Replication strategies for rare variant complex trait association studies via next-generation sequencing

American Journal of Human Genetics

Volumn 87, Issue 6, 2010, Pages 790-801

  Liu, Dajiang J ^a,b   Leal, Suzanne M ^a,b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b Rice University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE LOCUS; GENE MAPPING; GENE REPLICATION; GENE SEQUENCE; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; PRIORITY JOURNAL;

GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, GENETIC; PROBABILITY; SEQUENCE ANALYSIS, DNA;

EID: 78649775312     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2010.10.025     Document Type: Article

References (39)

1. J.C. Cohen, R.S. Kiss, A. Pertsemlidis, Y.L. Marcel, R. McPherson, and H.H. Hobbs Multiple rare alleles contribute to low plasma levels of HDL cholesterol Science 305 2004 869 872
2. J.C. Cohen, A. Pertsemlidis, S. Fahmi, S. Esmail, G.L. Vega, S.M. Grundy, and H.H. Hobbs Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels Proc. Natl. Acad. Sci. USA 103 2006 1810 1815
3. W. Ji, J.N. Foo, B.J. O'Roak, H. Zhao, M.G. Larson, D.B. Simon, C. Newton-Cheh, M.W. State, D. Levy, and R.P. Lifton Rare independent mutations in renal salt handling genes contribute to blood pressure variation Nat. Genet. 40 2008 592 599
4. S. Romeo, L.A. Pennacchio, Y. Fu, E. Boerwinkle, A. Tybjaerg-Hansen, H.H. Hobbs, and J.C. Cohen Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL Nat. Genet. 39 2007 513 516
5. S. Romeo, W. Yin, J. Kozlitina, L.A. Pennacchio, E. Boerwinkle, H.H. Hobbs, and J.C. Cohen Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans J. Clin. Invest. 119 2009 70 79
6. B. Li, and S.M. Leal Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data Am. J. Hum. Genet. 83 2008 311 321
7. S.B. Ng, K.J. Buckingham, C. Lee, A.W. Bigham, H.K. Tabor, K.M. Dent, C.D. Huff, P.T. Shannon, E.W. Jabs, and D.A. Nickerson Exome sequencing identifies the cause of a mendelian disorder Nat. Genet. 42 2010 30 35
8. S.B. Ng, E.H. Turner, P.D. Robertson, S.D. Flygare, A.W. Bigham, C. Lee, T. Shaffer, M. Wong, A. Bhattacharjee, and E.E. Eichler Targeted capture and massively parallel sequencing of 12 human exomes Nature 461 2009 272 276
9. L. Mamanova, A.J. Coffey, C.E. Scott, I. Kozarewa, E.H. Turner, A. Kumar, E. Howard, J. Shendure, and D.J. Turner Target-enrichment strategies for next-generation sequencing Nat. Methods 7 2010 111 118
10. O. Harismendy, P.C. Ng, R.L. Strausberg, X. Wang, T.B. Stockwell, K.Y. Beeson, N.J. Schork, S.S. Murray, E.J. Topol, S. Levy, and K.A. Frazer Evaluation of next generation sequencing platforms for population targeted sequencing studies Genome Biol. 10 2009 R32
11. I.P. Gorlov, O.Y. Gorlova, S.R. Sunyaev, M.R. Spitz, and C.I. Amos Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms Am. J. Hum. Genet. 82 2008 100 112
12. B.E. Madsen, and S.R. Browning A groupwise association test for rare mutations using a weighted sum statistic PLoS Genet. 5 2009 e1000384
13. A.P. Morris, and E. Zeggini An evaluation of statistical approaches to rare variant analysis in genetic association studies Genet. Epidemiol. 34 2010 188 193
14. I. Ionita-Laza, C. Lange, and N.M. Laird Estimating the number of unseen variants in the human genome Proc. Natl. Acad. Sci. USA 106 2009 5008 5013
15. B. Li, and S.M. Leal Discovery of rare variants via sequencing: implications for the design of complex trait association studies PLoS Genet. 5 2009 e1000481
16. R. Nielsen, I. Hellmann, M. Hubisz, C. Bustamante, and A.G. Clark Recent and ongoing selection in the human genome Nat. Rev. Genet. 8 2007 857 868 (Pubitemid 47609088)
17. A.R. Boyko, S.H. Williamson, A.R. Indap, J.D. Degenhardt, R.D. Hernandez, K.E. Lohmueller, M.D. Adams, S. Schmidt, J.J. Sninsky, and S.R. Sunyaev Assessing the evolutionary impact of amino acid mutations in the human genome PLoS Genet. 4 2008 e1000083
