Shifting Paradigm of Association Studies: Value of Rare Single-Nucleotide Polymorphisms

American Journal of Human Genetics

Volumn 82, Issue 1, 2008, Pages 100-112

  Gorlov, Ivan P ^a   Gorlova, Olga Y ^a   Sunyaev, Shamil R ^b   Spitz, Margaret R ^a   Amos, Christopher I ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CASE CONTROL STUDY; DISEASE PREDISPOSITION; GENE FREQUENCY; GENE IDENTIFICATION; GENETIC REGULATION; GENOTYPE; INFORMATION RETRIEVAL; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; GENETIC PREDISPOSITION; GENOME; HUMAN; MISSENSE MUTATION; POPULATION GENETICS;

CASE-CONTROL STUDIES; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; MUTATION, MISSENSE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 38749145596     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2007.09.006     Document Type: Article

References (64)

1. Risch N., and Merikangas K. The future of genetic studies of complex human diseases. Science 273 (1996) 1516-1517
2. Muller-Myhsok B., and Abel L. Genetic analysis of complex diseases. Science 275 (1997) 1328-1329
3. Scott W.K., Pericak-Vance M.A., and Haines J.L. Genetic analysis of complex diseases. Science 275 (1997) 1327
4. Long A.D., Grote M.N., and Langley C.H. Genetic analysis of complex diseases. Science 275 (1997) 1328
5. The International HapMap Consortium. The International HapMap Project. Nature 426 (2003) 789-796
6. The International HapMap Consortium. Integrating ethics and science in the International HapMap Project. Nat. Rev. Genet. 5 (2004) 467-475
7. Strittmatter W.J., and Roses A.D. Apolipoprotein E and Alzheimer's disease. Annu. Rev. Neurosci. 19 (1996) 53-77
8. Altshuler D., Hirschhorn J.N., Klannemark M., Lindgren C.M., Vohl M.C., Nemesh J., Lane C.R., Schaffner S.F., Bolk S., Brewer C., et al. The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat. Genet. 26 (2000) 76-80
9. Deeb S.S., Fajas L., Nemoto M., Pihlajamäki J., Mykkänen L., Kuusisto J., Laakso M., Fujimoto W., and Auwerx J. A Pro12Ala substitution in PPARgamma2 associated with decreased receptor activity, lower body mass index and improved insulin sensitivity. Nat. Genet. 20 (1998) 284-287
10. Florez J.C., Hirschhorn J., and Altshuler D. The inherited basis of diabetes mellitus: Implications for the genetic analysis of complex traits. Annu. Rev. Genomics Hum. Genet. 4 (2003) 257-291
11. Begovich A.B., Carlton V.E., Honigberg L.A., Schrodi S.J., Chokkalingam A.P., Alexander H.C., Ardlie K.G., Huang Q., Smith A.M., Spoerke J.M., et al. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am. J. Hum. Genet. 75 (2004) 330-337
12. Ogura Y., Bonen D.K., Inohara N., Nicolae D.L., Chen F.F., Ramos R., Britton H., Moran T., Karaliuskas R., Duerr R.H., et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 411 (2001) 603-606
13. Klein R.J., Zeiss C., Chew E.Y., Tsai J.Y., Sackler R.S., Haynes C., Henning A.K., SanGiovanni J.P., Mane S.M., Mayne S.T., et al. Complement factor H polymorphism in age-related macular degeneration. Science 308 (2005) 385-389
14. Edwards A.O., Ritter III R., Abel K.J., Manning A., Panhuysen C., and Farrer L.A. Complement factor H polymorphism and age-related macular degeneration. Science 308 (2005) 421-424
15. Li Y.Y., Xing J., Zhao L.S., Li Y.N., Wang Y.C., and Zhang W.M. [Screening and analysis of coding SNPs of HLA-DQA1 gene involved in susceptibility for cervical cancer]. Ai Zheng 25 (2006) 906-910
16. Andrew A.S., Nelson H.H., Kelsey K.T., Moore J.H., Meng A.C., Casella D.P., Tosteson T.D., Schned A.R., and Karagas M.R. Concordance of multiple analytical approaches demonstrates a complex relationship between DNA repair gene SNPs, smoking and bladder cancer susceptibility. Carcinogenesis 27 (2006) 1030-1037
17. Webb T. SNPs: Can genetic variants control cancer susceptibility?. J. Natl. Cancer Inst. 94 (2002) 476-478
18. Schubert E.L., Lee M.K., Newman B., and King M.C. Single nucleotide polymorphisms (SNPs) in the estrogen receptor gene and breast cancer susceptibility. J. Steroid Biochem. Mol. Biol. 71 (1999) 21-27
