A data-driven weighting scheme for family-based genome-wide association studies

European Journal of Human Genetics

Volumn 18, Issue 5, 2010, Pages 596-603

  Qin, Huaizhen ^a   Feng, Tao ^a,b   Zhang, Shuanglin ^a,b   Sha, Qiuying ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^b HEILONGJIANG UNIVERSITY   (China)

Author keywords

Data driven weighting; Linkage disequilibrium; Population stratification; Two stage

Indexed keywords

ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; FAMILY ASSESSMENT; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; HUMAN; PHENOTYPE; PRIORITY JOURNAL; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

DATABASES, GENETIC; FAMILY; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, STATISTICAL; PARENTS; PHENOTYPE;

EID: 77951619989     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2009.201     Document Type: Article

References (19)

1. Steen KV, McQueen MB, Herbert A et al: Genomic screening and replication using the same dataset in family-based association testing. Nat Genet 2005; 37: 683-691.
2. Ionita-Laza I, McQueen MB, Laird NM, Lange C: Genome-wide weighted hypothesis testing in family-based association studies, with an application to a 100k scan. Am J Hum Genet 2007; 81: 607-614.
3. Herbert A, Gerry NP, McQueen MB et al: A common genetic variant is associated with adult and childhood obesity. Science 2006; 312: 279-283.
4. Spielman RS, McGinnis RE, Ewens WJ: Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 1993; 52: 506-516.
5. Claton D, Jones H: Transmission/Disequilibrium test for extended marker haplotype. Am J Hum Genet 1999; 65: 1161-1169.
6. Schaid DJ, Rowland CM: Quantitative trait transmission disequilibrium test: allowance for missing parents. Genetic Epidemiol 1999; 17: S307-S312.
7. Zhao H, Zhang S, Merikangas KR et al: Transmission/disequilibrium test using multiple tightly linked markers. Am J Hum Genet 2000; 67: 936-946.
8. Selman H, Roeder K, Devlin B: Transmission/disequilibrium test meets measured haplotype analysis: family-based association guided by evolution of haplotype. Am J Hum Genet 2001; 68: 1250-1263.
9. Feng T, Zhang S, Sha Q: Two-stage association tests for genome-wide association studies based on family data with arbitrary family structure. Eu J Hum Genet 2007; 15: 169-1175.
10. Rubin D, van der Laan M, Dudoit S: Multiple testing approaches which are optimal at a simple alternative. Collection of Biostatistics Research Archive 2006, http://www.bepress.com/ucbbiostat/paper 171.
11. Roeder K, Devlin B, Wasserman L: Improving power in genome-wide association studies: weights tip the scale. Genet Epidemiol 2007; 31: 741-747.
12. Zhang S, Zhang K, Li J, Sun FZ, Zhao H: Test of linkage and association for quantitative traits in general pedigree: the quantitative pedigree disequilibrium test. Genetic Epi 2001; 18 (Suppl 1): 370-375.
13. Morley M, Molony CM, Weber T et al: Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430: 743-747.
14. Hudson RR: Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformations 2002; 18: 337-338.
15. Nordborg M, Tavare S: Linkage disequilibrium: what history has to tell us? Trends Genet 2002; 18: 83-90.
16. Kimmel G, Shamir R: A fast method for computing high significance disease association in large population-based studies. Am J Hum Genet 2006; 79: 481-492.
17. Balding DJ, Nichols RA: A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 1995; 96: 3-12.
18. Chung RH, Hauser ER, Martin ER: Interpretation of simultaneous linkage and family-based association tests in genome screens. Genet Epidemiol 2007; 31: 134-142.
19. Lasky-Su J, Lyon HN, Emilsson V et al.: On the replication of genetic associations: timing can be everything!. Am J Hum genet 2008; 82: 849-858.