Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3

Oncotarget
Cinzia BersaniTina Dalianis

Abstract

Human papillomavirus positive (HPV+) tonsillar cancer (TSCC), base of tongue cancer (BOTSCC) and unknown primary cancer of the head and neck (HNCUP) have better outcome than corresponding HPV- cancers. To find predictive markers for response to treatment, and correlations and differences in mutated oncogenes and suppressor genes between HPV+ TSCC/BOTSSCC and HPV+ HNCUP and HPV- TSCC/BOTSCC targeted next-generation sequencing was performed of frequently mutated regions in 50 cancer related genes. DNA from 348 TSCC/BOTSCC and 20 HNCUP from patients diagnosed 2000-2011, was sequenced by the Ion Proton sequencing platform using the Ion AmpliSeq Cancer Hotspot Panel v2 to identify frequently mutated regions in 50 cancer related genes. Ion Torrent Variant Caller software was used to call variants. 279 HPV+ TSCC/BOTSCC, 46 HPV- TSCC/BOTSCC and 19 HPV+ HNCUP samples qualified for further analysis. Mutations/tumor were fewer in HPV+ TSCC/BOTSCC and HNCUP, compared to HPV- tumors (0.92 vs. 1.32 vs. 1.68). Differences in mutation frequency of TP53 and PIK3CA were found between HPV+ TSCC/BOTSCC and HNCUP and HPV- TSCC/BOTSCC. In HPV+ TSCC/BOTSCC presence of FGFR3 mutations correlated to worse prognosis. Other correlations to survival withi...Continue Reading

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Citations

Jul 20, 2018·Diagnostic Pathology·Linnea HaeggblomAnders Näsman
Jul 16, 2020·International Journal of Molecular Sciences·Sebastian ZiębaMagdalena Kowalewska
Mar 7, 2021·Critical Reviews in Oncology/hematology·Adriana Castelo de MouraEliete Neves Silva Guerra
Dec 21, 2021·Frontiers in Genetics·Qunchao HuHaiyan Zhu

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Methods Mentioned

BETA
biopsy
biopsies
PCR
chip

Software Mentioned

Ion Torrent
Torrent Variant Caller ( TVC )
SPSS
Torrent Suite
Integrative Genomics Viewer ( IGV )
Ion Torrent Variant Caller Plugin

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