publication . Article . 2014

Combining information from linkage and association mapping for next-generation sequencing longitudinal family data

Balliu, Brunilda; Uh, Hae-Won; Tsonaka, Roula; Boehringer, Stefan; Helmer, Quinta; Houwing-Duistermaat, Jeanine J;
Open Access
  • Published: 01 Jun 2014 Journal: BMC Proceedings, volume 8 (eissn: 1753-6561, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
In this analysis, we investigate the contributions that linkage-based methods, such as identical-by-descent mapping, can make to association mapping to identify rare variants in next-generation sequencing data. First, we identify regions in which cases share more segments identical-by-descent around a putative causal variant than do controls. Second, we use a two-stage mixed-effect model approach to summarize the single-nucleotide polymorphism data within each region and include them as covariates in the model for the phenotype. We assess the impact of linkage disequilibrium in determining identical-by-descent states between individuals by using markers with and...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Chromosome 3, Bioinformatics, Association mapping, Linkage disequilibrium, DNA sequencing, Genetic association, Polymorphism (computer science), Medicine, business.industry, business, Nested association mapping, Imputation (statistics), Proceedings
Funded by
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| NIDDM Susceptibility Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01DK047482-13
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Identifying T2D Variants by DNA Sequencing in Multiethnic Samples
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U01DK085584-01
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Identification and Replication of Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085501-02
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Multiethnic Study of Type 2 Diabetes Genes
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085526-05
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES

Cantor, RM, Lange, K, Sinsheimer, JM. Prioritizing GWAS results: a review of statistical methods and recommendations for their application. Am J Hum Genet. 2010; 86: 6-33 [OpenAIRE] [PubMed] [DOI]

Browning, SR, Thompson, EA. Detecting rare variant associations by identity-by-descent mapping in case-control studies. Genetics. 2012; 190: 1521-1531 [OpenAIRE] [PubMed] [DOI]

Browning, BL, Browning, SR. A fast, powerful method for detecting identity by descent. Am J Hum Genet. 2011; 88: 173-182 [OpenAIRE] [PubMed] [DOI]

Tsonaka, R, van der Helm-van, Mil AHM, Houwing-Duistermaat, JJ. A two-stage mixed-effects model approach for gene-set analyses in candidate gene studies. Stat Med. 2011; 31: 1190-1202 [OpenAIRE] [PubMed]

Brown, MD, Glazner, CG, Zheng, C, Thompson, EA. Inferring coancestry in population samples in the presence of linkage disequilibrium. Genetics. 2012; 190: 1447-1460 [OpenAIRE] [PubMed] [DOI]

Thompson, EA. The IBD process along four chromosomes. Theor Popul Biol. 2008; 73: 369-373 [OpenAIRE] [PubMed] [DOI]

The IBD_Haplo software is part of MORGAN 3.1.

Chen, LS, Hutter, CM, Potter, JD, Liu, Y, Prentice, RL, Peters, U, Hsu, L. Insights into colon cancer etiology via regularized approach to gene set analysis of GWAS data. Am J Hum Genet. 2010; 86: 860-871 [OpenAIRE] [PubMed] [DOI]

Houwing-Duistermaat, JJ, Helmer, Q, Balliu, B, van de Akker, E, Tsonaka, R, Uh, HW. Gene analysis for longitudinal family data using nested random effects models. BMC Proc. 2014; 8 (suppl 2): S88 [OpenAIRE]

Soler, JMP, Blangero, J. Longitudinal familial analysis of blood pressure involving parametric (co)variance functions. BMC Genet. 2003; 4 (Suppl 1): S87 [OpenAIRE] [PubMed] [DOI]

The National Center for Biotechnology Information.

Speliotes, EK, Willer, CJ, Berndt, SI, Monda, KL, Thorleifsson, G, Jackson, AU, Lango Allen, H, Lindgren, CM, Luan, J, Mägi, R. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet. 2010; 42: 937-948 [OpenAIRE] [PubMed] [DOI]

Powered by OpenAIRE Research Graph
Any information missing or wrong?Report an Issue