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

Paper Id
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
Genome medicine 2012;4(7):56
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.
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Genes Analysed
Mutated Samples
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Genes Samples CDS Mutation AA Mutation
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This is a whole exome/systematic screen paper and the negatives for this paper should be inferred.

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Non-Mutant Samples Sample Id (COSS)
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Sample Name Mutation Count
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Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq
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Sample Gene Expression Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type Minor Allele Copy Number CN Segment Posn. Average Ploidy

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

2. For TCGA samples, the ASCAT algorithm was used to calculate the average ploidy.

3. For CGP samples, the PICNIC algorithm was used to calculate the average ploidy.

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Gene Sample Name Id Sample(COSS) CDS Mutation Somatic status Zygosity Validated Type