Supplementary Material for: Distribution and clinical significance of HPV16 variants in head and neck squamous cell carcinomas: data from a Portuguese cohort and systematic review

Introduction: Genomic variants of the human papillomavirus type 16 (HPV16) are thought to play differential roles in the susceptibility to head and neck squamous cell carcinomas (HNSCC) and its biological behaviour. This study aims to establish the prevalence of HPV16 variants in an HNSCC cohort and associate them with clinical-pathological characteristics and patient survival. Methods: We retrieved samples and clinical data from 68 HNSCC patients. DNA samples were available from tumour biopsy at the time of the primary diagnosis. Targeted next-generation sequencing (NGS) was used to obtain whole-genome sequences and variants were established based on phylogenetic classification. Results: 74.% of samples clustered in lineage A, 5.7% lineage B, 2.9% C and 17.1% D. Comparative genome analysis revealed 243 single nucleotide variations (SNVs). Of these one hundred were previously reported, according to our systematic review. No significant associations with clinical-pathological variables or patient survival were observed. The E6 amino acid variations E31G, L83V and D25E and E7 N29S, associated with cervical cancer, were not observed, except for N29S in a single patient. Discussion/Conclusion: These results provide a comprehensive genomic map of HPV16 in HSNCC, highlighting tissue-specific characteristics which will help design tailored therapies for cancer patients.

引言：人乳头瘤病毒16型（human papillomavirus type 16, HPV16）的基因组变异被认为在头颈部鳞状细胞癌（head and neck squamous cell carcinomas, HNSCC）的易感性及其生物学行为中发挥差异化作用。本研究旨在明确某头颈部鳞状细胞癌（HNSCC）队列中HPV16变异株的流行率，并分析其与患者临床病理特征及生存结局的关联。
方法：本研究从68名头颈部鳞状细胞癌（HNSCC）患者中获取样本及临床数据，所有DNA样本均取自初诊时的肿瘤活检组织。本研究采用靶向下一代测序（next-generation sequencing, NGS）技术获取全基因组序列，并基于系统发育分类对变异株进行分型。
结果：74.%的样本聚类于A谱系，5.7%聚类于B谱系，2.9%聚类于C谱系，17.1%聚类于D谱系。比较基因组分析共鉴定出243个单核苷酸变异（single nucleotide variations, SNVs）。根据本研究的系统综述，其中100个变异此前已有报道。未观察到该类变异与临床病理指标或患者生存结局存在显著关联。与宫颈癌相关的E6氨基酸变异E31G、L83V、D25E以及E7 N29S均未检出，仅1例患者存在N29S变异。
讨论与结论：本研究结果构建了头颈部鳞状细胞癌（HNSCC）中HPV16的全面基因组图谱，重点揭示了其组织特异性特征，可为癌症患者的个性化治疗方案设计提供参考。