Increased efficiency of case-control association analysis by using allele-sharing and covariate information

Human Heredity

Volumn 65, Issue 3, 2007, Pages 154-165

  Schmidt, Silke ^a   Schmidt, Michael A ^a   Qin, Xuejun ^a   Martin, Eden R ^a   Hauser, Elizabeth R ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Gene environment interaction; Genetic heterogeneity; Linkage analysis; Ordered subset analysis; Quantitative trait locus; SIMLA; Study design

Indexed keywords

ARTICLE; CASE CONTROL STUDY; COVARIANCE; DISEASE ASSOCIATION; ENVIRONMENTAL FACTOR; FAMILY; GENE INTERACTION; GENETIC HETEROGENEITY; GENETIC LINKAGE; GENETIC MARKER; GENETIC MODEL; GENOME ANALYSIS; GENOTYPE; LINKAGE ANALYSIS; QUANTITATIVE TRAIT LOCUS; RISK FACTOR; SIMULATION;

ANALYSIS OF VARIANCE; CASE-CONTROL STUDIES; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; LINKAGE (GENETICS); MODELS, GENETIC; MODELS, STATISTICAL; QUANTITATIVE TRAIT LOCI; SIBLINGS;

EID: 37149035176     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000109732     Document Type: Article

References (23)

1. Li M, Boehnke M, Abecasis GR: Efficient study designs for test of genetic association using sibship data and unrelated cases and controls. Am J Hum Genet 2006;78:778-792.
2. Risch N, Teng J: The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases: DNA pooling. Genome Res 1998;8:1273-1288.
3. Teng J, Risch N: The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases. II. Individual genotyping. Genome Res 1999;9:234-241.
4. Epstein MP, Veal CD, Trembath RC, Barker JN, Li C, Satten GA: Genetic association analysis using data from triads and unrelated subjects. Am J Hum Genet 2005;76:592-608.
5. Weinberg CR, Umbach DM: A hybrid design for studying genetic influences on risk of diseases with onset early in life. Am J Hum Genet 2005;77:627-636.
6. Laird NM, Lange C: Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 2006;7:385-394.
7. Schmidt MA, Hauser ER, Martin ER, Schmidt S: Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: Environmental covariates, gene-gene and gene-environment interaction. Stat Appl Genet Mol Biol 2005;4:Article 15 [Epub].
8. Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002;30:97-101.
9. Kong A, Cox NJ: Allele-sharing models: LOD scores and accurate linkage tests. Am J Hum Genet 1997;61:1179-1188.
10. Hauser ER, Watanabe RM, Duren WL, Bass MP, Langefeld CD, Boehnke M: Ordered subset analysis in genetic linkage mapping of complex traits. Genet Epidemiol 2004;27:53-63.
11. Fingerlin TE, Boehnke M, Abecasis GR: Increasing the power and efficiency of disease-marker case-control association studies through use of allele-sharing information. Am J Hum Genet 2004;74:432-443.
12. Schaid DJ: General score tests for associations of genetic markers with disease using cases and their parents. Genet Epidemiol 1996;13:423-449.
13. Sturmer T, Gefeller O, Brenner H: A computer program to estimate power and relative efficiency to assess multiplicative interactions in flexibly matched case-control studies. Comput Methods Programs Biomed 2004;74:261-265.
14. Saunders CL, Barrett JH: Flexible matching in case-control studies of gene-environment interactions. Am J Epidemiol 2004;159:17-22.
15. Chung RH, Hauser ER, Martin ER: Interpretation of simultaneous linkage and family-based association tests in genome screens. Genet Epidemiol 2007;31:134-142.
16. Schmidt S, Schmidt MA, Qin X, Martin ER, Hauser ER: Linkage analysis with gene-environment interaction: model illustration and performance of ordered subset analysis. Genet Epidemiol 2006;30:409-422.
17. Schmidt S, Qin X, Schmidt M, Martin ER, Hauser ER: Interpreting analyses of continuous covariates in affected sibling pair linkage studies. Genet Epidemiol 2007;April 4 [Epub ahead of print].
18. Qin X, Schmidt S, Schmidt M, Martin E, Hauser E: A visualization tool for genetic parameters in complex human traits. International Genetic Epidemiology Society, November 16-17, 2006, Tampa, FL.
19. Schmidt S, Hauser MA, Scott WK, Postel EA, Agarwal A, Gallins P, Wong F, Chen YS, Spencer K, Schnetz-Boutaud N, Haines JL, Pericak-Vance MA: Cigarette smoking strongly modifies the association of LOC387715 and age-related macular degeneration. Am J Hum Genet 2006;78:852-864.
20. Kotowski IK, Pertsemlidis A, Luke A, Cooper RS, Vega GL, Cohen JC, Hobbs HH: A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol. Am J Hum Genet 2006;78:410-422.
21. Cohen JC, Boerwinkle E, Mosley TH Jr, Hobbs HH: Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N Engl J Med 2006;354:1264-1272.
22. Romeo S, Pennacchio LA, Fu Y, Boerwinkle E, Tybjaerg-Hansen A, Hobbs HH, Cohen JC: Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet 2007.
23. Lou X, Schmidt S, Hauser ER: Evaluation of GIST and LAMP in the GAW15 simulated data. BMC Genetics, in press.