19. Cantor C.R. The use of genetic SNPs as new diagnostic markers in preventive medicine. Ann. N Y Acad. Sci. 1055 (2005) 48-57
20. Packer B.R., Yeager M., Burdett L., Welch R., Beerman M., Qi L., Sicotte H., Staats B., Acharya M., Crenshaw A., et al. SNP500Cancer: A public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res. 34 Database issue (2006) D617-D621
21. Packer B.R., Yeager M., Staats B., Welch R., Crenshaw A., Kiley M., Eckert A., Beerman M., Miller E., Bergen A., et al. SNP500Cancer: A public resource for sequence validation and assay development for genetic variation in candidate genes. Nucleic Acids Res. 32 Database issue (2004) D528-D532
22. Horng J.T., Hu K.C., Wu L.C., Huang H.D., Lin F.M., Huang S.L., Lai H.C., and Chu T.Y. Identifying the combination of genetic factors that determine susceptibility to cervical cancer. IEEE Trans. Inf. Technol. Biomed. 8 (2004) 59-66
23. Ott J. Association of genetic loci: Replication or not, that is the question. Neurology 63 (2004) 955-958
24. Smyth D.J., Cooper J.D., Bailey R., Field S., Burren O., Smink L.J., Guja C., Ionescu-Tirgoviste C., Widmer B., Dunger D.B., et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat. Genet. 38 (2006) 617-619
25. Breast Cancer Association Consortium. Commonly studied single-nucleotide polymorphisms and breast cancer: Results from the Breast Cancer Association Consortium. J. Natl. Cancer Inst. 98 (2006) 1382-1396
26. Thorisson G.A., Smith A.V., Krishnan L., and Stein L.D. The International HapMap Project Web site. Genome Res. 15 (2005) 1592-1593
27. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., and Sirotkin K. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29 (2001) 308-311
28. Sherry S.T., Ward M., and Sirotkin K. Use of molecular variation in the NCBI dbSNP database. Hum. Mutat. 15 (2000) 68-75
29. Park J., Hwang S., Lee Y.S., Kim S.C., and Lee D. SNP@Ethnos: A database of ethnically variant single-nucleotide polymorphisms. Nucleic Acids Res. 35 Database issue (2007) D711-D715
30. Sawyer S.L., Mukherjee N., Pakstis A.J., Feuk L., Kidd J.R., Brookes A.J., and Kidd K.K. Linkage disequilibrium patterns vary substantially among populations. Eur. J. Hum. Genet. 13 (2005) 677-686
31. Voight B.F., Kudaravalli S., Wen X., and Pritchard J.K. A map of recent positive selection in the human genome. PLoS Biol. 4 (2006) e72
32. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306 (2004) 636-640
33. Gabriel S.B., Schaffner S.F., Nguyen H., Moore J.M., Roy J., Blumenstiel B., Higgins J., DeFelice M., Lochner A., Faggart M., et al. The structure of haplotype blocks in the human genome. Science 296 (2002) 2225-2229
34. Reich D.E., Gabriel S.B., and Altshuler D. Quality and completeness of SNP databases. Nat. Genet. 33 (2003) 457-458
35. Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., Shaw N., Lane C.R., Lim E.P., Kalyanaraman N., et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22 (1999) 231-238
36. Mooney S. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief. Bioinform. 6 (2005) 44-56
37. Abushamaa A.M., Sporn T.A., and Folz R.J. Oxidative stress and inflammation contribute to lung toxicity after a common breast cancer chemotherapy regimen. Am. J. Physiol. Lung Cell. Mol. Physiol. 283 (2002) L336-L345
38. Ramensky V., Bork P., and Sunyaev S. Human non-synonymous SNPs: Server and survey. Nucleic Acids Res. 30 (2002) 3894-3900
39. Dagan T., Talmor Y., and Graur D. Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol. Biol. Evol. 19 (2002) 1022-1025
40. Dupont W.D., and Plummer Jr. W.D. Power and sample size calculations. A review and computer program. Control. Clin. Trials 11 (1990) 116-128
41. Ng P.C., and Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 31 (2003) 3812-3814
42. Pritchard J.K. Are rare variants responsible for susceptibility to complex diseases?. Am. J. Hum. Genet. 69 (2001) 124-137
