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Utilizing sequence and imputed genotype data to identify novel genetic susceptibility variants for colorectal cancer

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-68
Initial CDAS Request Approval
Mar 6, 2014
Title
Utilizing sequence and imputed genotype data to identify novel genetic susceptibility variants for colorectal cancer
Summary
Colorectal cancer (CRC) is the second leading cause of cancer death in the US. Linkage studies and genome-wide association studies (GWAS) have successfully identified high-penetrance mutations as well as low-penetrance variants. However, these variants explain only a fraction of the heritability of CRC. Contributions from large classes of genetic variation, specifically less frequent and rare single nucleotide variants (SNV) with allele frequency of 0.1-5%, insertion/deletions (indels), and copy number variants (CNVs), have not been systematically investigated across the genome. To identify these variants, we propose using the PLCO whole genome sequence data, and the PLCO GWAS data (imputed with the CRC whole genome sequence as part of the reference panel), which has been approved under EEMS Proposal 2010-00150.
Aims

This project aims to identify novel colorectal cancer (CRC) susceptibility variants using whole genome sequencing. Using sequencing data, we will impute the identified variants in an additional CRC cases and controls with GWAS data and subsequently test the associations between CRC risk and variants; these GWAS cases and controls include those from PLCO. We will also test whether known environmental risk factors for CRC modify genetic susceptibility to CRC. Directly genotype data, imputed GWAS, and a limited set of phenotype data will be shared by the Genetics & Epidemiology of Colorectal Cancer Consortium (GECCO) Coordinating Center at the Fred Hutchison Cancer Research Center with collaborators.

Collaborators

Goncalo Abecasis, University of Michigan
Suzanne Leal, Baylor College of Medicine