Classification of non-small cell lung cancer based on copy number alterations

Bi-Qing Li; Jin You; Tao Huang; Yu-Dong Cai

doi:10.1371/journal.pone.0088300

Classification of non-small cell lung cancer based on copy number alterations

PLoS One. 2014 Feb 5;9(2):e88300. doi: 10.1371/journal.pone.0088300. eCollection 2014.

Authors

Bi-Qing Li¹, Jin You², Tao Huang³, Yu-Dong Cai⁴

Affiliations

¹ Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.
² The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.
³ Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, New York, United States of America.
⁴ Institute of Systems Biology, Shanghai University, Shanghai, P.R. China.

Abstract

Lung cancer is one of the leading causes of cancer mortality worldwide and non-small cell lung cancer (NSCLC) accounts for the most part. NSCLC can be further divided into adenocarcinoma (ACA) and squamous cell carcinoma (SCC). It is of great value to distinguish these two subgroups clinically. In this study, we compared the genome-wide copy number alterations (CNAs) patterns of 208 early stage ACA and 93 early stage SCC tumor samples. As a result, 266 CNA probes stood out for better discrimination of ACA and SCC. It was revealed that the genes corresponding to these 266 probes were enriched in lung cancer related pathways and enriched in the chromosome regions where CNA usually occur in lung cancer. This study sheds lights on the CNA study of NSCLC and provides some insights on the epigenetic of NSCLC.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenocarcinoma / classification
Adenocarcinoma / genetics*
Adenocarcinoma / pathology
Carcinoma, Non-Small-Cell Lung / classification
Carcinoma, Non-Small-Cell Lung / genetics*
Carcinoma, Non-Small-Cell Lung / pathology
Carcinoma, Squamous Cell / classification
Carcinoma, Squamous Cell / genetics*
Carcinoma, Squamous Cell / pathology
DNA Copy Number Variations*
Gene Dosage
Humans
Lung / metabolism
Lung / pathology
Lung Neoplasms / classification
Lung Neoplasms / genetics*
Lung Neoplasms / pathology

Grants and funding

This work was supported by grants from National Basic Research Program of China (2011CB510101, 2011CB510102), Innovation Program of Shanghai Municipal Education Commission (12ZZ087), and the grant of “The First-class Discipline of Universities in Shanghai”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.