Genome wide analysis and clinical correlation of chromosomal and transcriptional mutations in cancers of the biliary tract Journal Article
| Authors: | Miller, G.; Socci, N. D.; Dhall, D.; D'Angelica, M.; DeMatteo, R. P.; Allen, P. J.; Singh, B.; Fong, Y.; Blumgart, L. H.; Klimstra, D. S.; Jarnagin, W. R. |
| Article Title: | Genome wide analysis and clinical correlation of chromosomal and transcriptional mutations in cancers of the biliary tract |
| Abstract: | Background. The pathogenesis of biliary cancers is ill-defined. This study investigates changes in gene expression and copy number in biliary cancers and correlates these changes with anatomical site of origin, histopathology and outcome. Methods. We performed gene expression and CGH analysis on 34 biliary tract cancer specimens. Results were confirmed by RT-PCR. Clinical-pathologic correlation was made using functional over-representation analysis of the top 100 mutations associated with each variable. Results. There were 545 genes with altered expression in extrahepatic cholangiocarcinoma, 2,354 in intrahepatic cholangiocarcinoma, and 1,281 in gallbladder cancer. Unsupervised hierarchical clustering analysis indicated there was no difference in the global gene expression patterns between each biliary cancer subgroup. CGH analysis revealed that short segments of chromosomes 1p, 3p, 6q, 8p, 9p, and 14q were commonly deleted across all cancer subtypes. Commonly amplified regions included segments of 1q, 3q, 5p, 7p, 7q, 8q, and 20q. Over-representation analysis revealed an association between altered expression of functional gene groupings and pathologic features. Conclusion. This study defined regions of the genome associated with changes in DNA copy number and gene expression in specific subtypes of biliary cancers. The findings have implications for identification of therapeutic targets, screening, and prognostication. © 2009 Miller et al; licensee BioMed Central Ltd. |
| Keywords: | adult; clinical article; controlled study; human tissue; aged; aged, 80 and over; middle aged; gene mutation; genetics; mutation; histopathology; lymph node metastasis; metabolism; disease association; reverse transcription polymerase chain reaction; gene expression; gene expression profiling; tumor markers, biological; chromosome 9p; genetic transcription; transcription, genetic; pathology; tumor marker; cancer invasion; rna; chromosome aberration; dna; oligonucleotide array sequence analysis; human genome; dna, neoplasm; genome; bile duct carcinoma; dna microarray; chromosome 8p; chromosome aberrations; gene dosage; nucleic acid hybridization; chromosomes, human; comparative genomic hybridization; gallbladder cancer; human chromosome; biliary tract cancer; chromosome 1q; biliary tract neoplasms; genomic dna; chromosome 3p; genome, human; chromosome 6q; complementary dna; complementary rna; chromosomal localization; chromosome 14q; chromosome 1p; chromosome 20q; chromosome 3q; chromosome 5p; chromosome 7p; chromosome 7q; chromosome 8q; genome wide analysis; biliary tract tumor |
| Journal Title: | Journal of Experimental & Clinical Cancer Research |
| Volume: | 28 |
| Issue: | 1 |
| ISSN: | 1756-9966 |
| Publisher: | Biomed Central Ltd |
| Date Published: | 2009-05-12 |
| Start Page: | epub |
| Language: | English |
| DOI: | 10.1186/1756-9966-28-62 |
| PUBMED: | 19435499 |
| PROVIDER: | scopus |
| PMCID: | PMC2698861 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 2" - "Export Date: 30 November 2010" - "Art. No.: 62" - "CODEN: JECRD" - "Source: Scopus" |
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