Genome-Wide Association Study of Base of Tongue Squamous Cell Carcinoma Risk

ABSTRACT Background Inherited genetic alterations, such as single nucleotide polymorphisms (SNPs), were described in association with oropharyngeal cancer risk. However, existing studies have analyzed a limited number of genetic variants. Base of tongue (BT) squamous cell carcinoma (SCC) is a common tumor of oropharynx; however, the association of SNPs and BTSCC risk is still not clarified and, therefore, this was the aim of the present study. Methods Genomic DNA of 49 BTSCC patients and 49 controls was extracted from peripheral blood samples using the QIamp kit (Qiagen®). Each sample was genotyped individually using DNA high-resolution microarrays containing 500.568 SNPs (SNP array 5.0, Affymetrix®). Further sample processing, including digestion, adaptor ligation, amplification, fragmentation, labeling, hybridization, washing and scanning was assayed according to the standard protocol. Genotype data were acquired by genotyping calling of samples using the crlmm algorithm provided by Bioconductor software. The differences between groups were analyzed by the logistic regression model. The SNPs localized in genes of interest were selected by data base analysis in DAVID and NCBI websites. The validation of selected SNPs was performed by RT-PCR, using TaqMan® SNP Genotyping Assays (Applied Biosystems®) in all samples studied. Results We observed 6.609 SNPs with distinct frequencies between BTSCC patients and controls. Fifty-two SNPs (0.8%) were located in coding sequence (CDS), 51 (0.8%) in 3' and 5'-untranslated regions (UTR), 3.461 (52.4%) in up or downstream regions (DWS) and 3.045 (46.0%) in introns. Ten SNPs were selected for validation and eight of them were validated, evidencing those localized in genes related to cell cycle (3'-UTR: ERP29, rs7114; MCC, rs7033; DWS: LEF1, rs2107028 and rs4245926; PTCH1, rs16909856 and rs16909859) and transcription process (CDS: IKBKAP, rs3204145; 3'-UTR: ZNF415, rs3814). Conclusions Our preliminary results suggest that SNPs in genes involved in tumor origin and development may predispose individuals to BTSCC in southeastern Brazil. However, the roles of these SNPs in BTSCC susceptibility should be confirmed by functional protein studies and validated in larger epidemiological studies from distinct parts of the world. Financial support: FAPESP and FINEP. Disclosure All authors have declared no conflicts of interest.