Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis.

Cancer Res. 2005 Jul 1;65(13):5561-70.. Published: 2005.06.30

Xiaojun Zhao, Barbara A. Weir, Thomas LaFramboise, Ming Lin, Rameen Beroukhim, Levi Garraway, Javad Beheshti, Jeffrey C. Lee, Katsuhiko Naoki, William G. Richards, David Sugarbaker, Fei Chen, Mark A. Rubin, Pasi A. Janne, Luc Girard, John Minna, David Christiani, Cheng Li, William R. Sellers and Matthew Meyerson

Abstract

Genome-wide copy number changes were analyzed in 70 primary human lung carcinoma specimens and 31 cell lines derived from human lung carcinomas, with high-density arrays representing approximately 115,000 single nucleotide polymorphism loci. In addition to previously characterized loci, two regions of homozygous deletion were found, one near the PTPRD locus on chromosome segment 9p23 in four samples representing both small cell lung carcinoma (SCLC) and non-small cell lung carcinoma (NSCLC) and the second on chromosome segment 3q25 in one sample each of NSCLC and SCLC. High-level amplifications were identified within chromosome segment 8q12-13 in two SCLC specimens, 12p11 in two NSCLC specimens and 22q11 in four NSCLC specimens. Systematic copy number analysis of tyrosine kinase genes identified high-level amplification of EGFR in three NSCLC specimens, FGFR1 in two specimens and ERBB2 and MET in one specimen each. EGFR amplification was shown to be independent of kinase domain mutational status.

Keywords:

Zhao 2005

Supplemental Data

Description Link/Filename
Raw data http://research2.dfci.harvard.edu/dfci/snp/
Supplemental data Zhao_2005_Suppl.pdf
dChip software http://biosun1.harvard.edu/~cli/dchip2004.exe
Manuscript Zhao_2005.pdf