Study

Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency

Study ID Alternative Stable ID Type
EGAS00001000149 Exome Sequencing

Study Description

Whole-exome sequencing (Exome-Seq) has been successfully applied in several recent studies. We here performed Exome-Seq of 15 pancreatic tumor-normal pairs. We captured 162,073 exons of 16,954 genes and sequenced the targeted regions to a mean coverage of 56 folds. This study identified a total of 1,517 somatic mutations and validated 934 of them by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among tumors. The diversity of mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-Seq revealed intensive genomic instability in a tumor with MLH1 homozygous deletion, indicated by a dramatically elevated mutation rate of somatic substitutions, small insertions/deletions (indels), as well as indels presented at microsatellites. Notably, we detected MLH1 allelic loss in 4 tumors. MLH1 expression was decreased by nearly half in these cases. While they were negative in the conventional microsatellite instability assay, they showed a 10.5-fold increase in the ... (Show More)

Study Datasets 4 datasets.

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Dataset ID Description Technology Samples
EGAD00001000042
Whole-Exome-Seq-Dataset
Illumina Genome Analyzer IIx 30
EGAD00001000043
RNA-Seq-Dataset
Illumina Genome Analyzer IIx 16
EGAD00010000050
Matched tumor-negative pancreas tissues
Affymetrix SNP 6.0 15
EGAD00010000051
Cell line derived from microdissected primary pancreatic ductal adenocarcinoma tissues
Affymetrix SNP 6.0 15

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