ArticleBMC proceedings2016
Omics-squared: human genomic, transcriptomic and phenotypic data for genetic analysis workshop 19.
Article in BMC proceedings, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed, 50 citations in OpenAlex.
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- Advances in the Genetics of Hypertension: The Effect of Rare Variants.International journal of molecular sciences · 2018Review
- Two-phase designs for joint quantitative-trait-dependent and genotype-dependent sampling in post-GWAS regional sequencing.Genetic epidemiology · 2018Article
- Data for GAW20: genome-wide DNA sequence variation and epigenome-wide DNA methylation before and after fenofibrate treatment in a family study of metabolic phenotypes.BMC proceedings · 2018Article
- Comparison of single-marker and multi-marker tests in rare variant association studies of quantitative traits.PloS one · 2017Article
- Progress in methods for rare variant association.BMC genetics · 2016Article
- Joint analysis of multiple phenotypes: summary of results and discussions from the Genetic Analysis Workshop 19.BMC genetics · 2016Article
- Family-based approaches: design, imputation, analysis, and beyond.BMC genetics · 2016Article
- Gene expression in large pedigrees: analytic approaches.BMC genetics · 2016Article
- Filtering genetic variants and placing informative priors based on putative biological function.BMC genetics · 2016Article
- Pathway-based analyses.BMC genetics · 2016Article
- Analysis of gene expression to predict dynamics of future hypertension incidence in type 2 diabetic patients.BMC proceedings · 2016Article
- Gene coexpression network analysis for family studies based on a meta-analytic approach.BMC proceedings · 2016Article
- Identifying regions of disease-related variants in admixed populations with the summation partition approach.BMC proceedings · 2016Article
- Identification of interactions using model-based multifactor dimensionality reduction.BMC proceedings · 2016Article
- Comparison of parametric and machine methods for variable selection in simulated Genetic Analysis Workshop 19 data.BMC proceedings · 2016Article
- Assessing transmission ratio distortion in extended families: a comparison of analysis methods.BMC proceedings · 2016Article
- Transmission and decorrelation methods for detecting rare variants using sequencing data from related individuals.BMC proceedings · 2016Article
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Authors and funding
34 authors at 12 institutions in 4 countries.
Funding
Abstract
backgroundThe Genetic Analysis Workshops (GAW) are a forum for development, testing, and comparison of statistical genetic methods and software. Each contribution to the workshop includes an application to a specified data set. Here we describe the data distributed for GAW19, which focused on analysis of human genomic and transcriptomic data.
methodsGAW19 data were donated by the T2D-GENES Consortium and the San Antonio Family Heart Study and included whole genome and exome sequences for odd-numbered autosomes, measures of gene expression, systolic and diastolic blood pressures, and related covariates in two Mexican American samples. These two samples were a collection of 20 large families with whole genome sequence and transcriptomic data and a set of 1943 unrelated individuals with exome sequence. For each sample, simulated phenotypes were constructed based on the real sequence data. 'Functional' genes and variants for the simulations were chosen based on observed correlations between gene expression and blood pressure. The simulations focused primarily on additive genetic models but also included a genotype-by-medication interaction. A total of 245 genes were designated as 'functional' in the simulations with a few genes of large effect and most genes explaining < 1 % of the trait variation. An additional phenotype, Q1, was simulated to be correlated among related individuals, based on theoretical or empirical kinship matrices, but was not associated with any sequence variants. Two hundred replicates of the phenotypes were simulated. The GAW19 data are an expansion of the data used at GAW18, which included the family-based whole genome sequence, blood pressure, and simulated phenotypes, but not the gene expression data or the set of 1943 unrelated individuals with exome sequence.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.