Ovarian cancer variant rs2072590 is associated with HOXD1 and HOXD3 gene expression
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Liyuan Guo1,*, Yan Peng2,*, Lei Sun3,*, Xia Han4, Juan Xu4 and Dongwei Mao4
1Department of Gynecological Oncology, Cancer Hospital of Harbin Medical University, Harbin, China
2Disease Prevention Center, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, China
3Department of Gynecology and Obstetrics, The Fourth Hospital of Harbin Medical University, Harbin, China
4Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen, China
*These authors contributed equally to this work
Dongwei Mao, email: [email protected]
Keywords: ovarian cancer, genome-wide association study, gene expression
Received: July 17, 2017 Accepted: September 21, 2017 Published: October 13, 2017
Ovarian cancer (OC) is a common cancer in women and the leading cause of deaths from gynaecological malignancies in the world. In addition to the candidate gene approach to identify OC susceptibility genes, the genome-wide association study (GWAS) methods have reported new variants that are associated with OC risk. The minor allele of rs2072590 at 2q31 was associated with an increased OC risk, and was primarily significant for serous subtype. The OC risk-associated SNP rs2072590 lies in non-coding DNA downstream of HOXD3 and upstream of HOXD1, and it tags SNPs in the HOXD3 3′ UTR. We think that the non-coding rs2072590 variant may contribute to OC susceptibility by regulating the gene expression of HOXD1 and HOXD3. In order to investigate this association, we performed a bioinformatics analysis by a functional annotation of rs2072590 variant using RegulomeDB (version 1.1), HaploReg (version 4.1), and PhenoScanner (version 1.1). Using HaploReg, we identified 19 genetic variants tagged by rs2072590 variant with with r2 >= 0.8. Using RegulomeDB, we identified that three genetic variants are likely to affect TF binding + any motif + DNase Footprint + DNase peak. Other genetic variants are likely to affect TF binding + DNase peak. Using PhenoScanner (version 1.1), we identified that these 19 genetic variants could significantly regulate the expression of nearby genes, especially the HOXD1 and HOXD3 in human ovary tissue.
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