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. 2018 Jan 15:11:5.
doi: 10.1186/s13039-018-0354-8. eCollection 2018.

Identification of genomic copy number variations associated with specific clinical features of head and neck cancer

Boris Zagradišnik  1 , Danijela Krgović  1 , Špela Stangler Herodež  1 , Andreja Zagorac  1 , Bogdan Ćižmarević  2 , Nadja Kokalj Vokač  1
Affiliations

Identification of genomic copy number variations associated with specific clinical features of head and neck cancer

Boris Zagradišnik et al. Mol Cytogenet. .

Abstract

Background: Copy number variations (CNSs) of large genomic regions are an important mechanism implicated in the development of head and neck cancer, however, for most changes their exact role is not well understood. The aim of this study was to find possible associations between gains/losses of genomic regions and clinically distinct subgroups of head and neck cancer patients.

Results: Array comparative genomic hybridization (aCGH) analysis was performed on DNA samples in 64 patients with cancer in oral cavity, oropharynx or hypopharynx. Overlapping genomic regions created from gains and losses were used for statistical analysis. Following regions were overrepresented: in tumors with stage I or II a gain of 2.98 Mb on 6p21.2-p11 and a gain of 7.4 Mb on 8q11.1-q11.23; in tumors with grade I histology a gain of 1.1 Mb on 8q24.13, a loss of a large part of p arm of chromosome 3, a loss of a 1.24 Mb on 6q14.3, and a loss of terminal 32 Mb region of 8p23.3; in cases with affected lymph nodes a gain of 0.75 Mb on 3q24, and a gain of 0.9 Mb on 3q26.32-q26.33; in cases with unaffected lymph nodes a gain of 1.1 Mb on 8q23.3, in patients not treated with surgery a gain of 12.2 Mb on 7q21.3-q22.3 and a gain of 0.33 Mb on 20q11.22.

Conclusions: Our study identified several genomic regions of interest which appear to be associated with various clinically distinct subgroups of head and neck cancer. They represent a potentially important source of biomarkers useful for the clinical management of head and neck cancer. In particular, the PIK3CA and AGTR1 genes could be singled out to predict the lymph node involvement.

Keywords: Array comparative genomic hybridization; Biomarkers; Copy number variations; Head and neck cancer.

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Conflict of interest statement

The study was approved by the Ethics committee of the University Medical Centre Maribor, where it was conducted. Each patient signed an informed consent prior to the study enrollment.All the participants accepted with the initial written informed consent the possibility that the results of this study could be published.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Chromosomal locations of genomic regions associated with various subgroups of patients
See this image and copyright information in PMC

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