Detecting Rare Variant Effects Using Extreme Phenotype Sampling in Sequencing Association Studies

Genetic Epidemiology

Volumn 37, Issue 2, 2013, Pages 142-151

  Barnett, Ian J ^a   Lee, Seunggeun ^a   Lin, Xihong ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Complex trait associations; Extreme phenotype sampling; Rare genetic variants; Selective sampling

Indexed keywords

ANALYTICAL ERROR; ARTICLE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; PHENOTYPE; SAMPLING; SEQUENCE ANALYSIS; SIMULATION; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ANGIOPOIETINS; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; HUMANS; MODELS, GENETIC; PHENOTYPE; SEQUENCE ANALYSIS, DNA; TRIGLYCERIDES;

EID: 84872410521     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21699     Document Type: Article

References (37)

1. Bansal V, Libiger O, Torkamani A, Schork NJ. 2010. Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet 11(11):773-785.
2. Basu S, Pan W. 2011. Comparison of statistical tests for disease association with rare variants. Genet Epidemiol 35(7):606-619.
3. Biesecker LG, Shianna KV, Mullikin JC. 2011. Exome sequencing: the expert view. Genome Biol 12(9):128-130.
4. Chen Z, Zheng G, Ghosh K, Li Z. 2005. Linkage disequilibrium mapping of quantitative-trait Loci by selective genotyping. Am J Hum Genet 77(4):661-669.
5. Cirulli ET, Goldstein DB. 2010. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11(6):415-425.
6. Clement K, Vaisse C, Manning BS, Basdevant A, Guy-Grand B, Ruiz J, Silver KD, Shuldiner AR, Froguel P, Strosberg AD. 1995. Genetic variation in the beta 3-adrenergic receptor and an increased capacity to gain weight in patients with morbid obesity. N Engl J Med 333(6):352-354.
7. Davies RB. 1980. The distribution of a linear combination of chi-square random variables. J R Stat Soc 29(3):323-333.
8. Gu C, Todorov AA, Rao DC. 1997. Genome screening using extremely discordant and extremely concordant sib pairs. Genet Epidemiol 14(6):791-796.
9. Hernandez RD. 2008. A flexible forward simulator for populations subject to selection and demography. Bioinformatics 24(23):2786-2787.
10. Hu S, Zhong Y, Hao Y, Luo M, Zhou Y, Guo H, Liao W, Wan D, Wei H, Gao Y and others. 2009. Novel rare alleles of ABCA1 are exclusively associated with extreme high-density lipoprotein-cholesterol levels among the Han Chinese. Clin Chem Lab Med 47(10):1239-1245.
11. Huang BE, Lin DY. 2007. Efficient association mapping of quantitative trait loci with selective genotyping. Am J Hum Genet 80(3):567-576.
12. Ioannidis JP, Thomas G, Daly MJ. 2009. Validating, augmenting and refining genome-wide association signals. Nat Rev Genet 10(5):318-329.
13. Ji W, Foo JN, O'Roak BJ, Zhao H, Larson MG, Simon DB, Newton-Cheh C, State MW, Levy D, Lifton RP. 2008. Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat Genet 40(5):592-599.
14. Khor CC, Goh DL. 2010. Strategies for identifying the genetic basis of dyslipidemia: genome-wide association studies vs. the resequencing of extremes. Curr Opin Lipidol 21(2):123-127.
15. Lee S, Emonds M, Bamshad M, Barnes K, Rieder M, Nickerson D, Christiani D, Wurfel M, Lin X. 2012a. Optimal unified approach for rare variant association testing with application to small sample case-control whole-exome sequencing studies. Am J Hum Genet 91(2):224-237.
16. Lee S, Wu MC, Lin X. 2012b. Optimal tests for rare variant effects in sequencing association studies. Biostatistics 13(4):762-775.
17. Li B, Leal SM. 2008. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83(3):311-321.
18. Li D, Lewinger JP, Gauderman WJ, Murcray CE, Conti D. 2011. Using extreme phenotype sampling to identify the rare causal variants of quantitative traits in association studies. Genet Epidemiol 35(8):790-799.
19. Liang KY, Huang CY, Beaty TH. 2000. A unified sampling approach for multipoint analysis of qualitative and quantitative traits in sib pairs. Am J Hum Genet 66(5):1631-1641.
20. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5(2):e1000384.
21. Maher B. 2008. Personal genomes: the case of the missing heritability. Nature 456(7218):18-21.
22. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A and others. 2009. Finding the missing heritability of complex diseases. Nature 461(7265):747-753.
23. Morgenthaler S, Thilly WG. 2007. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res 615(1-2):28-56.
24. Morris AP, Zeggini E. 2010. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34(2):188-193.
25. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, Orho-Melander M, Kathiresan S, Purcell SM, Roeder K, Daly MJ. 2011. Testing for an unusual distribution of rare variants. PLoS Genet 7(3):e1001322.
26. Nejentsev S, Walker N, Riches D, Egholm M, Todd JA. 2009. Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 324(5925):387-389.
27. Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, Li K, Axelrod N, Busam DA, Strausberg RL, Venter JC. 2008. Genetic variation in an individual human exome. PLoS Genet 4(8):e1000160.
28. Pan W. 2009. Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genet Epidemiol 33(6):497-507.
29. Price RA, Li WD, Zhao H. 2008. FTO gene SNPs associated with extreme obesity in cases, controls and extremely discordant sister pairs. BMC Med Genet 9:4-8.
30. Price AL, Kryukov GV, de Bakker PIW, Purcell SM, Staples J, Wei LJ, Sunyaev SR. 2010. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86(6):832-838.
31. Ramser J, Ahearn ME, Lenski C, Yariz KO, Hellebrand H, von Rhein M, Clark RD, Schmutzler RK, Lichtner P, Hoffman EP and others. 2008. Rare missense and synonymous variants in UBE1 are associated with X-linked infantile spinal muscular atrophy. Am J Hum Genet 82(1):188-193.
32. Risch N, Zhang H. 1995. Extreme discordant sib pairs for mapping quantitative trait loci in humans. Science 268(5217):1584-1589.
33. Slatkin M. 1999. Disequilibrium mapping of a quantitative-trait locus in an expanding population. Am J Hum Genet 64(6):1764-1772.
34. Tzeng JY, Zhang D. 2007. Haplotype-based association analysis via variance-components score test. Am J Hum Genet 81(5):927-938.
35. Victor RG, Haley RW, Willett DL, Peshock RM, Vaeth PC, Leonard D, Basit M, Cooper RS, Iannacchione VG, Visscher WA and others. 2004. The Dallas Heart Study: a population-based probability sample for the multidisciplinary study of ethnic differences in cardiovascular health. Am J Cardiol 93(12):1473-1480.
36. Wallace C, Chapman JM, Clayton DG. 2006. Improved power offered by a score test for linkage disequilibrium mapping of quantitative-trait loci by selective genotyping. Am J Hum Genet 78(3):498-504.
37. Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. 2011. Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 89(1):82-93.