Year: 2014
Type: article
Abstract: The electronic MEdical Records and GEnomics (eMERGE) network brings together DNA biobanks linked to electronic health records (EHRs) from multiple institutions. Approximately 51,000 DNA samples from distinct individuals have been genotyped using genome-wide SNP arrays across the nine sites of the network. The eMERGE Coordinating Center and the Genomics Workgroup developed a pipeline to impute and merge genomic data across the different SNP arrays to maximize sample size and power to detect associations with a variety of clinical endpoints. The 1000 Genomes cosmopolitan reference panel was used for imputation. Imputation results were evaluated using the following metrics: accuracy of imputation, allelic R (2) (estimated correlation between the imputed and true genotypes), and the relationship between allelic R (2) and minor allele frequency. Computation time and memory resources required by two different software packages (BEAGLE and IMPUTE2) were also evaluated. A number of challenges were encountered due to the complexity of using two different imputation software packages, multiple ancestral populations, and many different genotyping platforms. We present lessons learned and describe the pipeline implemented here to impute and merge genomic data sets. The eMERGE imputed dataset will serve as a valuable resource for discovery, leveraging the clinical data that can be mined from the EHR.
Source: Frontiers in Genetics
Authors: Shefali S. Verma, Mariza de Andrade, Gerard Tromp, Helena Kuivaniemi, Elizabeth Pugh, Bahram Namjou-Khales, Shubhabrata Mukherjee, Gail P. Jarvik, Leah C. Kottyan, Amber Burt, Yuki Bradford, Gretta D. Armstrong, Kimberly Derr, Dana C. Crawford, Jonathan L. Haines, Rongling Li, David Crosslin, Marylyn D. Ritchie
Institutions: Pennsylvania State University, Mayo Clinic, Geisinger Medical Center, Geisinger Health System, Johns Hopkins University, Cincinnati Children's Hospital Medical Center, University of Washington, Vanderbilt University, Case Western Reserve University, National Human Genome Research Institute
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,801
Funders: Children's Hospital of Philadelphia, Vanderbilt University, Northwestern University, Cincinnati Children's Hospital Medical Center, University of Washington, Johns Hopkins University, Pennsylvania State University, Broad Institute, National Human Genome Research Institute, National Institute of General Medical Sciences
Awards: G1039948199, G1085576015, G1119622688, G1271251741, G1329273205, G1350761991, EHR-based Genomic Discovery and Implementation, G1569664509, G1678063915, G1800770867, G1875582626, G2424387874, G2673102205, G2686867407, G2720851073, G2813733336, G2860569048, G2878691739, G2888548701, G303142226, G309706311, G330805887, G3326248413, G3420921512, G3425267393, G3543980300, G3606196707, G4203491109, G4246599211, G4503763930, G4880343153, G504300783, G5058729078, G556970706, G5683642332, G5871168253, G6071621673, G6135170989, Genetic Discovery and Application in a Clinical Setting Continuing a Partnership, G635500700, G6384197514, G7163342664, G8565821944, G858805679, G8754966041, G906879642, G911961363, G957155052
OpenAlex ID: W2068127873