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Genetic Analysis Workshop 17 mini-exome simulation
journal contribution
posted on 2023-05-17, 09:35 authored by Almasy, L, Dyer, TD, Peralta, JM, Kent Jr, JW, Jac CharlesworthJac Charlesworth, Curran, JE, Blangero, JThe data set simulated for Genetic Analysis Workshop 17 was designed to mimic a subset of data that might be produced in a full exome screen for a complex disorder and related risk factors in order to permit workshop participants to investigate issues of study design and statistical genetic analysis. Real sequence data from the 1000 Genomes Project formed the basis for simulating a common disease trait with a prevalence of 30% and three related quantitative risk factors in a sample of 697 unrelated individuals and a second sample of 697 individuals in large, extended pedigrees. Called genotypes for 24,487 autosomal markers assigned to 3,205 genes and simulated affection status, quantitative traits, age, sex, pedigree relationships, and cigarette smoking were provided to workshop participants. The simulating model included both common and rare variants with minor allele frequencies ranging from 0.07% to 25.8% and a wide range of effect sizes for these variants. Genotype-smoking interaction effects were included for variants in one gene. Functional variants were concentrated in genes selected from specific biological pathways and were selected on the basis of the predicted deleteriousness of the coding change. For each sample, unrelated individuals and family, 200 replicates of the phenotypes were simulated.
History
Publication title
BMC ProceedingsVolume
5Issue
Supplement 9Article number
S2Number
S2Pagination
1-9ISSN
1753-6561Department/School
Menzies Institute for Medical ResearchPublisher
BioMed Central Ltd.Place of publication
United KingdomRights statement
Copyright 2011 BioMed Central Ltd.Repository Status
- Restricted