Novel genetic locus at MHC region for esophageal squamous cell carcinoma in Chinese populationsReport as inadecuate




Novel genetic locus at MHC region for esophageal squamous cell carcinoma in Chinese populations - Download this document for free, or read online. Document in PDF available to download.

Background

Our previous genome-wide association study GWAS identified three independent single nucleotide polymorphisms SNPs in human major histocompatibility complex MHC region showing association with esophageal squamous cell carcinoma ESCC. In this study, we increased GWAS sample size on MHC region and performed validation in an independent ESCC cases and normal controls with aim to find additional loci at MHC region showing association with an increased risk to ESCC.

Methods

The 1,077 ESCC cases and 1,733 controls were genotyped using Illumina Human 610-Quad Bead Chip, and 451 cases and 374 controls were genotyped using Illumina Human 660W-Quad Bead Chip. After quality control, the selected SNPs were replicated by TaqMan genotyping assay on another 2,026 ESCC cases and 2,384 normal controls.

Results

By excluding low quality SNPs in primary GWAS screening, we selected 2,533 SNPs in MHC region for association analysis, and identified 5 SNPs with p <10−4. Further validation analysis in an independent case-control cohort confirmed one of the 5 SNPs rs911178 that showed significant association with ESCC. rs911178 PGWAS = 6.125E-04, OR = 0.644 and Preplication = 1.406E-22, OR = 0.489 was located at upstream of SCAND3.

Conclusion

The rs911178 SCAND3 gene in MHC region is significantly associated with high risk of ESCC. This study not only reveal the potential role of MHC region for the pathogenesis of ESCC, but also provides important clues for the establishment of tools and methods for screening high risk population of ESCC.



Author: Peng Zhang, Xin-Min Li, Xue-Ke Zhao, Xin Song, Ling Yuan, Fang-Fang Shen, Zong-Min Fan, Li-Dong Wang

Source: http://plos.srce.hr/



DOWNLOAD PDF




Related documents