TY - JOUR
T1 - Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix genechip mapping 10 K array
AU - Hu, Nan
AU - Wang, Chaoyu
AU - Hu, Ying
AU - Yang, Howard H.
AU - Kong, Li Hui
AU - Lu, Ning
AU - Su, Hua
AU - Wang, Quan Hong
AU - Goldstein, Alisa M.
AU - Buetow, Kenneth H.
AU - Emmert-Buck, Michael R.
AU - Taylor, Philip R.
AU - Lee, Maxwell P.
PY - 2006/11/29
Y1 - 2006/11/29
N2 - 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.
AB - 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.
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U2 - 10.1186/1471-2164-7-299
DO - 10.1186/1471-2164-7-299
M3 - Article
C2 - 17134496
AN - SCOPUS:33845678584
SN - 1471-2164
VL - 7
JO - BMC Genomics
JF - BMC Genomics
M1 - 299
ER -