Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array release_5inlb5efx5holgzd7wtrxk7fz4

by Nan Hu, Chaoyu Wang, Ying Hu, Howard H Yang, Li-Hui Kong, Ning Lu, Hua Su, Quan-Hong Wang, Alisa M Goldstein, Kenneth H Buetow, Michael R Emmert-Buck, Philip R Taylor (+1 others)

Published in BMC Genomics.

2006   Volume 7, p299

Abstract

Esophageal squamous cell carcinoma (ESCC) is a common malignancy worldwide. Comprehensive genomic characterization of ESCC will further our understanding of the carcinogenesis process in this disease. Genome-wide detection of chromosomal changes was performed using the Affymetrix GeneChip 10 K single nucleotide polymorphism (SNP) array, including loss of heterozygosity (LOH) and copy number alterations (CNA), for 26 pairs of matched germ-line and micro-dissected tumor DNA samples. LOH regions were identified by two methods--using Affymetrix's genotype call software and using Affymetrix's copy number alteration tool (CNAT) software--and both approaches yielded similar results. Non-random LOH regions were found on 10 chromosomal arms (in decreasing order of frequency: 17p, 9p, 9q, 13q, 17q, 4q, 4p, 3p, 15q, and 5q), including 20 novel LOH regions (10 kb to 4.26 Mb). Fifteen CNA-loss regions (200 kb to 4.3 Mb) and 36 CNA-gain regions (200 kb to 9.3 Mb) were also identified. These studies demonstrate that the Affymetrix 10 K SNP chip is a valid platform to integrate analyses of LOH and CNA. The comprehensive knowledge gained from this analysis will enable improved strategies to prevent, diagnose, and treat ESCC.
In text/plain format

Archived Files and Locations

application/pdf  3.7 MB
file_6yeywkcqinefxna5xdhc7gxhh4
europepmc.org (repository)
web.archive.org (webarchive)
application/pdf  7.5 MB
file_ceibt5uotjcolgq53djwkk5tgm
bmcgenomics.biomedcentral.com (publisher)
web.archive.org (webarchive)
Read Archived PDF
Preserved and Accessible
Type  article-journal
Stage   published
Date   2006-11-29
Language   en ?
Container Metadata
Open Access Publication
In DOAJ
In ISSN ROAD
In Keepers Registry
ISSN-L:  1471-2164
Work Entity
access all versions, variants, and formats of this works (eg, pre-prints)
Catalog Record
Revision: b5939109-d13e-406e-9ef6-13ffebac0506
API URL: JSON