This tab shows an overview of the selected study/paper [more details]
Reference

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes.

Paper Id
COSP28538
Authors
Zang ZJ,Cutcutache I,Poon SL,Zhang SL,McPherson JR,Tao J,Rajasegaran V,Heng HL,Deng N,Gan A,Lim KH,Ong CK,Huang D,Chin SY,Tan IB,Ng CC,Yu W,Wu Y,Lee M,Wu J,Poh D,Wan WK,Rha SY,So J,Salto-Tellez M,Yeoh KG,Wong WK,Zhu YJ,Futreal PA,Pang B,Ruan Y,Hillmer AM,Bertrand D,Nagarajan N,Rozen S,Teh BT and Tan P
Affiliation
Cellular and Molecular Research, National Cancer Centre, Singapore.
Journal
Nature genetics 2012;44(5):570-4
ISSN:1546-1718
PUBMED:22484628
Abstract
Gastric cancer is a major cause of global cancer mortality. We surveyed the spectrum of somatic alterations in gastric cancer by sequencing the exomes of 15 gastric adenocarcinomas and their matched normal DNAs. Frequently mutated genes in the adenocarcinomas included TP53 (11/15 tumors), PIK3CA (3/15) and ARID1A (3/15). Cell adhesion was the most enriched biological pathway among the frequently mutated genes. A prevalence screening confirmed mutations in FAT4, a cadherin family gene, in 5% of gastric cancers (6/110) and FAT4 genomic deletions in 4% (3/83) of gastric tumors. Frequent mutations in chromatin remodeling genes (ARID1A, MLL3 and MLL) also occurred in 47% of the gastric cancers. We detected ARID1A mutations in 8% of tumors (9/110), which were associated with concurrent PIK3CA mutations and microsatellite instability. In functional assays, we observed both FAT4 and ARID1A to exert tumor-suppressor activity. Somatic inactivation of FAT4 and ARID1A may thus be key tumorigenic events in a subset of gastric cancers.
Paper Status
Curated
Genes Analysed
816
Mutated Samples
15
Total No. of Samples
15
This tab shows genes with mutations in the selected study/paper [more details]
Genes Samples CDS Mutation AA Mutation
This tab shows genes without mutations in the selected study/paper [more details]
Non-Mutant Genes Gene Id (COSG)
This tab shows samples without mutations in the selected study/paper [more details]
Non-Mutant Samples Sample Id (COSS)
This tab shows mutated samples in the selected study/paper [more details]
Sample Name Mutation Count
This tab shows non coding variant in the selected study/paper [more details]
Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq
This tab shows the copy number variation data for this study. Only variants (classified as gain or loss) are listed. [more details]
CNV Gene Sample Position Minor Allele Copy Number Average Ploidy

1. N/A represents cases where average ploidy value is not available( mostly ICGC samples). For some TCGA samples where minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, Ascat algorithm is used to calculate the average ploidy.

3. For CGP samples, Picnic algorithm is used to calculate the average ploidy.

Type
This tab shows a table of count of samples having gain or loss for all genes [more details]
Gene Gain Samples Loss Samples Samples Tested
This tab shows the fusion mutations observed in this sample [more details]
Gene Sample Name Id Sample(COSS) CDS Mutation Somatic status Zygosity Validated Type