43. Pritchard J.K., and Cox N.J. The allelic architecture of human disease genes: Common disease-common variant...or not?. Hum. Mol. Genet. 11 (2002) 2417-2423
44. Reich D.E., and Lander E.S. On the allelic spectrum of human disease. Trends Genet. 17 (2001) 502-510
45. Kondrashov A.S. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Hum. Mutat. 21 (2003) 12-27
46. Nachman M.W., and Crowell S.L. Estimate of the mutation rate per nucleotide in humans. Genetics 156 (2000) 297-304
47. Peng B., and Kimmel M. Simulations provide support for the common disease-common variant hypothesis. Genetics 175 (2007) 763-776
48. Kryukov G.V., Pennacchio L.A., and Sunyaev S.R. Most rare missense alleles are deleterious in humans: Implications for complex disease and association studies. Am. J. Hum. Genet. 80 (2007) 727-739
49. Kotowski I.K., Pertsemlidis A., Luke A., Cooper R.S., Vega G.L., Cohen J.C., and Hobbs H.H. A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol. Am. J. Hum. Genet. 78 (2006) 410-422
50. Krawczak M., and Cooper D.N. The human gene mutation database. Trends Genet. 13 (1997) 121-122
51. Stenson P.D., Ball E.V., Mort M., Phillips A.D., Shiel J.A., Thomas N.S., Abeysinghe S., Krawczak M., and Cooper D.N. Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat. 21 (2003) 577-581
52. Crow J.F., and Kimura M. An Introduction to Population Genetics Theory (1970), Harper & Row
53. Zhang X.S., Wang J., and Hill W.G. Influence of dominance, leptokurtosis and pleiotropy of deleterious mutations on quantitative genetic variation at mutation-selection balance. Genetics 166 (2004) 597-610
54. Fan J.B., Gehl D., Hsie L., Shen N., Lindblad-Toh K., Laviolette J.P., Robinson E., Lipshutz R., Wang D., Hudson T.J., et al. Assessing DNA sequence variations in human ESTs in a phylogenetic context using high-density oligonucleotide arrays. Genomics 80 (2002) 351-360
55. Wicklow B.A., Ivanovich J.L., Plews M.M., Salo T.J., Noetzel M.J., Lueder G.T., Cartegni L., Kaback M.M., Sandhoff K., Steiner R.D., et al. Severe subacute GM2 gangliosidosis caused by an apparently silent HEXA mutation (V324V) that results in aberrant splicing and reduced HEXA mRNA. Am. J. Med. Genet. A. 127 (2004) 158-166
56. Xie J., Pabón D., Jayo A., Butta N., and González-Manchón C. Type I Glanzmann thrombasthenia caused by an apparently silent beta3 mutation that results in aberrant splicing and reduced beta3 mRNA. Thromb. Haemost. 93 (2005) 897-903
57. Pfarr N., Prawitt D., Kirschfink M., Schroff C., Knuf M., Habermehl P., Mannhardt W., Zepp F., Fairbrother W., Loos M., et al. Linking C5 deficiency to an exonic splicing enhancer mutation. J. Immunol. 174 (2005) 4172-4177
58. Denecke J., Kranz C., Kemming D., Koch H.G., and Marquardt T. An activated 5′ cryptic splice site in the human ALG3 gene generates a premature termination codon insensitive to nonsense-mediated mRNA decay in a new case of congenital disorder of glycosylation type Id (CDG-Id). Hum. Mutat. 23 (2004) 477-486
59. Carlini D.B., and Genut J.E. Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J. Mol. Evol. 62 (2006) 89-98
60. Gorlov I.P., Kimmel M., and Amos C.I. Strength of the purifying selection against different categories of the point mutations in the coding regions of the human genome. Hum. Mol. Genet. 15 (2006) 1143-1150
61. Wong G.K., Yang Z., Passey D.A., Kibukawa M., Paddock M., Liu C.R., Bolund L., and Yu J. A population threshold for functional polymorphisms. Genome Res. 13 (2003) 1873-1879
62. Wilson S.H., and Olden K. The environmental genome project: Phase I and beyond. Mol. Interv. 4 (2004) 147-156
63. Guengerich F.P. The Environmental Genome Project: Functional analysis of polymorphisms. Environ. Health Perspect. 106 (1998) 365-368
64. Taylor J.A., Xu Z.L., Kaplan N.L., and Morris R.W. How well do HapMap haplotypes identify common haplotypes of genes? A comparison with haplotypes of 334 genes resequenced in the environmental genome project. Cancer Epidemiol. Biomarkers Prev. 15 (2006) 133-137