Abstract:
The location at which tissue samples are obtained to determine whether cells exhibit characeristics associated with cell differentiation or cancer by molecular analysis is determined by illuminating a gross anotomic area of tissue with a light that  5  selectively distinguishes cancerous and precancerous tissue from normal tissue.

Description:
[0001]     This application is a Division of U.S.A patent application Ser. No. 10/017,007, filed Dec. 14, 2001, the disclosure of which is hereby incorporated by reference. 
     
    
       [0002]     This invention relates to a combined method for the early location and prognosis of tissue containing potentially invasive cancer cells, before the normal visual appearance of the tissue indicates potential development of invasive cancer, thus delaying a diagnosis of such tissue as precancerous or cancerous by conventional location, excision and histological procedures.  
         [0003]     In another respect, the invention relates to a combined method for location and detection of tissue containing such potentially invasive cancer cells, the normal visual appearance of which is anomalous, which may lead to delay in obtaining a diagnosis indicating treatment.  
       BACKGROUND OF THE INVENTION  
       [0004]     Patients who delay in obtaining a cancer consultation for at least two months have significantly higher relative hazards of death than do patients with a shorter delay. (See Cancer, 92[11]:2885-2891, 2001). Thus, if patients are more regularly subjected cancer screening, coupled with a definitive procedure for making an early prognosis or diagnosis, the mortality rate risks of cancer would be reduced.  
         [0005]     Accordingly, I provide prognostic and diagnostic methods for early prediction of eventual development of invasive cancer or for definitive diagnosis, which are stepwise, rapid, conclusive, and readily adaptable as a clinical protocol.  
         [heading-0006]     Development of Pre-Cancerous &amp; Cancerous Tissue:  
         [0007]     The development of tumors requires two separate mutational events. One of these events may occur in the germline and be inherited. The second then occurs somatically. Alternatively, the two mutational events may occur only in the somatic cell of an individual.  
       Cancer Screening Procedures  
       [heading-0008]     Conventional Visual Cancer Screening  
         [0009]     Cellular mutautions which are normally visible are well documented and may involve thickening, discoloration, atypical moles, or hardening. Several tissue features for differentiating early melanomas from benign melanocytic nevi are known to those skilled in the art. For example:  
                                                       Feature   Benign Mole   Melanoma                           Assymetry   No   Yes           Border Integrity   No   Yes           Color   Uniform, tan/brown   Variegated, black           Diameter   &lt;6 mm   May be &gt; 6 mm                      
 
 However, these normally visible features and their characteristics may not be apparent until the tissue involved is advanced on the normal progression pathway of cancer. Conseqently, a simple, rapid and relatively accurate screening method was needed to enable the clinician to locate suspect tissue before the normally visible characterstics of cancerous or precancerous tissue appear. 
 
 In Vivo Cancer Screening Procedures For Early Location of Potentially Cancerous Tissue 
 
         [0012]     In vivo screening techniques have now been developed to quickly and noninvasively identify gross or specific anatomical locations of a patient&#39;s body are likely to contain cells with the tumor or cancerous phenotype at stages before conventional visual observation of the tissue would reveal such suspect tissue. These in vivo screening techniques to locate such potentially canerous sites, particularly epithelial cancers, are fast and quite feasible, even for the general clinical practioner.  
         [0013]     Gross Anatomical Screening:  
         [0014]     One example of gross anatomical screening is the Polymerase Chain Reaction (PCR) analysis of a simple saliva sample. Saliva contains exfoliated cells that originate from the head and neck region—a large surface area—that is a common origin of cancer cells, especially in patients who expose these areas to nicotine, alcohol, and other known or suspected carcinogens. PCR analysis serves as a gross preliminary screening procedur, which determines whether exfoliated cells found in a patient&#39;s saliva exhibit a cancerous phenotype, indicating the development of cancer within this gross anatomical area. For example, see Spafford, M. F., et al, “Detection of Head and Neck Squamous Cell Carcinoma Among Exfoliated Mucosal Cells by Microsatellite Analysis”, Clin. Cancer Res. 2001, Mar. 7(3):607-612.  
