Mining for SNPs: Putting the common variants-common disease hypothesis to the test

Pharmacogenomics

Volumn 1, Issue 1, 2000, Pages 27-37

  Cargill, Michele ^a   Daley, George Q ^a  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

Complex diseases; Genetic association study; Heterozygosity; Human Genome Project; Linkage disequilibrium; Single nucleotide polymorphism (SNP)

Indexed keywords

GENE FREQUENCY; GENETIC DISORDER; GENETIC POLYMORPHISM; GENETICS; GENOME; HUMAN; MOLECULAR BIOLOGY; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

GENE FREQUENCY; GENETIC DISEASES, INBORN; GENOME, HUMAN; HUMANS; MOLECULAR BIOLOGY; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 0034139518     PISSN: 14622416     EISSN: None     Source Type: Journal    
DOI: 10.1517/14622416.1.1.27     Document Type: Review

References (38)

1. RISCH N, MERIKANGAS K: The future of genetic studies of complex human diseases. Science (1996) 273:1516-1517. This brief review presents convincing arguments that statistical tests of association provide enhanced power over traditional genetic linkage strategies for demonstrating the modest effects of weak alleles on disease phenotypes.
2. COLLINS FS, GUYER MS, CHARKRAVARTI A: Variations on a theme: cataloging human DNA sequence variation. Science (1997) 278:1580-1581. The argument for cataloguing human genetic variation put forth by opinion leaders in the Human Genome Project.
3. LI W-H: Molecular Evolution. Sinauer Associates, Canada (1997). Extremely helpful resource for issues in population genetic theory.
4. LANDER ES: The new genomics: global views of biology. Science (1996) 274:536-539. A vision of biology in the post-genome era.
5. STRITTMATTER WJ, SAUNDERS AM, SCHMECHEL D et al.: Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. Proc. Natl. Acad. Sci. USA (1993) 90:1977-1981. A classic study using a statistical test of association to suggest the role of the epsilon 4 allele of apolipoprotein E as a genetic risk factor in Alzheimer's disease. The apolipoprotein E locus had emerged as a candidate gene from the genomic region previously associated with linkage to late-onset familial Alzheimer's dementia.
6. CORDER EH, LANNFELT L, BOGDANOVIC N, FRATIGLIONI L, MORI H: The role of APOE polymorphisms in late-onset dementias. Cell Mol. Life Sci. (1998) 54:928-934.
7. LENDON CL, ASHALL F, GOATE AM: Exploring the etiology of Alzheimer's disease using molecular genetics. JAMA (1997) 277:825-831.
8. ROSES AD: Apolipoprotein E alleles as risk factors in Alzheimer's disease. Ann. Rev. Med. (1996) 47:387-400.
9. DEAN M, CARRINGTON M, WINKLER C et al.: Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science (1996) 273:1856-1802.
10. BERTINA RM, KOELEMAN BP, KOSTER T et al.: Mutation in blood coagulation Factor V associated with resistance to activated protein C. Nature (1994) 369:64-67.
11. NICKERSON DA, TAYLOR SL, WEISS KM et al.: DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nature Genet. (1998) 19:233-240. Extensive sequence cliaracterization of a single locus in many individuals documents the magnitude and type of variation in coding and intronic regions. The authors discuss how heterozygosity within a locus poses significant challenges to identification of which alleles influence trait variation.
12. COLLINS FS, PATRINOS A, JORDAN E, CHAKRAVARTI A, GESTELAND R, WALTERS L: New goals for the US Human Genome Project: 1998-2003. Science(1998) 282:682-689.
13. CHEE M, YANG R, HUBBELL E et al.: Accessing genetic information with high-density DNA arrays. Science (1996) 274:610-614. An explanation of the technology and principles of high-density oligonucleotide array analysis for resequencing of DNA.
14. COTTON RG: Slowly but surely towards better scanning for mutations [published erratum appears in Trends Genet. (1997) May 13(5):208]. Trends Genet. (1997) 13:43-46. An accessible discussion of the methodology of mutation detection.
15. TAYLOR GR: Enzymatic and chemical cleavage methods. Electrophoresis (1999) 20:1125-1130.
16. BUETOW K, EDMONSON M, CASSIDY A: Reliable identification of large numbers of candidate SNPs from public EST data. Nature Genet. (1999) 21:323-325. In silico strategies for SNP discovery.
17. PICOULT-NEWBERG L, IDEKER TE, POHL MG et al.: Mining SNPs from EST databases. Genome Res. (1999) 9:167-174. In silico strategies for SNP discovery.
18. NICKERSON DA, TOBE VO, TAYLOR SL: PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. (1997) 25:2745-2751. A description of the PolyPhred software package, which facilitates identification of SNPs through multiple sequence alignment and assessments of sequence quality.
