Unknown,Transcriptomics,Genomics,Proteomics

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Identification of a subgroup of head and neck cancers lacking numerical chromosomal aberrations

ABSTRACT: ABSTRACT Two major subgroups of head and neck squamous cell carcinomas (HNSCC) are currently distinguished based on etiology and pattern of genetic alterations; tumors with biologically active human papillomavirus (HPV) and tumors without. It is at present unclear whether additional genetically distinct subgroups exist within HPV-negative HNSCC. Aim of this study is to genetically classify HNSCC without HPV involvement and to correlate the genetically defined classes to tumor and patient characteristics. By means of array comparative genomic hybridization (aCGH) we determined DNA copy number variation in thirty-nine HPV-negative, but further unselected HNSCC. Unsupervised analysis of aCGH data distinguished two genetic groups in HPV-negative HNSCC, one characterized by a low level of chromosomal alterations (N=9), and another by a high level of chromosomal alterations (N=30). Absence of chromosomal aberrations was significantly associated with wild-type TP53, a low level of alcohol consumption, a female gender and a better prognosis. The tumors were negative for microsatellite instability. The discovery of this new class of HNSCC with unique genetic and clinical characteristics has important consequences for future basic and clinical studies. All DNAs are isolated from fresh frozen HNSCC specimen. All tissue specimens were microdissected to obtain at least 90% tumor DNA. All sampels are hybridized against a pool of reference DNA of normal individuals of the opposite gender.

ORGANISM(S): Homo sapiens

SUBMITTER: Serge Smeets

PROVIDER: E-GEOD-11929 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck.

Wilting Saskia M SM Smeets Serge J SJ Snijders Peter J F PJ van Wieringen Wessel N WN van de Wiel Mark A MA Meijer Gerrit A GA Ylstra Bauke B Leemans C René CR Meijer Chris J L M CJ Brakenhoff Ruud H RH Braakhuis Boudewijn J M BJ Steenbergen Renske D M RD

BMC medical genomics 20090601

<h4>Background</h4>It is well known that a persistent infection with high-risk human papillomavirus (hrHPV) is causally involved in the development of squamous cell carcinomas of the uterine cervix (CxSCCs) and a subset of SCCs of the head and neck (HNSCCs). The latter differ from hrHPV-negative HNSCCs at the clinical and molecular level.<h4>Methods</h4>To determine whether hrHPV-associated SCCs arising from different organs have specific chromosomal alterations in common, we compared genome-wid ...[more]

PMID: 19486517

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Dataset Information

Identification of a subgroup of head and neck cancers lacking numerical chromosomal aberrations

Publications

Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck.

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