         [heading-0015]     Selective Light In Vivo Cancer Screening Procedure  
         [0016]     Tissue containing tumor phenotypes, which may indicate the eventual development of invasive cancer, can be identified and located in vivo by visually identifying cellular mutation or lesions, using selective in vivo light examinations. For example, U.S. Pat. Nos. 5,179,938 and 5,329,938 to Lonky describe using an endoscopic instrument or speculum equipped with a chemiluminescent light source, to eliminate the disadvantages of using hot white light sources, to examine and locate suspect tissues. Lonky&#39;s light source radiates in the visible green, blue, and red spectrums, with spectral peaks at 450, 550, and 580 nanometers. The methods described by Lonky can be applied to the surfaces of body cavities, such as mucousal tissues and as well as epithelial discharges. The advantages of using the chemiluminescent light source include the elimination of a hot light source which can cause the patient discomfort, cellular damage, reduction of visual interference, such as shadowing, and, most importantly, the selective coloration of abnormal tissue which readily distinguishes it from adjacent normal tissue. Chemiluminescent solutions and the processes for manufacture of the solutions and devices have been described by U.S. Pat. Nos. 5,122,306 and 5,194,666.  
         [heading-0017]     Prognosis and Diagnosis Based on Molecular Analysis  
         [0018]     Mutations generally result from intramolecular gene reorganization, such as a substitution, addition, or deletion of a nucleotide, the subunit of DNA and RNA, respectively. Recently, however, genetic mapping has developed ways to detect mutations of nucleotides characteristic of cancer and precancer, such as the methylation patterns of DNA and RNA, and enzymatic activity, which is a direct consequence of alterations of the nucleotide sequence or the “genetic code”. It has also been determined that cancerous activity can be detected by changes in the mitochondria.  
       I. Genetic Mutations  
       [heading-0019]     DNA Analysis  
         [0020]     Analysis of DNA polymorphisms reveals a significant difference between normal cells and tumor cells: whereas normal cells are heterozygous at many loci, the tumors are homozygous at the same loci (loss of heterozygosity).  
         [0021]     Tumor suppressor genes are often associated with the loss of one chromosome or a part of a chromosome, resulting in a reduction to homozygosity, through elimination of one allele of a tumor suppressor gene as well as surrounding markers. The remaining tumor suppressor allele is inactivated by either an inherited or a somatic mutation. Some examples of well documented tumor suppression genes include: Adenomatous polyposis of the colon gene (APC), Familial breast/ovarian cancer genes 1 and 2 (BRCA1 and BRCA2), Cadherin 1 (epithelial cadherin or E-cadherin) gene (CDH1), Multiple endocrine neoplasia type 1 gene (MEN1), Neurofibromatosis type 1 gene (NF1), Protein kinase A type 1, alpha, regulatory subunit gene (PRKAR1A), Retinoblastoma gene (RB1), Serine/threonine kinase 11 gene (STK11), and von Hipple-Lindau syndrome gene (VHL). Thus, critical chromosome loci are predictors of the probable onset of invasive cancer.  
         [0022]     An example of DNA analysis includes Microsatellite Analysis for determining mutations or the instability of “chromosomal arms” or “microsatellites”. Microsatellites are short repetitive sequences of DNA that have been observed to contain nucleotide mispairs, misalignments, or nucleotide slippage (looping or shortening). Mutations, such as these, are termed microsatellite instability and have become acssociated with a number of epithelial cancers.  
         [0023]     More recent studies have identified new microsatellite markers for detecting loss of heterogeniety, before a cell undergoes abnormal morphological change. See Guo, Z., et al, “Allelic Losses in Ora Test-directed Biopsies of Patients with Prior Upper Aerodigestive Tract Malignancy”, Clinical Canc. Res. Vol. 7, 1963-1968, July 2001.  
         [0024]     Those skilled in the art understand that there are distinct differences, at the histologic level, at the genetic level and at the anatomic level in terms of right side/left side, between tumors with chromosomal instability and microsatellite instability. It is also known that in leukemias and lymphomas, major interstitial deletions and translocations occur at the gross chromosomal level. In various epithelial tumors such as, the changes occur differently, as major chromosomal arms have been shown to be lost. Tumors apparently progress down one pathway or the other but not both. (Oncology News International, Vol. 9, No. 8, Suppl. 2, August 2000) MSI analyses generally requires the use of five MS markers—two mononucleotide repeats and three dinucleotide repeats.  
