Base of tongue squamous cell carcinoma susceptibility: Novel candidate genetic polymorphisms identified in genome-wide association study.

Abstract

e16041 Background: Inherited genetic alterations, such as single nucleotide polymorphisms (SNPs), were described in association with oropharyngeal cancer risk in few reports with restrict number of SNPs analyzed. Base of tongue (BT) squamous cell carcinoma (SCC) is a common tumor of oropharynx; however, the association of SNPs and BTSCC risk is not clarified and, therefore, this was the aim of this study. Methods: DNA from 49 BTSCC patients and 49 controls was extracted 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 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 and validated in study, including those localized in genes related to cell cycle (3’-UTR: ERP29, rs7114; MCC, rs7033; DWS: LEF1, rs2107028 and rs4245926; PTCH1, rs16909856 and rs16909859), transcription process (CDS: IKBKAP, rs3204145; 3’-UTR: ZNF415, rs3814), and cell adhesion (CDS: COL22A1, rs2292927; DWS: LY6K, rs1995467). Conclusions: Our preliminary results suggest that SNPs in genes involved in tumor development may predispose individuals to BTSCC. However, these results should be confirmed by functional protein studies and validated in larger epidemiological studies. Financial support: FAPESP and FINEP.