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Series GSE49666 Query DataSets for GSE49666
Status Public on Nov 03, 2013
Title Distinct Mutational Patterns of Infection and Non-Infection-Related Bile Duct Cancers Revealed by Exome Sequencing
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary The impact of different carcinogenic exposures on the specific patterns of somatic mutations in human tumors remains unclear. To clarify this issue, we profiled 209 cholangiocarcinomas (CCAs) from Asia and Europe, including 108 cases caused by liver fluke Opisthorchis viverrini (OV)-infection and 101 cases due to non-OV etiologies. Whole-exome (N = 15) and prevalence screening (N = 194) revealed recurrent somatic mutations in BAP1 and ARID1A, neither of which has been previously reported to be mutated in CCA. Comparisons between intrahepatic OV and non-OV CCAs demonstrated statistically significant different mutation patterns: BAP1 and IDH1/2 were more frequently mutated in non-OV CCAs, while TP53 displayed the reciprocal pattern. Functional studies demonstrated tumor suppressive roles of BAP1 and ARID1A, establishing the role of chromatin modulators in CCA pathogenesis. These findings indicate that different causative etiologies may induce distinct somatic alterations even within the same tumor type.
 
Overall design Affymetrix SNP6 arrays were performed according to the manufacturer's directions on DNA extracted from the 15 tumors and the 15 matched normal discovery samples.
 
Contributor(s) Chan-on W, Teh BT
Citation(s) 24185513
Submission date Aug 08, 2013
Last update date Nov 27, 2018
Contact name Ioana Cutcutache
E-mail(s) ioana.cutcutache@duke-nus.edu.sg
Organization name Duke-NUS
Department Centre for Computational Biology
Lab Steve Rozen lab
Street address 8 College Rd
City Singapore
State/province Singapore
ZIP/Postal code 169857
Country Singapore
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (30)
GSM1204675 Cholangio non-malignant sample 17231203N SNP6
GSM1204676 Cholangio tumor sample 17231203T SNP6
GSM1204677 Cholangio non-malignant sample 2000861N SNP6
Relations
BioProject PRJNA214694

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49666_RAW.tar 918.9 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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