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Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array.
- Source :
-
BMC Genomics . 2006, Vol. 7, p299-16. 16p. 7 Diagrams, 8 Charts. - Publication Year :
- 2006
-
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 CNAgain 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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 7
- Database :
- Academic Search Index
- Journal :
- BMC Genomics
- Publication Type :
- Academic Journal
- Accession number :
- 28858735
- Full Text :
- https://doi.org/10.1186/1471-2164-7-299