title: Genome-wide analysis of recurrent copy-number alterations and copy-neutral loss of heterozygosity in head and neck squamous cell carcinoma.
abstract: BACKGROUND
  Head and neck squamous cell carcinoma (HNSCC) is the eighth most commonly diagnosed malignancy worldwide, and it is generally characterized by a poor prognosis. The aim of our study has been to identify possible recurring genomic abnormalities in this malignancy, likely to have a key role in pathogenesis.
  
  
  METHODS
  The single-nucleotide polymorphism (SNP)-array data relative to 19 HNSCC samples (submitted by Poage et al., PloS ONE 2010; 5: e9651), accessible at NCBI GEO database (GSE20939), were analyzed using criteria that take into account both genotyping and intensity data. By this method, we determined the number and localization of recurrent copy-neutral loss of heterozygosity (CN-LOH) regions and compared them with recurrent somatic copy-number alterations (CNAs).
  
  
  RESULTS
  Single-nucleotide polymorphism-array data analysis allowed us to detect, for the first time in HNSCC, chromosomal segment of CN-LOHs in addition to CNAs. Chromosomal alterations have been detected in 14 (73.7%) of 19 samples, and the 12.1% of all alterations observed (LOHs, gains, and CN-LOHs) were CN-LOHs. The most recurrent gain events, occurring in 78.5% of cases (11 samples), were harbored within 8q21.11-q21.13 and 8q23.1-q24.22 loci, while the most recurrent loss and CN-LOH events were present at 3p21.31-p21.1 (57.1%; 8 samples) and 17p13.3-p13.1 (28.6%; 4 samples) loci, respectively.
  
  
  CONCLUSIONS
  The investigated chromosomal regions, in particular those with CN-LOH, harbored some interesting genes, such as HIC1, DOCK8, KANK1, and NOTCH1 whose role, mutations and epigenetic modifications in HNSCC deserve to be investigated, in order to understand the significance of CN-LOH events in HNSCC pathogenesis.
authors.affiliation: Scuola Superiore di Catania, University of Catania, Catania, Italy.
authors.forename: Maria Sebastiana
authors.initials: MS
authors.lastname: Marescalco
authors.forename: Carmela
authors.initials: C
authors.lastname: Capizzi
authors.forename: Daniele Filippo
authors.initials: DF
authors.lastname: Condorelli
authors.forename: Vincenza
authors.initials: V
authors.lastname: Barresi
mesh_terms: D048868:Adaptor Proteins, Signal Transducing; D017089:Ankyrin Repeat / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics; D002893:Chromosomes, Human, Pair 3 / Q000235:genetics; D002898:Chromosomes, Human, Pair 8 / Q000235:genetics; D003598:Cytoskeletal Proteins; D056915:DNA Copy Number Variations / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics; D017353:Gene Deletion; D015894:Genome, Human / Q000235:genetics*; D005838:Genotype; D020662:Guanine Nucleotide Exchange Factors / Q000235:genetics; D006258:Head and Neck Neoplasms / Q000235:genetics*; D006801:Humans; D051741:Kruppel-Like Transcription Factors / Q000235:genetics; D019656:Loss of Heterozygosity / Q000235:genetics*; D009154:Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D051881:Receptor, Notch1 / Q000235:genetics; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D003598:Cytoskeletal Proteins; C516591:DOCK8 protein, human; D020662:Guanine Nucleotide Exchange Factors; C499808:HIC1 protein, human; C467739:KANK1 protein, human; D051741:Kruppel-Like Transcription Factors; C497761:NOTCH1 protein, human; D051881:Receptor, Notch1; D025521:Tumor Suppressor Proteins
keywords: SNP-array; copy-neutral loss of heterozygosity; genetic alterations; head and neck cancer