Are VNTRs co-localizing with breast cancer-associated SNPs?

Are VNTRs co-localizing with breast cancer-associated SNPs? Purpose Several common genetic variants (single-nucleotide polymorphisms, SNPs) have been shown to be associated with breast cancer (BC) risk in the general population, and to modify BC risk for BRCA1 and BRCA2 mutation carriers. Co- localization of variable number of tandem repeats (VNTRs) with these BC-associated SNPS has not been comprehensively studied. Methods Cross referencing of genome-wide VNTRs with the known BC genome-wide association studies (GWAS) SNPs significantly associated with increased risk for developing breast cancer was carried out. Analysis was based on the overlap between the VNTRs and 10-kb windows around these BC-susceptibility SNPs. Results Cross referencing of the 1.2 million TR with the 161 known BC-associated SNPs in the general population led to 690 matches. Of those, in 17 VNTRs, the SNP was within the VNTR. Analysis restricted to loci known to modify BC pen- etrance in BRCA1 (n = 31) and BRCA2 (n = 33) mutation carriers led to 139 and 170 co-localization matches, respectively. For these, none of the SNPs were within the VNTR. The distances between the SNPs and the VNTRs were not significantly different from what was expected to occur by chance alone ( p = 0.61; p = 0.44; p = 0.25, respectively). Conclusion There is no evidence that VNTRs co-localize with http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Breast Cancer Research and Treatment Springer Journals

Are VNTRs co-localizing with breast cancer-associated SNPs?

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Publisher
Springer US
Copyright
Copyright © 2017 by Springer Science+Business Media, LLC, part of Springer Nature
Subject
Medicine & Public Health; Oncology
ISSN
0167-6806
eISSN
1573-7217
D.O.I.
10.1007/s10549-017-4588-7
Publisher site
See Article on Publisher Site

Abstract

Purpose Several common genetic variants (single-nucleotide polymorphisms, SNPs) have been shown to be associated with breast cancer (BC) risk in the general population, and to modify BC risk for BRCA1 and BRCA2 mutation carriers. Co- localization of variable number of tandem repeats (VNTRs) with these BC-associated SNPS has not been comprehensively studied. Methods Cross referencing of genome-wide VNTRs with the known BC genome-wide association studies (GWAS) SNPs significantly associated with increased risk for developing breast cancer was carried out. Analysis was based on the overlap between the VNTRs and 10-kb windows around these BC-susceptibility SNPs. Results Cross referencing of the 1.2 million TR with the 161 known BC-associated SNPs in the general population led to 690 matches. Of those, in 17 VNTRs, the SNP was within the VNTR. Analysis restricted to loci known to modify BC pen- etrance in BRCA1 (n = 31) and BRCA2 (n = 33) mutation carriers led to 139 and 170 co-localization matches, respectively. For these, none of the SNPs were within the VNTR. The distances between the SNPs and the VNTRs were not significantly different from what was expected to occur by chance alone ( p = 0.61; p = 0.44; p = 0.25, respectively). Conclusion There is no evidence that VNTRs co-localize with

Journal

Breast Cancer Research and TreatmentSpringer Journals

Published: Nov 22, 2017

References

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