@article{c6367e8c6d854fee80bcc5396b321c66,
title = "Omics-squared: Human genomic, transcriptomic and phenotypic data for genetic analysis workshop 19",
abstract = "Background: The 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. Methods: GAW19 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.",
author = "John Blangero and Teslovich, {Tanya M.} and Xueling Sim and Almeida, {Marcio A.} and Goo Jun and Dyer, {Thomas D.} and Matthew Johnson and Peralta, {Juan M.} and Alisa Manning and Wood, {Andrew R.} and Christian Fuchsberger and Kent, {Jack W.} and Aguilar, {David A.} and Below, {Jennifer E.} and Farook, {Vidya S.} and Rector Arya and Sharon Fowler and Blackwell, {Tom W.} and Sobha Puppala and Satish Kumar and Glahn, {David C.} and Moses, {Eric K.} and Curran, {Joanne E.} and Farook Thameem and Jenkinson, {Christopher P.} and DeFronzo, {Ralph A.} and Lehman, {Donna M.} and Craig Hanis and Goncalo Abecasis and Michael Boehnke and Harald G{\"o}ring and Ravindranath Duggirala and Laura Almasy",
note = "Funding Information: The GAW19 exome and whole genome sequence data were provided by the T2D-GENES Consortium, which is supported by NIH grants U01 DK085524, U01 DK085584, U01 DK085501, U01 DK085526, and U01 DK085545. Additional genetic and phenotypic data for GAW19 were provided by the San Antonio Family Heart Study and San Antonio Family Diabetes/ Gallbladder Study, which are supported by NIH grants R01 HL0113323, P01 HL045222, R01 DK047482, and R01 DK053889. Additional Starr County genotype and phenotype data were supported by NIH grants R01 DK073541 and R01 HL102830. The VAGES study was supported by a Veterans Administration Epidemiologic grant. The FIND-SA study was supported by NIH grant U01 DK57295. SAFHS gene expression assays were supported by a donation from the Azar and Shepperd families. We would also like to acknowledge the contributions and leadership of the late Dr. Hanna E. Abboud, Principal Investigator of the FIND study (San Antonio Component). Andrew R Wood is supported by the European Research Council grant: SZ-245 50371-GLUCOSEGENES-FP7-IDEAS-ERC. The Genetic Analysis Workshop is supported by NIH grant R01 GM031575. Publisher Copyright: {\textcopyright} 2016 The Author(s).",
year = "2016",
doi = "10.1186/s12919-016-0008-y",
language = "English (US)",
volume = "10",
journal = "BMC Proceedings",
issn = "1753-6561",
publisher = "BioMed Central",
}