publication . Article . 2014

Two-stage family-based designs for sequencing studies

Zhao Yang; Duncan C Thomas;
Open Access English
  • Published: 01 Jun 2014 Journal: BMC Proceedings, volume 8, issue Suppl 1, page S32 (issn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
Abstract
The cost of next-generation sequencing is now approaching that of the first generation of genome-wide single-nucleotide genotyping panels, but this is still out of reach for large-scale epidemiologic studies with tens of thousands of subjects. Furthermore, the anticipated yield of millions of rare variants poses serious challenges for distinguishing causal from noncausal variants for disease. We explore the merits of using family-based designs for sequencing substudies to identify novel variants and prioritize them for their likelihood of causality. While the sharing of variants within families means that family-based designs may be less efficient for discovery ...
Subjects
free text keywords: Proceedings, General Biochemistry, Genetics and Molecular Biology, General Medicine, Causality, Bioinformatics, First generation, Score test, Cosegregation, Genotyping, Medicine, business.industry, business, Systolic blood pressure measurement, Data sequences
Funded by
NIH| GENETICS OF GALLBLADDER DISEASE IN MEXICAN AMERICANS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01DK053889-04
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Methods for Pathway Modeling with Application to Folate
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01ES019876-02
  • Funding stream: NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
,
NIH| Identifying variants causal for Type 2 Diabetes in Major human populations
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085545-02
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Discovery of Functional Variants in Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085524-05
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Design and Analysis of 2 Stage GWAS Study Using Next Generation Sequence Technolo
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U01HG005927-01
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
29 references, page 1 of 2

Witte, JS, Gauderman, WJ, Thomas, DC. Asymptotic bias and efficiency in case-control studies of candidate genes and gene-environment interactions: basic family designs. Am J Epidemiol. 1999; 149: 693-705 [OpenAIRE] [PubMed] [DOI]

Ionita-Laza, I, Ottman, R. Study designs for identification of rare disease variants in complex diseases:the utility of family-based designs. Genetics. 2011; 189: 1061-1068 [OpenAIRE] [PubMed] [DOI]

Shi, G, Rao, DC. Optimum designs for next-generation sequencing to discover rare variants for common complex disease. Genet Epidemiol. 2011; 35: 572-579 [OpenAIRE] [PubMed]

Feng, T, Elston, RC, Zhu, X. Detecting rare and common variants for complex traits: sibpair and odds ratio weighted sum statistics (SPWSS, ORWSS). Genet Epidemiol. 2011; 35: 398-409 [OpenAIRE] [PubMed] [DOI]

Zhu, X, Feng, T, Li, Y, Lu, Q, Elston, RC. Detecting rare variants for complex traits using family and unrelated data. Genet Epidemiol. 2010; 34: 171-187 [OpenAIRE] [PubMed] [DOI]

Li, Y, Willer, C, Sanna, S, Abecasis, G. Genotype imputation. Annu Rev Genomics Hum Genet. 2009; 10: 387-406 [OpenAIRE] [PubMed] [DOI]

Murphy, A, Weiss, ST, Lange, C. Screening and replication using the same data set: testing strategies for family-based studies in which all probands are affected. PLoS Genet. 2008; 4: e1000197 [OpenAIRE] [PubMed] [DOI]

Van Steen, K, McQueen, MB, Herbert, A, Raby, B, Lyon, H, Demeo, DL, Murphy, A, Su, J, Datta, S, Rosenow, C. Genomic screening and replication using the same data set in family-based association testing. Nat Genet. 2005; 37: 683-691 [OpenAIRE] [PubMed] [DOI]

Feng, T, Zhang, S, Sha, Q. Two-stage association tests for genome-wide association studies based on family data with arbitrary family structure. Eur J Hum Genet. 2007; 15: 1169-1175 [OpenAIRE] [PubMed] [DOI]

Lange, C, DeMeo, D, Silverman, EK, Weiss, ST, Laird, NM. Using the noninformative families in family-based association tests: a powerful new testing strategy. Am J Hum Genet. 2003; 73: 801-811 [OpenAIRE] [PubMed] [DOI]

Wason, JM, Dudbridge, F. A general framework for two-stage analysis of genome-wide association studies and its application to case-control studies. Am J Hum Genet. 2012; 90: 760-773 [OpenAIRE] [PubMed] [DOI]

Yang, F, Thomas, DC. Two-stage design of sequencing studies for testing association with rare variants. Hum Hered. 2011; 71: 209-220 [OpenAIRE] [PubMed] [DOI]

Petersen, GM, Parmigiani, G, Thomas, D. Missense mutations in disease genes: a Bayesian approach to evaluate causality. Am J Hum Genet. 1998; 62: 1516-1524 [OpenAIRE] [PubMed] [DOI]

Ionita-Laza, I, Makarov, V, Yoon, S, Raby, B, Buxbaum, J, Nicolae, DL, Lin, X. Finding disease variants in mendelian disorders by using sequence data: methods and applications. Am J Hum Genet. 2011; 89: 701-712 [OpenAIRE] [PubMed] [DOI]

Schifano, ED, Epstein, MP, Bielak, LF, Jhun, MA, Kardia, SLR, Peyser, PA, Lin, X. SNP set association analysis for familial data. Genet Epidemiol. 2012; 36: 797-810 [OpenAIRE]

