Building a large imputation panel for a publicly available server to impute GWAS data
Principal Investigator
Name
Ulrike Peters
Degrees
Ph.D, M.P.H
Institution
Fred Hutchinson Cancer Center
Position Title
Associate Director, Public Health Sciences
Email
About this CDAS Project
Study
PLCO
(Learn more about this study)
Project ID
PLCO-70
Initial CDAS Request Approval
Mar 20, 2014
Title
Building a large imputation panel for a publicly available server to impute GWAS data
Summary
Efforts are underway to construct a large reference panel of roughly 15,000 samples with whole genome sequencing data, which will allow researchers to impute rarer variants with higher certainty than currently possible with the available smaller reference panels (e.g. HapMap or 1000 Genome Project). The imputation platform will be available to the general research community so that individuals can receive imputed results for their GWAS data without obtaining individual level data from the reference panel. This is made possible through an imputation server that allows researchers to submit their GWAS data to the server, which then imputes the GWAS using the large whole genome sequencing reference panel. After imputation is complete, the imputed GWAS data are returned to the investigators and deleted from the imputation server. We aim to include whole genome sequence data from PLCO samples, along with additional sequence data from of the Genetics & Epidemiology of Colorectal Cancer Consortium (GECCO).
Aims
To include PLCO whole genome sequence data into a larger reference panel as part of a imputation platform, which will allow researchers to receive imputed GWAS results, while by-passing the need for the distribution and downloading of individual level study data.
Collaborators
Goncalo Abecasis at the University of Michigan
Jonathan Marchini at the University of Oxford
Richard Durbin at Wellcome Trust Sanger