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Systematic Review ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00723

Genome and transcriptome analysis highlights the association of rs2180341 variant with breast cancer

 Yuqin Ye1, 2*, Shihou Sheng3*, Keren Wang3, Zhaoying Yang3, Guang Sun3, Ning Liu3, Chunni Fan3 and Lu Tang3*
  • 1Jilin University, China
  • 2First Affiliated Hospital of Jilin University, China
  • 3China-Japan Union Hospital, Jilin University, China

Abstract
In 2008, a breast cancer genetic variant rs2180341 in 6q22.33 was first identified in Ashkenazi Jews population with P=2.90E-08. However, other studies reported controversial findings. Here, we conducted a three-stage analysis. In stage 1, we used the genome-wide association study datasets and candidate gene study datasets to evaluate the potential association between rs2180341 and breast cancer. In stage 2, we conducted an expression quantitative trait loci (eQTLs) analysis to further evaluate whether rs2180341 is associated with the expression of nearby genes. In stage 3, we evaluated the potential different expression of these nearby genes using case-control gene expression dataset. Our findings showed significant heterogeneity in all these selected genome-wide association study datasets and candidate gene study datasets. The breast cancer variant rs2180341 identified in Ashkenazi Jews population may not be directly replicated in other populations. Meanwhile, eQTLs analysis provides strong evidence implicating rs2180341 as a risk variant regulating the expression of nearby genes involved in kinds of cancers. However, few nearby genes showed significant different expression in breast cancer cases and controls.

Keywords: breast cancer, rs2180341, Meta-analysis, eQTLs analysis, Genome-Wide Association Study

Received: 04 Apr 2019; Accepted: 10 Jul 2019.

Edited by:

Liang Cheng, Harbin Medical University, China

Reviewed by:

Guiyou Liu, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
Junwei Han, Harbin Medical University, China
Keshen Li, Jinan University, China  

Copyright: © 2019 Ye, Sheng, Wang, Yang, Sun, Liu, Fan and Tang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Prof. Yuqin Ye, Jilin University, Changchun, China, dearlea88@126.com
Dr. Shihou Sheng, China-Japan Union Hospital, Jilin University, Changchun, 130033, Jilin Province, China, sheng897237@163.com
Dr. Lu Tang, China-Japan Union Hospital, Jilin University, Changchun, 130033, Jilin Province, China, tanglu_06@163.com