Using extreme phenotype sampling to identify the rare causal variants of quantitative traits in association studies

Genetic Epidemiology

Volumn 35, Issue 8, 2011, Pages 790-799

  Li, Dalin ^a   Lewinger, Juan Pablo ^b   Gauderman, William J ^b   Murcray, Cassandra Elizabeth ^b   Conti, David ^b  

^a CEDARS SINAI MEDICAL CENTER   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Extreme phenotype sampling; Next generation sequencing; Rare variants

Indexed keywords

ARTICLE; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; EXTREME PHENOTYPE SAMPLING; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC VARIABILITY; HUMAN; PHENOTYPE; QUANTITATIVE TRAIT; SAMPLING; STATISTICAL MODEL;

COST-BENEFIT ANALYSIS; GENE FREQUENCY; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE;

EID: 82355169007     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20628     Document Type: Article

References (40)

1. Asimit J, Zeggini E. 2010. Rare variant association analysis methods for complex traits. Annu Rev Genet 44:293-308.
2. Bansal V, Libiger O, Torkamani A, Schork NJ. 2010. Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet 11:773-785.
3. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2008. GenBank. Nucleic Acids Res 36:D25-30.
4. Chen Z, Zheng G, Ghosh K, Li Z. 2005. Linkage disequilibrium mapping of quantitative-trait loci by selective genotyping. Am J Hum Genet 77:661-669.
5. Chobanian AV, Bakris GI, Black HR, Cushman WC, Green LA, Izzo Jr JL, Jones DW, Materson BJ, Oparil S, Wright JT, Rocella EJ, Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure; National Heart, Lung, and Blood Institute; National High Blood Pressure Education Program Coordinating Committee. 2003. Seventh report of the joint national committee on prevention, detection, evaluation, and treatment of high blood pressure. Hypertension 42:1206-1252.
6. Cirulli ET, Goldstein DB. 2010. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11:415-425.
7. Expert Committee on the Diagnosis and Classification of Diabetes Mellitus. 2003. Report of the expert committee on the diagnosis and classification of diabetes mellitus. Diabetes Care 26:S5-S20.
8. Frazer KA, Murray SS, Schork NJ, Topol EJ. 2009. Human genetic variation and its contribution to complex traits. Nat Rev Genet 10:241-251.
9. Gauderman WJ, Morrison JM. 2006. QUANTO 1.1: a computer program for power and sample size calculations for genetic-epidemiology studies. .
10. Gu C, Todorov AA, Rao DC. 1997. Genome screening using extremely discordant and extremely concordant sib pairs. Genet Epidemiol 14:791-796.
11. Hindorff LA, Junkins HA, Hall PN, Mehta JP, Manolio TA. 2010. A catalog of published genome-wide association studies. Accessed December.
12. Huang BE, Lin DY. 2007. Efficient association mapping of quantitative trait loci with selective genotyping. Am J Hum Genet 80:567-576.
13. Ioannidis JP, Thomas G, Daly MJ. 2009. Validating, augmenting and refining genome-wide association signals. Nat Rev Genet 10:318-329.
14. 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 40:592-599.
15. Johnson NL, Kotz S. 1970. Continuous Univariate Distributions-1. San Francisco: Wiley.
16. Kiefer J. 1953. Sequential minimax search for a maximum. Proc Am Math Soc 4:502-506.
17. Li D, Conti DV. 2009. Enriching the gold dust: EPS in the post GWAS era. 18th IGES Annual Meeting, Hawaii (Abstract).
18. 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 83:311-321.
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 66:1631-1641.
20. Lin Y, Li P, Cai L, Zhang B, Tang X, Zhang X, Li Y, Xian Y, Yang Y, Wang L, Lu F, Liu X, Rao S, Chen M, Ma S, Shi Y, Bao M, Wu J, Yang Y, Yang J, Yang Z. 2010. Association study of genetic variants in eight genes/loci with type 2 diabetes in a Han Chinese population. BMC Med Genet 11:97-102.
21. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5:e1000384.
22. Maher B. 2008. Personal genomes: the case of the missing heritability. Nature 456:18-21.
23. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN. 2008. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9:356-369.
24. 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 324:387-389.
25. 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:e1000160.
26. Niu WQ, Guo SJ, Zhang Y, Gao PJ, Zhu DL. 2010. Genetic and functional analyses of aldosterone synthase gene C-344T polymorphism with essential hypertension. Genetic and functional analyses of aldosterone synthase gene C-344T polymorphism with essential hypertension. J Hum Hypertens 24:427-429.
27. Ollier W, Sprosen T, Peakman T. 2005. UK Biobank: from concept to reality. Pharmacogenomics 6:639-646.
28. Ramser J, Ahearn ME, Lenski C, Yariz KO, Hellebrand H, von Rhein M, Clark RD, Schmutzler RK, Lichtner P, Hoffman EP, Meindl A, Baumbach-Reardon L. 2008. Rare missense and synonymous variants in UBE1 are associated with X-linked infantile spinal muscular atrophy. Am J Hum Genet 82:188-193.
29. Reich DE, Lander ES. 2001. On the allelic spectrum of human disease. Trends Genet 17:502-510.
30. Risch N, Zhang H. 1995. Extreme discordant sib pairs for mapping quantitative trait loci in humans. Science 268:1584-1589.
31. Salam MT Li YF, Langholz B, Gilliland FD. 2004. Children's Health Study. Early-life environmental risk factors for asthma: findings from the Children's Health Study. Environ Health Perspect 112:760-765.
32. Schleinitz D, Carmienke S, Böttcher Y, Tönjes A, Berndt J, Klöting N, Enigk B, Müller I, Dietrich K, Breitfeld J, Scholz GH, Engeli S, Stumvoll M, Blüher M, Kovacs P. 2010. Role of genetic variation in the cannabinoid type 1 receptor gene (CNR1) in the pathophysiology of human obesity. Pharmacogenomics 11:693-702.
33. Skol AD, Scott LJ, Abecasis GR, Boehnke M. 2006. Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 38: 209-213.
34. Slatkin M. 1999. Disequilibrium mapping of a quantitative-trait locus in an expanding population. Am J Hum Genet 64:1765-1773.
35. Song R, Zhou H, Kosorok MR. 2009. On semiparametric efficient inference for two-stage outcome-dependent sampling with a continuous outcome. Biometrika 96:221-228.
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 78:498-504.
37. Xing C, Xing G. 2009. Power of selective genotyping in genome-wide association studies of quantitative traits. BMC Proc 3:S23.
38. Yamada Y, Matsuo H, Segawa T, Watanabe S, Kato K, Hibino T, Yokoi K, Ichihara S, Metoki N, Yoshida H, Satoh K, Nozawa Y. 2006. Assessment of the genetic component of hypertension. Am J Hypertens 19:1158-1165.
39. Zawistowski M, Gopalakrishnan S, Ding J, Li Y, Grimm S, Zöllner S. 2010. Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. Am J Hum Genet 87:604-617.
40. Zhou H, Song R, Wu Y, Qin J. 2011. Statistical inference for a two-stage outcome-dependent sampling design with a continuous outcome. Biometrics 67:194-202.