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

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, Maxwell P. Lee

Research output: Contribution to journalArticle

33 Scopus citations

Abstract

Background: 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. Results: 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. Conclusion: 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.

Original languageEnglish (US)
Article number299
JournalBMC Genomics
Volume7
DOIs
StatePublished - Nov 29 2006
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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    Hu, N., Wang, C., Hu, Y., Yang, H. H., Kong, L. H., Lu, N., Su, H., Wang, Q. H., Goldstein, A. M., Buetow, K. H., Emmert-Buck, M. R., Taylor, P. R., & Lee, M. P. (2006). Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix genechip mapping 10 K array. BMC Genomics, 7, [299]. https://doi.org/10.1186/1471-2164-7-299