         [heading-0025]     RNA Analysis  
         [0026]     It is now possible to detect one somatic mutant mRNA molecule in a background of 1000 wild type mRNA molecules. This technique measures gene expression levels in samples containing as few as 10-20 cells, together with the capability for detection of somatic point mutations at several loci known to be altered with high frequency. Thus, it is possible to observe microheterogeneity in gene expression profiles in small clusters of cells in dysplasia and cancer.  
         [0027]     Sequence detection was accomplished on oligonucleotide microarrays, using a target-directed DNA ligation step coupled to a Rolling Circle Amplification (RCA) unimolecular detection system. The DNA ligation step is adaptable to the detection of mRNAs containing point mutations. Lizardi, P. M., “Messenger RNA Profiling by Single Molecule Counting”, Yale University, (2000), http://otir.cancer.gov/tech/imat_awards.html, (Nov. 28, 2001).  
         [heading-0028]     Telomeric DNA and Associative Protein, Telomerase  
         [0029]     Telomeres are the DNA sequences, which are the specialized complexes at the ends of chromosomes. Telomerase, the ribonucleoprotein that helps maintain telomeres, is inactive in many adult human cell types, but is highly activated in most human cancers. It has been determined that a disruption or mutation in either the telomeric DNA or telomerase, or the intermediary RNA, can uncap the telomere, causing further damage to the DNA. Thus, it is known that a molecular analysis can detect either abnormal telomeric nucleotides or abnormal enzymatic activity of telomerase, which are equally associated with the proliferation of pre-cancerous cells. See, e.g., Kim, M. M., et al., “A Low Threshold Level of Expression of Mutant-template Telomerase RNA Inhibits Human Tumor Cell Proliferation”, Proc. Natl. Acad. Sci. USA: Vol. 98, No. 14, 7982-7987, (July 2001).  
       II. Epigenetic Mutations  
       [0030]     Aberrant promoter methylation was recently discovered to be a fundamental molecular abnormality leading to transcriptional silencing of tumor suppressor genes, DNA repair genes and metastasis inhibitor genes, and is linked to the predisposition of genetic alterations of other cancer-associated genes.  
         [0031]     Somatic epigenetic alterations in DNA methylation are tightly linked to development, cell differentiation and neoplastic transformation. For instance, hypermethylation of CpG islands in promoter regions has been increasingly associated with transcriptional inactivation of tumor suppressor genes in carcinogenesis. Although techniques to measure methylation in specific DNA segments or in total DNA have been available, Yamamoto developed a method called “Methylation Sensitive-Amplified Fragment Length Polymorphism” (MS-AFLP) for identifying changes in methylation in the entire genome. This polymerase chain reaction (PCR)-based unbiased DNA fingerprinting technique permits the identification of the cleavage sites that exhibit DNA methylation alterations and subsequently allows the isolation of DNA fragments with these sites at their ends. Decreases or increases of band intensity, or differences in banding pattern, were specifically linked with the tumor phenotype.  
         [0032]     Thus, methylation alteration provides identification of epigenetic alterations associated with cell differentiation and cancer. DNA mutation or loss of heterogeneity can be alternatively detected by measuring DNA methylation. SeeYamamoto, F., Ph.D., “Technology to Detect Genome-wide DNA Methylation Changes”, Burnham Institute, http://otir.cancer.gov/tech/imat_awards.html, (Nov. 28, 2001).  
       III. Mitochondrial Mutations  
       [0033]     More recently, another cancer detection method was developed, based on the finding that mitchondrial DNA (mtDNA) exhibits mutations when derived from human cancerous cells.  
