publication . Article . Conference object . 2014

A 2-step penalized regression method for family-based next-generation sequencing association studies

David Fardo;
Open Access English
  • Published: 01 Jun 2014 Journal: BMC Proceedings, volume 8, issue Suppl 1, pages S25-S25 (eissn: 1753-6561, Copyright policy)
  • Publisher: BioMed Central
Abstract
Large-scale genetic studies are often composed of related participants, and utilizing familial relationships can be cumbersome and computationally challenging. We present an approach to efficiently handle sequencing data from complex pedigrees that incorporates information from rare variants as well as common variants. Our method employs a 2-step procedure that sequentially regresses out correlation from familial relatedness and then uses the resulting phenotypic residuals in a penalized regression framework to test for associations with variants within genetic units. The operating characteristics of this approach are detailed using simulation data based on a la...
Subjects
free text keywords: Proceedings, General Biochemistry, Genetics and Molecular Biology, General Medicine, Group lasso, Genetic association, Data mining, computer.software_genre, computer, Text mining, business.industry, business, Regression, Correlation, DNA sequencing, Pedigree chart, Medicine
Funded by
NIH| KY IDeA Networks of Biomedical Research Excellence
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 8P20GM103436-12
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
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| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
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
,
NIH| Statistical Genetics Methods for Mixed Pathologies
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5K25AG043546-02
  • Funding stream: NATIONAL INSTITUTE ON AGING

Zhu, Y, Xiong, M. Family-based association studies for next-generation sequencing. Am J Hum Genet. 2012; 90: 1028-1045 [OpenAIRE] [PubMed] [DOI]

Aulchenko, YS, De Koning, D-J, Haley, C. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics. 2007; 177: 577-585 [OpenAIRE] [PubMed] [DOI]

Sinnwell, JP, Therneau, TM, Atkinson, EJ, Schaid, DJ, Matsumoto, ME, McDonnell, SK. Kinship2: an enhancement to the kinship R package with additional pedigree utilities. 2011

Aulchenko, YS, Ripke, S, Isaacs, A, Van Duijn, CM. GenABEL: an R library for genome-wide association analysis. Bioinformatics. 2007; 23: 1294-1296 [OpenAIRE] [PubMed] [DOI]

Wu, TT, Lange, K. Coordinate descent algorithms for lasso penalized regression. Ann Appl Stat. 2008; 2: 224-244 [OpenAIRE] [DOI]

Wu, TT, Chen, YF, Hastie, T, Sobel, E, Lange, K. Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics. 2009; 25: 714-721 [OpenAIRE] [PubMed] [DOI]

Friedman, J, Hastie, T, Tibshirani, R. A note on the group lasso and a sparse group lasso. 2010: 8

Zhou, H, Sehl, ME, Sinsheimer, JS, Lange, K. Association screening of common and rare genetic variants by penalized regression. Bioinformatics. 2010; 26: 2375-2382 [OpenAIRE] [PubMed] [DOI]

Lange, K, Cantor, R, Horvath, S, Perola, M, Sabatti, C, Sinsheimer, JSE. MENDEL version 4.0: a complete package for the exact genetic analysis of discrete traits in pedigree and population data sets. Am J Hum Genet. 2001; 69: 504 [OpenAIRE] [PubMed] [DOI]

Zhou, H, Alexander, DH, Sehl, ME, Sinsheimer, JS, Sobel, EM, Lange, K. Penalized regression for genome-wide association screening of sequence data. Pac Symp Biocomput. 2011: 106-117 [OpenAIRE] [PubMed]

Powered by OpenAIRE Open Research Graph
Any information missing or wrong?Report an Issue
publication . Article . Conference object . 2014

A 2-step penalized regression method for family-based next-generation sequencing association studies

David Fardo;