GRCh38 · COSMIC v87

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
Genetic analysis of 779 advanced differentiated and anaplastic thyroid cancers.
Paper ID
COSP45225
Authors
Pozdeyev N, Gay L, Sokol ES, Hartmaier RJ, Deaver KE, Davis SN, French JD, Vanden Borre P, LaBarbera DV, Tan AC, Schweppe RE, Fishbein L, Ross JS, Haugen BR and Bowles DW
Affiliation
Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus nikitapozdeyev@gmail.com.
Journal
Clinical cancer research : an official journal of the American Association for Cancer Research 2018
ISSN:1078-0432
PUBMED:29615459
Abstract
Purpose: To define the genetic landscape of advanced differentiated and anaplastic thyroid cancer and identify genetic alterations of potential diagnostic, prognostic and therapeutic significance.The genetic profiles of 583 advanced differentiated and 196 anaplastic thyroid cancers (ATC) generated with targeted next-generation sequencing cancer-associated gene panels MSK-IMPACT and FoundationOne were analyzed.Results: ATC had more genetic alterations per tumor, and pediatric papillary thyroid cancer had fewer genetic alterations per tumor when compared to other thyroid cancer types. DNA mismatch repair deficit and activity of APOBEC cytidine deaminases were identified as mechanisms associated with high mutational burden in a subset of differentiated and anaplastic thyroid cancers. Copy number losses and mutations of <i>CDKN2A</i> and <i>CDKN2B</i>, amplification of <i>CCNE1</i>, amplification of receptor tyrosine kinase genes <i>KDR, KIT</i> and <i>PDGFRA</i>, amplification of immune evasion genes <i>CD274, PDCD1LG2</i> and <i>JAK2</i> and activating point mutations in small GTPase <i>RAC1</i> were associated with ATC. An association of <i>KDR, KIT</i> and <i>PDGFRA</i> amplification with the sensitivity of thyroid cancer cells to lenvatinib was shown <i>in vitro</i> Three genetically distinct types of ATC are proposed.Conclusions: This large-scale analysis describes genetic alterations in a cohort of thyroid cancers enriched in advanced cases. Many novel genetic events previously not seen in thyroid cancer were found. Genetic alterations associated with anaplastic transformation were identified. An updated schematic of thyroid cancer genetic evolution is proposed.
Paper Status
Curated
Genes Analysed
751
Mutated Samples
604
Total No. of Samples
630

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]

Table Information

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This is a whole exome/systematic screen paper and the negatives for this paper should be inferred.

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)