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Series GSE49656 Query DataSets for GSE49656
Status Public on Oct 20, 2013
Title Distinct Mutational Patterns of Infection and Non-Infection-Related Bile Duct Cancers Revealed by Exome Sequencing
Organism Homo sapiens
Experiment type Methylation profiling by 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 Illumina 450k methylation array profiling performed on wild-type (n=23) and mutant (n=9) CCA (cholangiocarcinoma) samples, with adjacent normal tissue (n=4)
Contributor(s) Chan-On W, Teh BT
Citation(s) 24185513
Submission date Aug 08, 2013
Last update date Mar 22, 2019
Contact name Weng Khong Lim
Organization name National Cancer Centre Singapore
Department Department of Medical Sciences
Lab NCCS-VARI Translational Research Laboratory
Street address 11 Hospital Drive
City Singapore
State/province Singapore
ZIP/Postal code 169610
Country Singapore
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (40)
GSM1204490 CCA_Tumor_Sample [17137053T]
GSM1204491 CCA_Tumor_Sample [19286759T]
GSM1204492 CCA_Tumor_Sample [90866096T]
BioProject PRJNA214647

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
GSE49656_RAW.tar 183.1 Mb (http)(custom) TAR
GSE49656_SignalFile.txt.gz 131.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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