Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Somatic copy number alterations (CNAs) play a significant role in the development of this lethal cancer. In this study, we present a meta-analysis of CNAs for a total of 1,395 HNSCC samples. Publicly available R packages and in-house scripts were used for genomic array data processing, including normalization, segmentation and CNA calling. We detected 125 regions of significant gains or losses using GISTIC algorithm and found several potential driver genes in these regions. The incidence of chromothripsis in HNSCC was estimated to be 6%, and the chromosome pulverization hotspot regions were detected. We determined 323 genomic locations significantly enriched for breakpoints, which indicate HNSCC-specific genomic instability regions. Unsupervised clustering of genome-wide CNA data revealed a sub-cluster predominantly composed of nasopharynx tumors and presented a large proportion of HPV-positive samples. These results will facilitate the discovery of therapeutic candidates and extend our molecular understanding of HNSCC.
Highlights
Head and neck squamous cell carcinoma (HNSCC) has an incidence of over 600,000 new diagnoses per year worldwide, with a mortality rate of nearly 50% [1, 2]
The most notable focal copy number alterations (CNAs) was the overrepresentation of 11q13, which may be associated with oncogene CCND1 amplification [44, 45]
We further investigated the frequency of arm-level alterations, which were defined as a single CNA that encompasses >50% of a chromosomal arm
Summary
Head and neck squamous cell carcinoma (HNSCC) has an incidence of over 600,000 new diagnoses per year worldwide, with a mortality rate of nearly 50% [1, 2]. It consists of a heterogeneous group of epithelial tumors arising from oral cavity, nasal cavity, pharynx, larynx, paranasal sinuses and salivary glands. Tobacco use and excessive alcohol consumption are well-established major risk factors for the development of HNSCC. Human papillomavirus (HPV) infection has been recognized as an increasingly important risk factor for HNSCC [3, 4]. A more detailed understanding of the genetic mechanisms of HNSCC is needed to improve prevention and treatment of this cancer
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