publication . Article . 2012

Genetic Association Analysis Using Sibship Data: A Multilevel Model Approach

Yang Zhao; Hao Yu; Ying Zhu; Monica Ter-Minassian; Zhihang Peng; Hongbing Shen; Nancy Diao; Feng Chen;
Open Access
  • Published: 01 Feb 2012 Journal: PLoS ONE, volume 7, page e31134 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
  • Country: United States
Abstract
Family based association study (FBAS) has the advantages of controlling for population stratification and testing for linkage and association simultaneously. We propose a retrospective multilevel model (rMLM) approach to analyze sibship data by using genotypic information as the dependent variable. Simulated data sets were generated using the simulation of linkage and association (SIMLA) program. We compared rMLM to sib transmission/disequilibrium test (S-TDT), sibling disequilibrium test (SDT), conditional logistic regression (CLR) and generalized estimation equations (GEE) on the measures of power, type I error, estimation bias and standard error. The results ...
Subjects
free text keywords: public health, genomics, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Population stratification, Statistics, Genome-wide association study, Linkage disequilibrium, Standard error, Sample size determination, Multilevel model, Type I and type II errors, Genetics, Odds ratio, Mathematics, Research Article, Biology, Human Genetics, Computer Science, Computerized Simulations, Medicine, Clinical Research Design, Epidemiology, R, Science, Q
31 references, page 1 of 3

Laird, NM, Lange, C. Family-based designs in the age of large-scale gene-association studies.. Nat Rev Genet. 2006; 7: 385-394 [PubMed]

McGinnis, R, Shifman, S, Darvasi, A. Power and efficiency of the TDT and case-control design for association scans.. Behav Genet. 2002; 32: 135-144 [PubMed]

Benyamin, B, Visscher, PM, McRae, AF. Family-based genome-wide association studies.. Pharmacogenomics. 2009; 10: 181-190 [PubMed]

Cirulli, ET, Goldstein, DB. Uncovering the roles of rare variants in common disease through whole-genome sequencing.. Nat Rev Genet. 2010; 11: 415-425 [OpenAIRE] [PubMed]

Spielman, RS, Ewens, WJ. The TDT and other family-based tests for linkage disequilibrium and association.. Am J Hum Genet. 1996; 59: 983-989 [OpenAIRE] [PubMed]

Spielman, RS, Ewens, WJ. A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test.. Am J Hum Genet. 1998; 62: 450-458 [OpenAIRE] [PubMed]

Horvath, S, Laird, NM. A discordant-sibship test for disequilibrium and linkage: no need for parental data.. Am J Hum Genet. 1998; 63: 1886-1897 [OpenAIRE] [PubMed]

Siegmund, KD, Langholz, B, Kraft, P, Thomas, DC. Testing linkage disequilibrium in sibships.. Am J Hum Genet. 2000; 67: 244-248 [OpenAIRE] [PubMed]

Hancock, DB, Martin, ER, Li, YJ, Scott, WK. Methods for interaction analyses using family-based case-control data: conditional logistic regression versus generalized estimating equations.. Genet Epidemiol. 2007; 31: 883-893 [PubMed]

Goldstein, H. 2010

Goldstein, H. Multilevel mixed linear model analysis using iterative generalized least squares.. Biometrika. 1986: 43-56

Goldstein, H, Browne, W, Rasbash, J. Multilevel modelling of medical data.. Stat Med. 2002; 21: 3291-3315 [PubMed]

Rasbash, JR, Charlton, C, Browne, WJ, Healy, M, Cameron, B. MLwiN.. 2009 [OpenAIRE]

Hu, FB, Goldberg, J, Hedeker, D, Flay, BR, Pentz, MA. Comparison of population-averaged and subject-specific approaches for analyzing repeated binary outcomes.. Am J Epidemiol. 1998; 147: 694-703 [OpenAIRE] [PubMed]

