GRCh38 · COSMIC v89

Overview

This section shows a general overview of information for the selected study (COSU identifier) or publication (COSP identifier). Studies may have been performed by the Sanger Institute Cancer Genome Project, or imported from the ICGC/TCGA. You can see more information on the help pages.

Reference
Mutational landscape of combined hepatocellular-cholangiocarcinoma and its clinicopathological significance.
Paper ID
COSP42266
Authors
Sasaki M, Sato Y and Nakanuma Y
Affiliation
Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan. m8sasaki@med.kanazawa-u.ac.jp.
Journal
Histopathology, 2016
ISSN: 1365-2559
PMID: 27634656 (view at PubMed or Europe PMC)
Abstract
Combined hepatocellular-cholangiocarcinoma (cHC-CC), which generally has a poor prognosis, comprises of hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and diverse components with intermediate features between HCC and CC. Histological subtypes with stem cell features (the SC subtype) have different clinicopathological significance in cHC-CC. The mutational status may reflect the clinicopathological subgroup of cHC-CC together with the histological subtype.Methods: We examined the mutational statuses of KRAS, IDH1 or 2 (IDH1/2), ARID1A, the TERT promoter, and p53 and their relationships with clinicopathological features in 53 patients with cHC-CC. Background liver diseases were hepatitis B (n=9), hepatitis C (22), alcohol (5), nonalcoholic fatty liver disease (NAFLD) (8), and unknown (9).Results: Mutations in KRAS, IDH1/2, ARID1A, the TERT promoter and p53 were detected in 4 (7.5%), 6 (11.8%) 7 (13.2%), 16 (31.3%), and 24 patients (45.3%), respectively. KRAS mutations correlated with higher histological diversity scores and a higher M-factor (p<0.05). ARID1A mutations correlated with alcohol, smaller tumor sizes, lower grade of co-existent HCC, and AFP-positivity and were associated with cholangiolocellular carcinoma subtype-predominant (p<0.05). TERT promoter mutations correlated with hepatitis B, an intermediate subtype-predominant histology, higher clinical stage, and higher N-factor (p<0.05) and were associated with gender (female-predominant) and previous therapy. p53 mutations correlated with AFP-positivity (p<0.05).Conclusion: The results of the mutational analysis revealed that cHC-CC has diverse types of mutations and also that mutations in the TERT promoter and ARID1A may reflect etiological impact, different histological subtypes, histogenesis and tumor aggressiveness. These results suggest the potential efficacy of molecular-based subclassification of cHC-CC. This article is protected by copyright. All rights reserved.
Paper Status
Curated
Genes Analysed
4
Mutated Samples
23
Total No. of Samples
51

Mutation Matrix

This section shows the correlation plot between the top 20 genes and samples. There is more information in our help pages.

Genes

This table shows genes with mutations in the selected study/paper [more details]
Genes Mutated Samples
This table shows genes without mutations in the selected study/paper [more details]
Non-Mutant Genes Gene Id (COSG)

Variants

This tab shows genes with mutations in the selected study/paper [more details]

Genes Samples CDS Mutation AA Mutation

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 FATHMM-MKL

This tab shows the gene expression and copy number variation data for this study [more details]

Table Information

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The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

Click here to include all copy number data. For more detailed information about copy number data and gain/loss definitions click here.

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.

CNV

This table lists the samples in the selected study which have low/high methylation for each gene. [more details]

No data

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

Samples

This table shows mutated samples in the selected study/paper.

Sample Name Mutation Count

This table shows samples without mutations in the selected study/paper.

Non-Mutant Samples Sample Id (COSS)