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Recently, we read the article by Ma et al with great interest. They conducted a comprehensive meta-analysis that nominated 62 variants in 50 candidate genes with high level of cumulative evidence for genetic susceptibility to colorectal cancer (CRC).1 Interestingly, the authors found that 10 variants in 7 genes were graded strong and moderate association with CRC risk. However, functional annotations of these variants remain largely unknown. To investigate their functional relevance, we annotated the variants and their high related single nucleotide polymorphisms (SNPs) (linkage disequilibrium, r2>0.9) using publicly available The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus datasets.
After exclusion of the variants with minor allele frequency <0.05, a total of four SNPs (rs1801155, rs1569686, rs1800734 and rs2736100) were included in further analysis (table 1). We then evaluated the effect of risk alleles on gene epigenetic and expression alterations in CRC tumour tissues from TCGA. Three SNPs (rs1569686, rs1800734 and rs2736100) were identified as methylation quantitative trait loci (meQTL) in the 500 kb upstream and …
Footnotes
GM, YG and DG contributed equally to this work. ZZ and MW co-supervised this work.
Twitter Follow Yuqiu Ge at @gutjnl-2015-311299
Contributors ZZ and MW are co-responders for this paper. Study concept and design: MW and GM. Acquisition of data: GM and YG. Analysis and interpretation of data: MD, DG and HC. Drafting of the manuscript: GM and YG. Critical revision of the manuscript for important intellectual content: ZZ, MW and JC. Statistical analysis: GM and YG. Obtained funding: ZZ and MW. Approval of the final version of the manuscript: MW and ZZ.
Funding This study was partly supported by National Natural Science Foundation of China (81373091, 81230068 and 81201570), Distinguished Young Scholars of Nanjing (JQX13005) and the Priority Academic Program Development of Jiangsu Higher Education Institutions (Public Health and Preventive Medicine).
Competing interests None declared.
Patient consent Obtained.
Provenance and peer review Not commissioned; internally peer reviewed.