Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility
Previous genome-wide association studies
(GWAS) have shown several risk alleles to be associated
with breast cancer. However, the variants identified so far
contribute to only a small proportion of disease risk. The
objective of our GWAS was to identify additional novel
breast cancer susceptibility variants and to replicate these
findings in an independent cohort. We performed a twostage
association study in a cohort of 3,064 women from
Alberta, Canada. In Stage I, we interrogated 906,600 single
nucleotide polymorphisms (SNPs) on Affymetrix SNP 6.0
arrays using 348 breast cancer cases and 348 controls. We
used single-locus association tests to determine statistical
significance for the observed differences in allele frequencies
between cases and controls. In Stage II, we
attempted to replicate 35 significant markers identified in
Stage I in an independent study of 1,153 cases and 1,215
controls. Genotyping of Stage II samples was done using
Sequenom Mass-ARRAY iPlex platform. Six loci from
four different gene regions (chromosomes 4, 5, 16 and 19)
showed statistically significant differences between cases
and controls in both Stage I and Stage II testing, and also in
joint analysis. The identified variants were from
EDNRA,
ROPN1L, C16orf61 and
ZNF577 gene regions. The presented
joint analyses from the two-stage study design were
not significant after genome-wide correction. The SNPs
identified in this study may serve as potential candidate loci
for breast cancer risk in a further replication study in Stage
III from Alberta population or independent validation in
Caucasian cohorts elsewhere.
Citation
B. Sehrawat,
M. Sridharan,
S. Ghosh,
P. Robson,
C. Cass,
J. Mackey,
R. Greiner,
S. Damaraju.
"Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility".
Human Genetics, March 2011.
| Keywords: |
SNP, bioinformatics, medical informatics, association, breast cancer |
| Category: |
In Journal |
| Web Links: |
DOI |
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BibTeX
@article{Sehrawat+al:HumanGenetics11,
author = {Badan Sehrawat and Malinee Chakrava Sridharan and Sunita Ghosh and
Paula Robson and Carol Cass and John Mackey and Russ Greiner and
Sambasivarao Damaraju},
title = {Potential novel candidate polymorphisms identified in genome-wide
association study for breast cancer susceptibility},
journal = {Human Genetics},
year = 2011,
}Last Updated: September 21, 2012
Submitted by Russ Greiner 
