publication . Article . 2011

Penalized-regression-based multimarker genotype analysis of Genetic Analysis Workshop 17 data

Ayers, Kristin L; Mamasoula, Chrysovalanto; Cordell, Heather J;
Open Access English
  • Published: 01 Nov 2011 Journal: BMC Proceedings, volume 5, issue Suppl 9, page S92 (issn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
  • Country: Mexico
Abstract
<p>Abstract</p> <p>Testing for association between multiple markers and a phenotype can not only capture untyped causal variants in weak linkage disequilibrium with nearby typed markers but also identify the effect of a combination of markers. We propose a sliding window approach that uses multimarker genotypes as variables in a penalized regression. We investigate a penalty with three separate components: (1) a group least absolute shrinkage and selection operator (LASSO) that selects multimarker genotypes in a gene to be included in or excluded from the model, (2) an allele-sharing penalty that encourages multimarker genotypes with similar alleles to have simi...
Subjects
free text keywords: Medicine, R, Science, Q, Proceedings, General Biochemistry, Genetics and Molecular Biology, General Medicine, Genetic association, Quantitative trait locus, Model selection, Regression, Linkage disequilibrium, Single-nucleotide polymorphism, Bioinformatics, Lasso (statistics), Sliding window protocol, business.industry, business
Funded by
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
,
WT
Project
  • Funder: Wellcome Trust (WT)

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