Genetic Analysis Workshop 17 mini-exome simulation.
Genetic Analysis Workshop 17 mini-exome simulation.
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DOI：
10.1186/1753-6561-5-s9-s2
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发表时间：
2011-11-29
期刊：
影响因子：
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通讯作者：
Blangero J
中科院分区：
文献类型：
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作者：
Almasy L;Dyer TD;Peralta JM;Kent JW Jr;Charlesworth JC;Curran JE;Blangero J
遗传分析研讨会17模拟的数据集旨在模拟可能在复杂疾病和相关风险因素的全外显子组筛选中产生的数据子集，以允许研讨会参与者调查研究设计和统计遗传分析问题。来自1000基因组计划的真实序列数据构成了模拟697个不相关个体样本和697个大型扩展谱系个体样本中患病率为30%的常见疾病特征和三个相关定量风险因素的基础。为研讨会参与者提供了24,487个常染色体标记的基因型，分配给3,205个基因，并模拟了情感状态，数量性状，年龄，性别，系谱关系和吸烟情况。模拟模型包括常见和罕见变异，等位基因频率在0.07%至25.8%之间，这些变异的效应量范围很广。基因型-吸烟相互作用效应包括在一个基因变异。功能变异集中在从特定生物学途径中选择的基因中，并根据预测的编码变化的危害性进行选择。对于每个样本，不相关的个体和家庭，模拟了200个表型重复。
The 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.