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Reference

Cancer of the ampulla of Vater: analysis of the whole genome sequence exposes a potential therapeutic vulnerability.

Paper Id
COSP29197
Authors
Demeure MJ,Craig DW,Sinari S,Moses TM,Christoforides A,Dinh J,Izatt T,Aldrich J,Decker A,Baker A,Cherni I,Watanabe A,Koep L,Lake D,Hostetter G,Trent JM,Von Hoff DD and Carpten JD
Affiliation
Journal
Genome medicine 2012;4(7):56
ISSN:1756-994X
PUBMED:22762308
Abstract
ABSTRACT: BACKGROUND: Recent advances in the treatment of cancer have focused on targeting genomic aberrations with selective therapeutic agents. In rare tumors, where large-scale clinical trials are daunting, this targeted genomic approach offers a new perspective and hope for improved treatments. Cancers of the ampulla of Vater are rare tumors that comprise only about 0.2% of gastrointestinal cancers. Consequently, they are often treated as either distal common bile duct or pancreatic cancers. METHODS: We analyzed a DNA from a resected cancer of the ampulla of Vater and whole blood DNA, from a 63 year-old man who underwent a pancreaticoduodenectomy, by whole genome sequencing achieving 37 and 40x coverage respectively. We determined somatic mutations and structural alterations. RESULTS: We identified relevant aberrations including deleterious mutations of KRAS and SMAD4 as well as a homozygous focal deletion of the PTEN tumor suppressor gene. These findings suggest that these tumors have a distinct oncogenesis than either common bile duct cancer or pancreatic cancer. Furthermore, this combination of genomic aberrations suggests a therapeutic context for dual mTOR/PI3K inhibition. CONCLUSIONS: Whole genome sequencing can elucidate an oncogenic context and expose potential therapeutic vulnerabilities in rare cancers.
Paper Status
Curated
Genes Analysed
43
Mutated Samples
1
Total No. of Samples
1
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Genes Samples CDS Mutation AA Mutation
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Non-Mutant Genes Gene Id (COSG)
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Non-Mutant Samples Sample Id (COSS)
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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