18. D.Y. Lin, and D. Zeng Meta-analysis of genome-wide association studies: no efficiency gain in using individual participant data Genet. Epidemiol. 34 2010 60 66
19. Y. Shen, Z. Wan, C. Coarfa, R. Drabek, L. Chen, E.A. Ostrowski, Y. Liu, G.M. Weinstock, D.A. Wheeler, R.A. Gibbs, and F.A. Yu A SNP discovery method to assess variant allele probability from next-generation resequencing data Genome Res. 20 2010 273 280
20. P. Scheet, and M. Stephens Linkage disequilibrium-based quality control for large-scale genetic studies PLoS Genet. 4 2008 e1000147
21. S.M. Leal Detection of genotyping errors and pseudo-SNPs via deviations from Hardy-Weinberg equilibrium Genet. Epidemiol. 29 2005 204 214
22. J.A. Douglas, M. Boehnke, and K. Lange A multipoint method for detecting genotyping errors and mutations in sibling-pair linkage data Am. J. Hum. Genet. 66 2000 1287 1297
23. R.D. Hernandez A flexible forward simulator for populations subject to selection and demography Bioinformatics 24 2008 2786 2787
24. J.K. Pritchard Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet. 69 2001 124 137
25. A. Eyre-Walker, and P.D. Keightley High genomic deleterious mutation rates in hominids Nature 397 1999 344 347
26. G.V. Kryukov, A. Shpunt, J.A. Stamatoyannopoulos, and S.R. Sunyaev Power of deep, all-exon resequencing for discovery of human trait genes Proc. Natl. Acad. Sci. USA 106 2009 3871 3876
27. W. Bodmer, and C. Bonilla Common and rare variants in multifactorial susceptibility to common diseases Nat. Genet. 40 2008 695 701
28. J.D. Browning, L.S. Szczepaniak, R. Dobbins, P. Nuremberg, J.D. Horton, J.C. Cohen, S.M. Grundy, and H.H. Hobbs Prevalence of hepatic steatosis in an urban population in the United States: impact of ethnicity Hepatology 40 2004 1387 1395
29. R.G. Victor, R.W. Haley, D.L. Willett, R.M. Peshock, P.C. Vaeth, D. Leonard, M. Basit, R.S. Cooper, V.G. Iannacchione, W.A. Visscher Dallas Heart Study Investigators The Dallas Heart Study: a population-based probability sample for the multidisciplinary study of ethnic differences in cardiovascular health Am. J. Cardiol. 93 2004 1473 1480
30. B. Kerem, O. Chiba-Falek, and E. Kerem Cystic fibrosis in Jews: frequency and mutation distribution Genet. Test. 1 1997 35 39
31. M.C. King, S. Rowell, and S.M. Love Inherited breast and ovarian cancer. What are the risks? What are the choices? JAMA 269 1993 1975 1980
32. V. Bansal, O. Harismendy, R. Tewhey, S.S. Murray, N.J. Schork, E.J. Topol, and K.A. Frazer Accurate detection and genotyping of SNPs utilizing population sequencing data Genome Res. 20 2010 537 545
33. B. Ewing, and P. Green Base-calling of automated sequencer traces using phred. II. Error probabilities Genome Res. 8 1998 186 194 (Pubitemid 28177230)
34. B. Ewing, L. Hillier, M.C. Wendl, and P. Green Base-calling of automated sequencer traces using phred. I. Accuracy assessment Genome Res. 8 1998 175 185 (Pubitemid 28177229)
35. A.K. Daly, P.T. Donaldson, P. Bhatnagar, Y. Shen, I. Pe'er, A. Floratos, M.J. Daly, D.B. Goldstein, S. John, M.R. Nelson DILIGEN Study International SAE Consortium HLA-B5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin Nat. Genet. 41 2009 816 819
36. J. Mitsui, I. Mizuta, A. Toyoda, R. Ashida, Y. Takahashi, J. Goto, Y. Fukuda, H. Date, A. Iwata, and M. Yamamoto Mutations for Gaucher disease confer high susceptibility to Parkinson disease Arch. Neurol. 66 2009 571 576
37. S.B. Ng, A.W. Bigham, K.J. Buckingham, M.C. Hannibal, M.J. McMillin, H.I. Gildersleeve, A.E. Beck, H.K. Tabor, G.M. Cooper, and H.C. Mefford Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome Nat. Genet. 42 2010 790 793
38. C. Gilissen, H.H. Arts, A. Hoischen, L. Spruijt, D.A. Mans, P. Arts, B. van Lier, M. Steehouwer, J. van Reeuwijk, and S.G. Kant Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome Am. J. Hum. Genet. 87 2010 418 423
39. K. Bilgüvar, A.K. Oztürk, A. Louvi, K.Y. Kwan, M. Choi, B. Tatli, D. Yalnizolu, B. Tüysüz, A.O. Calayan, and S. Gökben Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations Nature 467 2010 207 210