         [0034]     There are an estimated 1000 different proteins in the mitochondria. Defects in such proteins can be characterized as “metabolic diseases”, causing defects in transport mechanisms and ion channels, most notably, defects in the electron transport chain and oxidative phosphorylation. Nuclear mutations can affect mtDNA replication and repair, transcription, protein synthesis in the matrix, protein import, and other properties of the mitochondria See, e.g., Fliss, et al., “Facile Detection of Mitochondrial DNA Mutations in Tumors and Bodily Fluids”, Science 287, 2017-2019, (2000). In this study, DNA was extracted from autopsy-derived brain samples from 14 individuals, ranging in age from 23 to 93 years and tested for the three mutations by PNA-directed PCR clamping. The ability to detect very low levels of point mutations in mtDNA by PNA-directed PCR clamping, permitted analysis of the presence or absence of, e.g., the A8344G, A3253G and T414G, point mutations in tissues from individuals of varying ages. Lung cancer cases corresponded with mutant mtDNA bands, that were detected using a sensitive oligonucleotide-mismatch ligation assay and gel electrophoresis.  
         [0035]     Thus, mutations within the mitochondrial genome are still another method for detecting cancerous activity in human cells. See also Parrella, P., et al., “Detection of Mitochondrial DNA Mutations in Primary Breast Cancer and Fine-Needle Aspirates”, Cancer Res. 61, 7623-7626, (October, 2001). Advantageously, abnormal chromosomal expression, associated with cancer, can be detected with common molecular analysis at very early stages of pathogenic expression and with a very few number of affected cells.  
         [0036]     However, given the expanse of the human body&#39;s cellular tissue that could possibly propagate invasive cancer tissue, diagnostic techniques such as genetic, epigenetic, or mitochondrial molecular analysis are not effective early cancer detection methods, because the effectiveness of these techniques directly depend on obtaining tissue samples from the specific tissue sites containing cells which are propagating cancer. Moreover, although some of the prior art screening methods are capable of identifying specific sites of suspect cancerous and precancerous tissue, the location and identification of such suspect tissue was, heretofore, generally followed by conventional histological examination of the suspect tissue such as lighted microscopy. Often, such conventional histological examination indicated that some of the locations identified by prior art techniques were not cancerous or precancerous, when, in fact, cells from these locations exhibited the markers for eventual development of cancer at that location, markers which could have been identified by molecular analysis, i.e., genetic code, (DNA or RNA), epi-genetic patterns, or mitochondrial DNA (mtDNA), characteristic of cancer cell propagation.  
         [0037]     For example, subsequent application of molecular analysis techniques to cells derived from suspect tissue samples located by mitochondrial dye staining—cells that were originally determined by conventional histology to be “false positives” of the Mashberg dye-staining protocol—revealed that a high proportion of these cells in fact contained markers that were the earliest indication of the eventual development of cancer at those suspect sites.  
       BRIEF STATEMENT OF THE INVENTION  
       [0038]     I have now discovered an improved prognostic and diagnostic method for detecting pre-cancerous and cancerous growth in human tissue which combines the advantages of prior art selective light “location screening” technologies and/or gross anatomical screening techniques, such as saliva testing, with the precise prognostic and diagnostic” technologies of cellular molecular analysis.  
         [0039]     Briefly, my method comprises various combinations and subcombinations of up to three steps: (1) conducting a screening test that subjects saliva to polymerase chain reaction (PCR) analysis to determmine whether head or neck cancer in this gross anatomical region is probable; (2) illuminating a gross anatomical region with light for selective visualization of the specific location of suspect tissue, to enable cell extraction or a biospy of the cells in such specific suspect location; and (3) subjecting cells obtained from such suspect location to molecular analysis, to determine whether said extracted cells exhibit characteristics associated with cell differentiation or cancer.  
         [0040]     According to one embodiment of the invention, in vivo selective light examination of a gross anatomical region is conducted to identify specific suspect tissue location(s), is combined with molecular analysis of cells from the thus-located suspect tissue.  
         [0041]     Yet another embodiment of the invention includes conducting a saliva screening test to determine whether the patient may or has developed head/neck cancer, followed in vivo selective light examination of the head and neck region to specifically locate suspect sites, followed by molecular analysis of cells from specific suspect sites to confirm whether the specifically identified suspect tissue contains cells which exhibit characteristics associated with cancer or the eventual development of cancer.  
