 Y‐STRs was obtained. This estimate is slightly higher than those obtained in previous pedigree studies in other populations. The haplotypes identified in Samaritan paternal lineages that belong to the same haplogroup were used to estimate the number of generations elapsed since their most recent common ancestor (MRCA). The estimate of 80 generations corresponds with accepted traditions of the origin of this sect.
Human Chromosome 17 in Essential Hypertension
Authors: Knight J. , Munroe P. B. , Pembroke J. C. , Caulfield M. J.
Published: March 2003

Hypertension affects up to 30% of the adult population in Western societies and is a major risk factor for kidney disease, stroke and coronary heart disease. It is a complex trait thought to be influenced by a number of genes and environmental factors, although the precise aetiology remains unknown at this time. A number of methods have been successfully used to identify mutations that cause Mendelian traits and these are now being applied to the investigation of complex diseases. This review summarises the data gathered, using such approaches, that suggest there is a gene or genes on chromosome 17 causing human essential hypertension.

 Studies in rodent models are discussed first, followed by studies of human hypertension that include the investigation of pseudohypoaldosteronism type II, a monogenic trait that manifests with hypertension alongside other phenotypic variables. In addition, candidate gene studies, genome screens and linkage studies based on comparative mapping are outlined. To date no gene has been identified on human chromosome 17 that influences blood pressure and causes human essential hypertension. However, results of ongoing fine mapping and candidate gene studies in both rodents and man are eagerly awaited.
Side effects of botanical insecticides on predatory mite Amblyseius andersoni (Chant)
Authors: Castagnoli M. , Angeli G. , Liguori M. , Forti D. , Simoni S.
Published: March 2003

The effects of the botanical insecticides Biopiren plus, Piresan plus and Neemazal T/S on the predatory mite Amblyseius andersoni (Chant) were tested under laboratory, semi‐field, and field conditions. The tests carried out in the laboratory allowed detection of the direct toxicity on eggs and females as well as the effects on fecundity, whereas semi‐field trials assessed their residual toxicity. In laboratory and semi‐field tests, pyrethrins, particularly Piresan plus, proved to have the highest toxicity with E value, concerning both female mortality and fecundity, of 100 % and 45 %, respectively. The same product tested in the field only caused a significant reduction in the phytoseiid population shortly after the treatment. The relevant escape rate registered in semi‐field tests could explain the lack of phytoseiid eradication in the field after treatment with pyrethrins.
Species differences in bradykinin receptor‐mediated responses of the airways
Authors: Ellis K. M. , Fozard J. R.
Published: March 2003

Summary 1 Bradykinin (BK) is a nine amino acid peptide (Arg‐Pro‐Pro‐Gly‐Phe‐Ser‐Pro‐Phe‐Arg) formed from the plasma precursor kininogen during inflammation and tissue injury. The actions of BK are mediated by G protein‐coupled cell surface receptors, designated B1 and B2.

2 BK has a plethora of effects in the airways including bronchoconstriction, bronchodilation, stimulation of cholinergic and sensory nerves, mucus secretion, cough and oedema resulting from promotion of microvascular leakage. These airway effects are mediated in the main by the B2 receptor subtype.

3 BK acts mainly indirectly, primarily through airway nerve activation, but also by the release of prostanoids, thromboxanes and nitric oxide (NO).

4 Airway responses to BK have been studied in detail in guinea‐pigs, mice, sheep and rats. This review describes the effects of BK in these species and draws comparison with its effects in normal humans and patients with respiratory diseases.

5 Despite its many and varied effects in the airways of animals and man, the exact contribution of BK to airways disease remains unclear.
Dual adrenergic control of in vivo choline levels in the mouse major salivary glands
Authors: Murai S. , Saito H. , Shirato R. , Kawaguchi T.
Published: March 2003

1 The purpose of this study was to demonstrate that the adrenergic nervous system regulates the in vivo choline levels in the mouse major salivary glands.

2 Methoxamine (α1‐adrenoceptor agonist, 2.5–20 mg kg−1, s.c.) elevated choline levels dose‐dependently and the effect of methoxamine (10 mg kg−1) was completely inhibited by the α‐adrenoceptor antagonist phentolamine (5 mg kg−1, i.p.) but not by the β‐adrenoceptor antagonist propranolol (3 mg kg−1, i.p.).

3 In contrast, isoprenaline (β‐adrenoceptor agonist 0.25–20 mg kg−1, s.c.) lowered choline levels and the effect of isoprenaline (2 mg kg−1) was inhibited by propranolol, but not by phentolamine.

4 Noradrenaline (1–4 mg kg−1, s.c.) manifested both the α‐ and β‐adrenergic actions depending on its dose. Noradrenaline at 1–2 mg kg−1, lowered choline levels and the effect of noradrenaline (1 mg kg−1) was inhibited by propranolol, but not by phentolamine. On the other hand, noradrenaline (4 mg kg−1) elevated choline levels and the effect was blocked by phentolamine, but not by propranolol.

5 Tyramine (5–80 mg kg−1, s.c.) elicited the release of noradrenaline from sympathetic nerve terminals and induced essentially the same effects on the choline levels as noradrenaline. Tyramine (10 mg kg−1) lowered choline levels and the effect was inhibited by propranolol, but not by phentolamine. However, tyramine (80 mg kg−1) elevated choline levels and the effect was inhibited by phentolamine, but not by propranolol.

6 These results suggest that choline levels in the salivary glands may be under separate α‐ and β‐adrenergic control and suggest a possibility that the neurotransmitter noradrenaline released for sympathetic nerve terminals can manage the dual control of choline levels in some autonomic organs in a characteristic dose‐dependent manner.