Oncotarget

Research Papers:

Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites

Junfeng Jiang, Peilin Jia, Bairong Shen and Zhongming Zhao _

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Oncotarget. 2014; 5:6168-6177. https://doi.org/10.18632/oncotarget.2179

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Abstract

Junfeng Jiang1,2,*, Peilin Jia1,3,*, Bairong Shen2 and Zhongming Zhao1,3,4,5

1 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA

2 Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China

3 Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA

4 Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA

5 Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA

* These authors contribute equally to this work

Correspondence:

Zhongming Zhao, email:

Bairong Shen, email:

Keywords: prostate cancer, genome-wide association studies, eQTL, TFBS, regulatory variants

Received: May 18, 2014 Accepted: July 7, 2014 Published: July 9, 2014

Abstract

While genome-wide association studies (GWAS) have revealed thousands of disease risk single nucleotide polymorphisms (SNPs), their functions remain largely unknown. Recent studies have suggested the regulatory roles of GWAS risk variants in several common diseases; however, the complex regulatory structure in prostate cancer is unclear.

We investigated the potential regulatory roles of risk variants in two prostate cancer GWAS datasets by their interactions with expression quantitative trait loci (eQTL) and/or transcription factor binding sites (TFBSs) in three populations.

Our results indicated that the moderately associated GWAS SNPs were significantly enriched with cis-eQTLs and TFBSs in Caucasians (CEU), but not in African Americans (AA) or Japanese (JPT); this was also observed in an independent pan-cancer related SNPs from the GWAS Catalog. We found that the eQTL enrichment in the CEU population was tissue-specific to eQTLs from CEU lymphoblastoid cell lines. Importantly, we pinpointed two SNPs, rs2861405 and rs4766642, by overlapping results from cis-eQTL and TFBS as applied to the CEU data.

These results suggested that prostate cancer associated SNPs and pan-cancer associated SNPs are likely to play regulatory roles in CEU. However, the negative enrichment results in AA or JPT and the potential mechanisms remain to be elucidated in additional samples.


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