TY - JOUR
T1 - Deep sequencing of human papillomavirus positive loco-regionally advanced oropharyngeal squamous cell carcinomas reveals novel mutational signature
AU - Grønhøj, Christian
AU - Jensen, David H
AU - Agander, Tina
AU - Kiss, Katalin
AU - Høgdall, Estrid
AU - Specht, Lena
AU - Bagger, Frederik Otzen
AU - Nielsen, Finn Cilius
AU - von Buchwald, Christian
PY - 2018/6/7
Y1 - 2018/6/7
N2 - BACKGROUND: The genetic profile for human papilloma virus positive (HPV+) oropharyngeal squamous cell carcinomas (OPSCC) remains largely unknown. The purpose of this study was to sequence tissue material from a large cohort of locoregionally-advanced HPV+ OPSCCs.METHODS: We performed targeted deep sequencing of 395 cancer-associated genes in 114 matched tumor/normal loco-regionally advanced HPV+ OPSCCs. Mutations and copy number aberrations were determined.RESULTS: We identified a total of 3459 mutations with an average of 10 mutations per megabase and a median of 28 variants per sample. The most frequently mutated genes were KALRN (28%), SPTBN1 (32%), KMT2A (31%), ZNRF3 (9%), BNC2 (12%), NOTCH2 (25%), FGFR2 (12%), SMAD2 (6%), and AR (13%). Our findings were dominated by COSMIC signature 5 and 12, represented in other head and neck cancers and in hepatocellular carcinomas, respectively.CONCLUSIONS: We have identified multiple genetic aberrations in HPV+ OPSCCs, and the COSMIC signature 12 as most prevalent. The mutations harbour both therapeutic and prognostic potential.
AB - BACKGROUND: The genetic profile for human papilloma virus positive (HPV+) oropharyngeal squamous cell carcinomas (OPSCC) remains largely unknown. The purpose of this study was to sequence tissue material from a large cohort of locoregionally-advanced HPV+ OPSCCs.METHODS: We performed targeted deep sequencing of 395 cancer-associated genes in 114 matched tumor/normal loco-regionally advanced HPV+ OPSCCs. Mutations and copy number aberrations were determined.RESULTS: We identified a total of 3459 mutations with an average of 10 mutations per megabase and a median of 28 variants per sample. The most frequently mutated genes were KALRN (28%), SPTBN1 (32%), KMT2A (31%), ZNRF3 (9%), BNC2 (12%), NOTCH2 (25%), FGFR2 (12%), SMAD2 (6%), and AR (13%). Our findings were dominated by COSMIC signature 5 and 12, represented in other head and neck cancers and in hepatocellular carcinomas, respectively.CONCLUSIONS: We have identified multiple genetic aberrations in HPV+ OPSCCs, and the COSMIC signature 12 as most prevalent. The mutations harbour both therapeutic and prognostic potential.
KW - Biomarkers, Tumor/genetics
KW - DNA Mutational Analysis
KW - High-Throughput Nucleotide Sequencing
KW - Humans
KW - Oropharyngeal Neoplasms/genetics
KW - Papillomavirus Infections/complications
KW - Squamous Cell Carcinoma of Head and Neck/genetics
KW - Transcriptome
U2 - 10.1186/s12885-018-4567-3
DO - 10.1186/s12885-018-4567-3
M3 - Journal article
C2 - 29879932
SN - 1471-2407
VL - 18
SP - 1
EP - 10
JO - BMC Cancer
JF - BMC Cancer
IS - 1
M1 - 640
ER -