         [0042]     According to still another embodiment of the invention the selective light examination of a gross anatomical region is followed by topical application of a selective staining dye to the suspect tissue location, to further confirm that it is suspected of containing cancerous or precancerous cells and to provide additional time to view the suspect tissue, before performing a biopsy to obtain cells for molecular analysis.  
         [heading-0043]     “Molecular Analysis” 
         [0044]     As used herein, the term “molecular analysis” means a procedure for identifiying cellular abnormalities which indicate cancer or the probable eventual development of cancer. Illustratively, these procedures include those which identify such abnormalities in the genetic code, i.e. DNA or RNA, in epi-genetic patterns, or in mitochondrial DNA (mtDNA), of suspect cells. Thus, although countless nucleotides within and exterior to a cell&#39;s nucleus can be observed to detect mutations, the term “molecular analysis” is limited to those procedures which determine whether a tumor phenotype is present in the suspect cells. Accordingly, target nucleotides or associated proteins and patterns, as well as the various other detection techniques known to one skilled in the art, are to be considered within the scope of the term “molecular analysis.” 
         [0045]     While the saliva screening test, Step 1, is specific to detecting only head and neck cancers, Steps 2-3 can be applied to any cells capable of visual inspection in vivo, including topical or internal tissues that may be observed within an internal cavity of the body or individual cells distributed within plasma fluid. Such combination of steps provides a simple clinical protocol that can identify the locations of precancerous, as well as suspect sites, well before onset of otherwise visible indications. 
     
    
     DETAILED DESCRIPTION OF THE INVENTION  
       [0046]     My method comprises sequentially examining cells to first locate and identify tissue having suspect cells and then to examine cells from such suspect tissue to detect the presence of a cancerous or tumor phenotype. Tumor phenotypes include any mutation, e.g. allelic loss, loss of heterogeneity, mutation of tumor suppressor genes, abnormal DNA methylation, or abnormal mtDNA, associated with cancer.  
         [0047]     The following detailed description of these sequential steps are provided to enable those skilled in the art to practice the invention and to indicate the presently preferred embodiments thereof. This description is not to be understood as limiting the scope of the invention, which is limited only by the appended claims.  
       Step 1: Saliva Screening for Head and Neck Cancer  
       [0048]     Saliva samples can be collected in a number of ways. It is most important that the collection apparatus complies with the requirements of polymerase chain reaction (PCR) analysis and that the integrity of nucleic acids is not destroyed before analysis.  
         [0049]     The PCR analysis detect an increase or decrease in short repetitive sequences, called microsatellite DNA. The microsatellite DNA correspond to an allele because of their location on the DNA. Mutations in microsatellite DNA are found to be most common in epithelial cancer phenotypes, and so is a particularly appropriate analysis of exfoliated cells found in saliva A thorough description of this analysis is provided by U.S. Pat. No. 6,291,163, to Sidransky, incorporated herein by reference.  
         [0050]     PCR analysis has become somewhat automated, as is described in U.S. Pat. No. 6,326,147, incorporated herein by reference. PCR is considered a method for nucleic acid amplification which allows for DNA and RNA sequencing with a minute amount of nucleic acid sequence. Two U.S. Pat. Nos. 5,981,293 and 6,241,689, describe apparatus suitable for collecting saliva samples.  
         [0051]     Even though a patient may be found to positively exhibit signs of a cancerous phenotype upon saliva screening, the location of the cancer cells must then be identified before proper prognosis and treatment can be effected. Alternatively, even though a patient&#39;s saliva screen results in negative, meaning no cancer indications, the patient should still undergo a thorough visual examination (described in Step 2: Cellular Staining Location) for common and recurring cancer types.  
       Step 2: Location by Selective Light Examination  
       [0052]     Step 2 enables a practitioner to precisely locate and select suspect cells in vivo, for later molecular analysis, providing the clinician with a view of the suspect site, enabling the practitioner to select suspect tissues from surrounding normal tissue to direct the biopsy procedure for obtaining cells for the molecular analysis, Step 3.  
         [0053]     Another embodiment of the invention employs the in vivo Mashberg Protocol or similar dye-staining selective location protocols as a further adjuct to the initial selective light location step. These selective dye-staining protocols are advantageously employed to give the practicioner a more sustained view of the suspect and surrounding tissue, thereby facilitating the biopsy procedure.  