29 references, page 1 of 2
Abstract
The cost of next-generation sequencing is now approaching that of the first generation of genome-wide single-nucleotide genotyping panels, but this is still out of reach for large-scale epidemiologic studies with tens of thousands of subjects. Furthermore, the anticipated yield of millions of rare variants poses serious challenges for distinguishing causal from noncausal variants for disease. We explore the merits of using family-based designs for sequencing substudies to identify novel variants and prioritize them for their likelihood of causality. While the sharing of variants within families means that family-based designs may be less efficient for discovery ...
Subjects
free text keywords: Proceedings, General Biochemistry, Genetics and Molecular Biology, General Medicine, Causality, Bioinformatics, First generation, Score test, Cosegregation, Genotyping, Medicine, business.industry, business, Systolic blood pressure measurement, Data sequences
Funded by
NIH| GENETICS OF GALLBLADDER DISEASE IN MEXICAN AMERICANS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01DK053889-04
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Methods for Pathway Modeling with Application to Folate
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01ES019876-02
  • Funding stream: NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
,
NIH| Identifying variants causal for Type 2 Diabetes in Major human populations
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085545-02
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Discovery of Functional Variants in Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085524-05
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Design and Analysis of 2 Stage GWAS Study Using Next Generation Sequence Technolo
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U01HG005927-01
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
29 references, page 1 of 2

Witte, JS, Gauderman, WJ, Thomas, DC. Asymptotic bias and efficiency in case-control studies of candidate genes and gene-environment interactions: basic family designs. Am J Epidemiol. 1999; 149: 693-705 [OpenAIRE] [PubMed] [DOI]

Ionita-Laza, I, Ottman, R. Study designs for identification of rare disease variants in complex diseases:the utility of family-based designs. Genetics. 2011; 189: 1061-1068 [OpenAIRE] [PubMed] [DOI]

Shi, G, Rao, DC. Optimum designs for next-generation sequencing to discover rare variants for common complex disease. Genet Epidemiol. 2011; 35: 572-579 [OpenAIRE] [PubMed]

Feng, T, Elston, RC, Zhu, X. Detecting rare and common variants for complex traits: sibpair and odds ratio weighted sum statistics (SPWSS, ORWSS). Genet Epidemiol. 2011; 35: 398-409 [OpenAIRE] [PubMed] [DOI]

Zhu, X, Feng, T, Li, Y, Lu, Q, Elston, RC. Detecting rare variants for complex traits using family and unrelated data. Genet Epidemiol. 2010; 34: 171-187 [OpenAIRE] [PubMed] [DOI]

Li, Y, Willer, C, Sanna, S, Abecasis, G. Genotype imputation. Annu Rev Genomics Hum Genet. 2009; 10: 387-406 [OpenAIRE] [PubMed] [DOI]

Murphy, A, Weiss, ST, Lange, C. Screening and replication using the same data set: testing strategies for family-based studies in which all probands are affected. PLoS Genet. 2008; 4: e1000197 [OpenAIRE] [PubMed] [DOI]

Van Steen, K, McQueen, MB, Herbert, A, Raby, B, Lyon, H, Demeo, DL, Murphy, A, Su, J, Datta, S, Rosenow, C. Genomic screening and replication using the same data set in family-based association testing. Nat Genet. 2005; 37: 683-691 [OpenAIRE] [PubMed] [DOI]

Feng, T, Zhang, S, Sha, Q. Two-stage association tests for genome-wide association studies based on family data with arbitrary family structure. Eur J Hum Genet. 2007; 15: 1169-1175 [OpenAIRE] [PubMed] [DOI]

Lange, C, DeMeo, D, Silverman, EK, Weiss, ST, Laird, NM. Using the noninformative families in family-based association tests: a powerful new testing strategy. Am J Hum Genet. 2003; 73: 801-811 [OpenAIRE] [PubMed] [DOI]

Wason, JM, Dudbridge, F. A general framework for two-stage analysis of genome-wide association studies and its application to case-control studies. Am J Hum Genet. 2012; 90: 760-773 [OpenAIRE] [PubMed] [DOI]

Yang, F, Thomas, DC. Two-stage design of sequencing studies for testing association with rare variants. Hum Hered. 2011; 71: 209-220 [OpenAIRE] [PubMed] [DOI]

Petersen, GM, Parmigiani, G, Thomas, D. Missense mutations in disease genes: a Bayesian approach to evaluate causality. Am J Hum Genet. 1998; 62: 1516-1524 [OpenAIRE] [PubMed] [DOI]

Ionita-Laza, I, Makarov, V, Yoon, S, Raby, B, Buxbaum, J, Nicolae, DL, Lin, X. Finding disease variants in mendelian disorders by using sequence data: methods and applications. Am J Hum Genet. 2011; 89: 701-712 [OpenAIRE] [PubMed] [DOI]

Schifano, ED, Epstein, MP, Bielak, LF, Jhun, MA, Kardia, SLR, Peyser, PA, Lin, X. SNP set association analysis for familial data. Genet Epidemiol. 2012; 36: 797-810 [OpenAIRE]

29 references, page 1 of 2
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