Detecting rare and common variants for complex traits: Sibpair and odds ratio weighted sum statistics (SPWSS, ORWSS)

Genetic Epidemiology

Volumn 35, Issue 5, 2011, Pages 398-409

  Feng, Tao ^a   Elston, Robert C ^a   Zhu, Xiaofeng ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Affected sibpairs; Association; Rare variants

Indexed keywords

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; FRAMINGHAM RISK SCORE; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HYPERTENSION; INSULIN DEPENDENT DIABETES MELLITUS; ODDS RATIO WEIGHTED SUM STATISTICS; SIBPAIR WEIGHTED SUM STATISTIC; STATISTICAL PARAMETERS;

ANGIOTENSINOGEN; CASE-CONTROL STUDIES; DATABASES, GENETIC; DEAD-BOX RNA HELICASES; DIABETES MELLITUS, TYPE 1; FEMALE; GENE FREQUENCY; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; HYPERTENSION; MALE; MODELS, GENETIC; MODELS, STATISTICAL; ODDS RATIO; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; SIBLINGS;

EID: 79958077854     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20588     Document Type: Article

References (38)

1. Welcome Trust Case Control Consortium. 2007. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 447:661-678.
2. Agresti A. 2002. Categorical Data Analysis. New York: Wiley-Interscience.
3. Bansal V, Libiger O, Torkamani A, Schork NJ. 2010. Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet 11:773-785.
4. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
5. Browning SR, Browning BL. 2007. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097.
6. Cohen J, Pertsemlidis A, Kotowski IK, Graham R, Garcia CK, Hobbs HH. 2005. Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat Genet 37:161-165.
7. Cohen JC, Pertsemlidis A, Fahmi S, Esmail S, Vega GL, Grundy SM, Hobbs HH. 2006. Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels. Proc Natl Acad Sci USA 103:1810-1815.
8. Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
9. Feng T, Zhu X. 2010. Genome-wide searching of rare genetic variants in WTCCC data. Hum Genet 128:269-280.
10. Forrester T, McFarlane-Anderson N, Bennet F, Wilks R, Puras A, Cooper R, Rotimi C, Durazo R, Tewksbury D, Morrison L. 1996. Angiotensinogen and blood pressure among blacks: findings from a community survey in Jamaica. J Hypertens 14:315-321.
11. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, and others. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861.
12. Gibson G. 2010. Hints of hidden heritability in GWAS. Nat Genet 42:558-560.
13. Guo W, Lin S. 2008. Generalized linear modeling with regularization for detecting common disease rare haplotype association. Genet Epidemiol 33:308-316.
14. Han F, Pan W. 2010. A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered 70:42-54.
15. Haseman JK, Elston RC. 1972. The investigation of linkage between a quantitative trait and a marker locus. Behav Genet 2:3-19.
16. Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, Steinthorsdottir V, Thorleifsson G, Zillikens MC, Speliotes EK, Magi R, Workalemahu T, White C, Bouatia-Naji N, Harris T, Berndt S, Ingelsson E, Willer C, Weedon M, Luan J, Vedantam S, Esko T, Kilpeläinen T, Kutalik Z, Li S, Monda K. 2010. Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet 42:949-960.
17. Hoffmann TJ, Marini NJ, Witte JS. 2010. Comprehensive approach to analyzing rare genetic variants. PLoS One 5:e13584.
18. Inoue I, Nakajima T, Williams CS, Quackenbush J, Puryear R, Powers M, Cheng T, Ludwig EH, Sharma AM, Hata A, Jeunemaitre X, Lalouel JM. 1997. A nucleotide substitution in the promoter of human angiotensinogen is associated with essential hypertension and affects basal transcription in vitro. J Clin Invest 99:1786-1797.
19. Jeunemaitre X, Soubrier F, Kotelevtsev YV, Lifton RP, Williams CS, Charru A, Hunt SC, Hopkins PN, Williams RR, Lalouel JM, and others. 1992. Molecular basis of human hypertension: role of angiotensinogen. Cell 71:169-180.
20. 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.
21. Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, Rivadeneira F, Willer CJ, Jackson AU, Vedantam S, Raychaudhuri S, and others. 2010. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467:832-838.
22. Levy D, Ehret GB, Rice K, Verwoert GC, Launer LJ, Dehghan A, Glazer NL, Morrison AC, Johnson AD, Aspelund T, and others. 2009. Genome-wide association study of blood pressure and hypertension. Nat Genet 41:677-687.
23. 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.
24. Li Y, Byrnes AE, Li M. 2010. To identify associations with rare variants, just WHaIT: weighted haplotype and imputation-based tests. Am J Hum Genet 87:728-735.
25. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5:e1000384.
26. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotmi C, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eicheler EE, Gibson G, Haines JL, Mackay T, McCarroll SA, Visscher PM. 2009. Finding the missing heritability of complex diseases. Nature 461:747-753.
27. Momozawa Y, Mni M, Nakamura K, Coppieters W, Almer S, Amininejad L, Cleynen I, Colombel JF, de Rijk P, Dewit O, Finkel Y, Gaassull MA, Goossens D, Laukens D, Lemann M, Libioulle C, O'Morain C, Reenaers C, Rutgeerts P, Tsysk C, Zelenika D, Lathrop M, Del-Favero J, Hugot JP, de Vos M, Franchimont D, Vermeire S, Louis E, Georges M. 2011. Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease. Nat Genet 43:43-47.
28. 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 615:28-56.
29. Morris AP, Zeggini E. 2010. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34:188-193.
30. 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.
31. Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. 2010. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86:832-838.
32. Pritchard JK. 2001. Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 69:124-137.
33. Rotimi C, Morrison L, Cooper R, Oyejide C, Effiong E, Ladipo M, Osotemihen B, Ward R. 1994. Angiotensinogen gene in human hypertension. Lack of an association of the 235T allele among African Americans. Hypertension 24:591-594.
34. Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, Lin X. 2010. Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet 86:929-942.
35. Zawistowski M, Gopalakrishnan S, Ding J, Li Y, Grimm S, Zollner S. 2010. Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. Am J Hum Genet 87:604-617.
36. Zhu X, Chang YP, Yan D, Weder A, Cooper R, Luke A, Kan D, Chakravarti A. 2003. Associations between hypertension and genes in the renin-angiotensin system. Hypertension 41:1027-1034.
37. Zhu X, Fejerman L, Luke A, Adeyemo A, Cooper RS. 2005. Haplotypes produced from rare variants in the promoter and coding regions of angiotensinogen contribute to variation in angiotensinogen levels. Hum Mol Genet 14:639-643.
38. Zhu X, Feng T, Li Y, Lu Q, Elston RC. 2010. Detecting rare variants for complex traits using family and unrelated data. Genet Epidemiol 34:171-187.