         [0054]     The Mashberg dye-staining protocol is described in detail in U.S. Pat. No. 6,086,852. The protocol employs toluidine blue O (TBO) dye to selectively stain cancerous and precancerous tissue. This original diagnostic screening test was described in the U.S. Pat. No. 4,321,251 to Mashberg and in the U.S. Pat. No. 5,372,801 to Tucci et al, incorporated herein by reference. Other cationic dyes, e.g. Azure B, Azure C and Brilliant Cresyl Blue, have been identified as useful for selectively marking cancerous and precancerous cells. See, for example, U.S. Pat. No. 5,882,672, to Pomerantz, incorporated here by reference.  
         [0055]     After the dye-staining step is perform, surgical excision biopsy of the suspect tissue is performed and a subsequent molecular analysis, herein described in “Step3: Molecular Analysis Diagnosis-Prognosis” follows, to yield a prognosis/diagnosis of cancer or eventual development of cancer, if the molecular analysis determines that cells from the abnormal tissue are malignant or precancerous.  
       Step 3: Molecular Analysis Diagnosis-Prognosis  
       [0056]     Cell samples for molecular analysis are derived from a variety of biopsy techniques, which, in general terms, involve the removal of a small piece of suspect tissue for molecular analysis. The method of tissue removal or extraction varies with the various types of biopsies. For example, the biopsy sample can comprise portions or skin lesions or isolated blood cells, e.g., erythrocytes, leukocytes, and lymphocytes, parathyroid tissue; salivary gland tissue; nasal mucosal tissue, oropharynx tissue, open lung tissue, small bowel tissues, etc. Molecular analysis is then performed to confirm whether the biopsy sample of suspect tissue is cancerous or precancerous.  
         [0057]     The target of molecular analysis, i.e., DNA, mRNA, DNA methylation, telemorase activity, or mtDNA analysis is selected based on access to instrumentation, qualified analysts, or the nature of the cell sample. The molecular analysis of the cell sample entails a choice among various procedures. Gel electrophoresis, the polymerase chain reaction (PCR) based chemistry, Rolling Circle Amplification (RCA) unimolecular detection system, flourescence tagging, immunohistochemical staining, mass spectroscopy, and colorimetry are representative examples of effective molecular analysis procedures. The nature of the cell sample, the extraction, and nucleic acid digestion will influence the choice of specific molecular analysis procedure for the optimum analysis.  
         [0058]     In the presently preferred embodiment of the invention, the molecular analysis procedure employed is the procedure for identifying microsatellite markers, i.e., repetitive sequences of the DNA, via PCR analysis. It should be understood, however, that the method of the invention may include any reliable molecular analysis technique for determining whether a cell&#39;s constituents exhibit a cancerous or wild-type phenotype.  
         [heading-0059]     I. Polymerase Chain Reaction (PCR), Commonly Microsatellite Instability (MSI)-Testing  
         [0060]     MSI is identified by electrophoretic resolution of amplified microsatellite DNA sequences. To perform MSI testing, blocks of surgically resected tumor tissue—either a fresh frozen specimen or a formalin-fixed, parafiin-embedded specimen is obtained. The tumor tissue is microdissected to separate neoplastic tissue from normal tissue, and DNA is extracted from both Samples of genomic DNA from these samples are amplified for a panel of specific mono- and di-nucleotide microsatellite loci using PCR.  
         [0061]     PCR products are then analyzed by electrophoresis. Additional bands in the PCR products of the tumor DNA not observed in the normal DNA is scored as instability at that locus (or specific site). According to industry standards, MSI analyses require the use of five MS markers, two mononucleotide repeats and three di-nucleotide repeats. According to the National Cancer Institute&#39;s consensus statement on MSI testing, any pair of samples that display instability at two or more of five different loci is scored as high MSI. For details, see Guo, Z., Yamaguchi, K., Sanchez-Cespedes, M., Westra, W. H., Koch, W. M., Sidransky, D., “Allelic Losses in OraTest-directed Biopsies of Patients with Prior Upper Aerodigestive Tract Malignancy”, Clinical Cancer Res., 7: 1963-1968, 2001. Further detail to enable one skilled in the art to perform the microsatellite analysis is disclosed in U.S. Pat. No. 6,291,163, to Sidransky, incorporated herein by reference. Automated PCR analysis is described in U.S. Pat. No. 6,326,147, incorporated herein by reference.  
