A Pilot Study Of Human Whole-exome Sequencing On Gene Chip For Oral Cancer SNPS

Objectives：To study the Single Nucleotide Polymorphisms （SNPs） ofprimary oral cancer, its lymphatic metastasis and peripheral blood of healthyvolunteers using Genome Wide Association Studies （GWAS） based on humanwhole-exome sequencing technique on gene chip; to identify susceptibility genes oforal cancer or its metastasis, and lay a foundation for further experiments.Method： Primary oral cancer and their lymph node metastasis samples of10cases, and peripheral blood from24healthy volunteers were collected as primarygroup, metastasis group and healthy control group. Sample DNA was extracted andwhole-exome sequencing on gene chip was performed afterwards. Alternativevisualization and brief analysis of raw data were achieved in Genomestudio usingsample sheets. Genome Wide Association Studies （GWAS） of case-controlcomparisons were carried out in PLINK and Haploview softwares. The SNPs of oralcancer and its metastasis susceptibility genes were identified by Chi-square tests andmultiple adjustions in comparisons of DNA genotyping.Results: Whole-exome sequencing was successfully performed for44DNA sampleson the gene chips. Alternative visualization and brief analysis of individual raw datawere achieved in Genomestudio. There was no SNP of significant differencesbetween groups after multiple adjustments in the following comparisons （p>0.05）：comparison between primary cancer group and metastasis group （10primary oral cancers and their lymph node metastases）, that between primary group and healthycontrol group（10primary oral cancers and24healthy controls）, and that betweenmetastasis group and healthy control group（10lymph node metastases and24healthycontrols）. However, in the comparison between cases （including10primary cancersand their metastases） and healthy control group,622candidate SNPs were screeningout of242901chosen SNPs （p<0.005）. After multiple adjustments, two SNPs（exm530670representing NM₀05514of HLA-B on6p21.3, p=0.025; andexm1415896representing NM₁98534.2of C19orf45，p=0.036; all p<0.05） werehighly correlated with oral cancer. In published literature, C19orf45was mutated inboth cancer and human induced stem cells, while HLA-B was conformed associatedwith head and neck squamous cell carcinoma and its metastasis significantly.Conclusions: HLA-B and C19orf45, human protein coding genes, areclosely related with oral cancer. Through the pilot experiment we have successfullyhandled the techique of whole-exome sequencing on genchip and afterward analysis,which lays the foundation for further identification of mutant genes of oral cancermetastasis and their functions.