Unraveling the genetic basis of nasopharyngeal carcinoma using next-generation sequencing approaches

Abstract

BACKGROUND: Nasopharyngeal carcinoma (NPC) is an epithelial malignancy that originates in the nasopharynx. This cancer is highly prevalent in Asia, especially southern China. Familiar genetic predisposition is observed in 5-10% of NPC patients. It is well-accepted that host genetics, EBV infection, and environmental factors together contribute to NPC development. PURPOSE: The genetic basis of NPC has not been fully elucidated. Therefore, we aim to use next-generation sequencing approaches to identify genes or pathways associated with NPC risk and to understand the genetic basis of NPC. METHODS: In the discovery cohort, 67 family history-positive (FH+) NPC cases from 56 families, 39 early-age onset cases, and 51 sporadic cases were subjected to whole-exome sequencing (WES). WES data of additional 415 non-cancer controls were obtained from non-cancer studies. Two strategies, mixed model association analysis and systematic filtering methods, were used for the analysis. The LightSNiP assay, which detects variants by melting curve analysis, and targeted sequencing approach were applied in an independent validation cohort. RESULTS: Association analysis identified a 3’ UTR variant in G protein-coupled receptor 114 (GPR114) with genome-wide significance (p-value 1.1x10-8). The risk allele was observed in 10 cases from 5 FH+ families and 1 sporadic case, but was not found in controls and public databases. In the validation study, LightSNiP assay identified the variant in 4 out of 210 FH+ cases, 25 out of 1725 sporadic cases, and 11 out of 1849 controls. The odds ratios are 3.1 and 2.35 for FH+ and sporadic cases, respectively. All the variants identified were validated by Sanger sequencing. GPR114 is expressed in both NPC and normal nasopharyngeal tissues. Further functional studies are now underway for GPR114. Using the systematic filtering analysis strategy, we identified the genes with rare damaging variants (minor allele frequency≤0.01) in at least four FH+ families and excluded the genes which are likely to be false positive signals in WES or not expressed in NPC or normal nasopharyngeal tissues. In total 455 genes were identified. Gene ontology analysis identified enriched terms including chromatin modification (FDR=0.02) and extracellular matrix (FDR=0.006). Targeted sequencing of candidate genes in about 300 additional FH+ cases and 300 age- and gender-matched controls is underway. CONCLUSIONS: In our study, a GPR114 3’ UTR variant was found to be associated with increased risk of NPC in both familiar and sporadic cases. We also identified rare damaging variants enriched in chromatin modification and extracellular matrix. Our study provides an enhanced road map for comprehensive understanding of the genetic basis of NPC.