         [heading-0062]     II. Gel Electrophoresis  
         [0063]     Nucleic acid strands are first selectively digested and then subjected to electrophoresis in which molecules (as proteins and nucleic acids) migrate through a gel (e.g., a polyacrylamide gel) and separate into bands according to size.  
         [heading-0064]     III. RCA  
         [0065]     Rolling circle amplification (RCA) is a surface-anchored DNA replication reaction that can display single molecular recognition events. RCA successfully visualizes target DNA sequences as small as 50 nts in peripheral blood lymphocytes or in stretched DNA fibers. Signal amplification by RCA can be coupled to nucleic acid hybridization and multicolor fluorescence imaging to detect single nucleotide changes in DNA within a cytological context or in single DNA molecules, enabling direct physical haplotyping and the analysis of somatic mutations on a cell-by-cell basis. Each amplified DNA molecule generated by RCA may be localized and imaged as a discrete fluorescent signal, indicating of a specific molecular ligation event. Expression profiles may be generated as histograms of single molecule counts, as well. The U.S. Pat. Nos. 6,329,150 and 6,210,884 to Lizardi, are incorporated herein by reference to provide ample detial to enable one skilled in the art to practice the disclosed invention employing RCA techniques.  
         [heading-0066]     IV. Southern Blotting  
         [0067]     Southern blotting can identify differences between normal and mutant alleles and identify genes that are related in other genomes. In a Southern blot, cloned or amplified DNA is digested with a restriction enzyme. The large variety of DNA fragments is separated according to size by electrophoresis and transferred onto a nitrocellulose filter. The fragments are then hybridized with a probe, but only those DNA fragments containing sequences homologous, or identical in base sequence, to the probe are detected. Single-base differences between individuals are detected when that base change creates or destroys a site for the restriction enzyme used to digest the DNA. Deletions or DNA insertions that change the size of the fragment created by the restriction enzyme(s) may also be detected in this manner. U.S. Pat. No. 5,811,2391, incorporated herein by reference, describes a method for single base-pair DNA sequence variation detection by Southern blot.  
         [heading-0068]     V. Flourescent Tagging  
         [0069]     Exact base sequence of a cloned or PCR-amplified DNA fragment is determined by a method called DNA sequencing. DNA sequencing has been automated by using differentially colored fluorescent markers for each of the four DNA bases whereby the fluorescent signal emitted by each of these chromosome “paints” can be read by a sensitive scanner and analyzed by a computer.  
         [heading-0070]     VI. DNA Probes  
         [0071]     A probe is a stretch of DNA or other nucleic acid that has been tethered to a stable material. The probe is then exposed to a target of free nucleic acid whose identity is being detected (by the probe) through a hybridization reaction (for terminology, see Phimster B: Nat Genet 21[Suppl]:1-60, 1999). The probe is generally labeled with a radioactive isotope or a chemical than can be detected after the hybridization takes place. For example, chemiluminescent labels, e.g. 1,2-dioxetanes, alkaline phosphate, or biotin, may be used as hybridization probes to detect nucleotide sequence ladders on membranes generated by the sequencing protocol of Church and Gilbert. See Church, G. M., Gilbert, W., Proc. Natl. Acad. Sci., USA 81, 1991-1995, (1984).  
         [heading-0072]     VII. Microarrays  
         [0073]     DNA microarrays made of high-speed robotics on inert materials, such as glass or nylon, may be used to identity genes and gene mutations. Preselected probes are exposed to “target” DNA and subsequently analyzed for hybridization patterns using a variety of visualization and information-processing programs and strategies. Identification of genes or gene mutations and the levels of gene expression can be detected and analyzed for many genes simultaneously and more rapidly than by many other techniques.  
         [0074]     Various names have been given to these microarrays, such as genome chip, biochip, DNA chip, DNA microarray, gene array, and GeneChip®® (registered trademark of “Affymetrix”).