Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2006-11-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/7/299 |
| _version_ | 1818766243981688832 |
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| author | Goldstein Alisa M Wang Quan-Hong Su Hua Lu Ning Kong Li-Hui Yang Howard H Hu Ying Wang Chaoyu Hu Nan Buetow Kenneth H Emmert-Buck Michael R Taylor Philip R Lee Maxwell P |
| author_facet | Goldstein Alisa M Wang Quan-Hong Su Hua Lu Ning Kong Li-Hui Yang Howard H Hu Ying Wang Chaoyu Hu Nan Buetow Kenneth H Emmert-Buck Michael R Taylor Philip R Lee Maxwell P |
| author_sort | Goldstein Alisa M |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-18T08:30:54Z |
| format | Article |
| id | doaj.art-1f0846e2917a498c967c67d66fc0578a |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T08:30:54Z |
| publishDate | 2006-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-1f0846e2917a498c967c67d66fc0578a2022-12-21T21:14:28ZengBMCBMC Genomics1471-21642006-11-017129910.1186/1471-2164-7-299Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K arrayGoldstein Alisa MWang Quan-HongSu HuaLu NingKong Li-HuiYang Howard HHu YingWang ChaoyuHu NanBuetow Kenneth HEmmert-Buck Michael RTaylor Philip RLee Maxwell P<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/7/299 |
| spellingShingle | Goldstein Alisa M Wang Quan-Hong Su Hua Lu Ning Kong Li-Hui Yang Howard H Hu Ying Wang Chaoyu Hu Nan Buetow Kenneth H Emmert-Buck Michael R Taylor Philip R Lee Maxwell P Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array BMC Genomics |
| title | Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array |
| title_full | Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array |
| title_fullStr | Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array |
| title_full_unstemmed | Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array |
| title_short | Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array |
| title_sort | genome wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the affymetrix genechip mapping 10 k array |
| url | http://www.biomedcentral.com/1471-2164/7/299 |
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