19. HARRIS H, HOPKINSON DA, ROBSON EB: The incidence of rare alleles determining electrophoretic variants: data on 43 enzyme loci in man. Ann. Hum. Genet. (1974) 37:237-253.
20. HARRIS H, HOPKINSON DA: Average heterozygosity per locus in man: an estimate based on the incidence of enzyme polymorphisms. Ann. Hum. Genet. (1972) 36:9-20.
21. CLARK AG, WEISS KM, NICKERSON DA et al.: Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. (1998) 63:595-612.
22. HALUSHKA MK, FAN JB, BENTLEY K et al.: Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nature Genet. (1999) 22:239-247. Among the first large-scale surveys of DNA sequence variation within the coding regions of a large number of genes. These studies represent the earliest attempts to assemble a catalogue of genetic variants in candidate genes for specific diseases.
23. CARGILL M, ALTSHULER D, IRELAND J et al.: Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genet. (1999) 22:231-238. Among the first large-scale surveys of DNA sequence variation within the coding regions of a large number of genes. These studies represent the earliest attempts to assemble a catalogue of genetic variants in candidate genes for specific diseases.
24. TAKAHATA N, SATTA Y, KLEIN J: Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol. (1995) 48:198-221.
25. AYALA FJ, ESCALANTE A, O'HUIGIN C, KLEIN J: Molecular genetics of speciation and human origins. Proc. Natl. Acad. Sci. USA (1994) 91:6787-6794.
26. WATTERSON GA, GUESS HA: Is the most frequent allele the oldest? Theor. Popul. Biol. (1977) 11:141-160.
27. HUDSON RR, KREITMAN M, AGUADE M: A test of neutral molecular evolution based on nucleotide data. Genetics (1987) 116.153-159.
28. KRUGLYAK L: Prospects for whole-genome linkage-disequilibrium mapping of common disease genes. Nature Genet. (1999) 22:139-144. A cogent theoretical model of the extent of linkage disequilibrium among markers in human genes, arguing that only minimal blocks of LD likely exist and therefore dense maps consisting of hundreds of thousands of SNPs will be needed for genome-wide mapping strategies.
29. EWENS WJ, SPIELMAN RS: The transmission/disequilibrium test: history, subdivision, and admixture. Am. J. Hum. Genet. (1995) 57:455-464. A discussion of how to employ allelic transmission analysis in study populations of parents and affected offspring to negate the problems of population admixture that plague case-control studies.
30. SMITH J, MODRICH P: Mutation detection with MutH, MutL, and MutS mismatch repair proteins. Proc. Natl. Acad. Sci. USA (1996) 93:4374-4379.
31. CAMBIEN F, POIRIER O, NICAUD V et al.: Sequence diversity in 36 candidate genes for cardiovascular disorders. Am. J. Hum. Genet. (1999) 65:183-191. An extensive survey of variation in candidate genes for cardiovascular disease and genotyping of 750 individuals. The results suggest a high degree of non-random association among polymorphic sites reflecting the presence of ancestral haplotypes within this population.
32. KAESSMANN H, HEISSIG F, VON HAESELER A, PAABO S: DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nature Genet. (1999) 22:78-81. An assessment of X chromosome sequence variation that documents the high population diversity within Africa, and provides information about the date of common genetic ancestry and human origins.
33. LI WH, SADLER LA: Low nucleotide diversity in man. Genetics (1991) 129:513-523. Data arguing that the human species harbours limited genetic diversity, likely reflecting its recent evolutionary emergence and small effective population size.
34. NACHMAN MW, BAUER VL, CROWELL SL, AQUADRO CF: DNA variability and recombination rates at X-linked loci in humans. Genetics (1998) 150:1133-1141.
35. RIEDER MJ, TAYLOR SL, CLARK AG, NICKERSON DA: Sequence variation in the human angiotensin converting enzyme. Nature Genet. (1999) 22:59-62. Sequence analysis of a 24 kilobase region of the ACE gene represents the longest contiguous scan for sequence variation within the human genome to date.
36. TAILLON-MILLER P, GU Z, LI Q, HILLIER L. KWOK PY: Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res. (1998) 8:748-754.
37. WANG DG, FAN JB, SIAO CJ et al.: Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science (1998) 280:1077-1082. The first large-scale application of VDAs in the discovery and genotyping of SNPs, resulting in the construction of a SNP-based genetic map consisting of over 2000 markers.
38. ZIETKIEWICZ E, YOTOVA V, JARNIK M et al.: Nuclear DNA diversity in worldwide distributed human populations. Gene (1997) 205:161-171.