Hanley, JA, Negassa, A, Edwardes, MD, Forrester, JE. Statistical analysis of correlated data using generalized estimating equations: an orientation.. Am J Epidemiol. 2003; 157: 364-375 [PubMed]

31 references, page 1 of 3
Related research
Abstract
Family based association study (FBAS) has the advantages of controlling for population stratification and testing for linkage and association simultaneously. We propose a retrospective multilevel model (rMLM) approach to analyze sibship data by using genotypic information as the dependent variable. Simulated data sets were generated using the simulation of linkage and association (SIMLA) program. We compared rMLM to sib transmission/disequilibrium test (S-TDT), sibling disequilibrium test (SDT), conditional logistic regression (CLR) and generalized estimation equations (GEE) on the measures of power, type I error, estimation bias and standard error. The results ...
Subjects
free text keywords: public health, genomics, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Population stratification, Statistics, Genome-wide association study, Linkage disequilibrium, Standard error, Sample size determination, Multilevel model, Type I and type II errors, Genetics, Odds ratio, Mathematics, Research Article, Biology, Human Genetics, Computer Science, Computerized Simulations, Medicine, Clinical Research Design, Epidemiology, R, Science, Q
31 references, page 1 of 3

Laird, NM, Lange, C. Family-based designs in the age of large-scale gene-association studies.. Nat Rev Genet. 2006; 7: 385-394 [PubMed]

McGinnis, R, Shifman, S, Darvasi, A. Power and efficiency of the TDT and case-control design for association scans.. Behav Genet. 2002; 32: 135-144 [PubMed]

Benyamin, B, Visscher, PM, McRae, AF. Family-based genome-wide association studies.. Pharmacogenomics. 2009; 10: 181-190 [PubMed]

Cirulli, ET, Goldstein, DB. Uncovering the roles of rare variants in common disease through whole-genome sequencing.. Nat Rev Genet. 2010; 11: 415-425 [OpenAIRE] [PubMed]

Spielman, RS, Ewens, WJ. The TDT and other family-based tests for linkage disequilibrium and association.. Am J Hum Genet. 1996; 59: 983-989 [OpenAIRE] [PubMed]

Spielman, RS, Ewens, WJ. A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test.. Am J Hum Genet. 1998; 62: 450-458 [OpenAIRE] [PubMed]

Horvath, S, Laird, NM. A discordant-sibship test for disequilibrium and linkage: no need for parental data.. Am J Hum Genet. 1998; 63: 1886-1897 [OpenAIRE] [PubMed]

Siegmund, KD, Langholz, B, Kraft, P, Thomas, DC. Testing linkage disequilibrium in sibships.. Am J Hum Genet. 2000; 67: 244-248 [OpenAIRE] [PubMed]

Hancock, DB, Martin, ER, Li, YJ, Scott, WK. Methods for interaction analyses using family-based case-control data: conditional logistic regression versus generalized estimating equations.. Genet Epidemiol. 2007; 31: 883-893 [PubMed]

Goldstein, H. 2010

Goldstein, H. Multilevel mixed linear model analysis using iterative generalized least squares.. Biometrika. 1986: 43-56

Goldstein, H, Browne, W, Rasbash, J. Multilevel modelling of medical data.. Stat Med. 2002; 21: 3291-3315 [PubMed]

Rasbash, JR, Charlton, C, Browne, WJ, Healy, M, Cameron, B. MLwiN.. 2009 [OpenAIRE]

Hu, FB, Goldberg, J, Hedeker, D, Flay, BR, Pentz, MA. Comparison of population-averaged and subject-specific approaches for analyzing repeated binary outcomes.. Am J Epidemiol. 1998; 147: 694-703 [OpenAIRE] [PubMed]

Hanley, JA, Negassa, A, Edwardes, MD, Forrester, JE. Statistical analysis of correlated data using generalized estimating equations: an orientation.. Am J Epidemiol. 2003; 157: 364-375 [PubMed]

31 references, page 1 of 3
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