GRCh38 · COSMIC v91

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
Genetics of Breast Implant-Associated Anaplastic Large Cell Lymphoma (BIA-ALCL).
Paper ID
COSP46322
Authors
Oishi N, Miranda RN and Feldman AL
Affiliation
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.
Journal
Aesthetic surgery journal, 2019;39(Supplement_1):S14-S20
ISSN: 1527-330X
PMID: 30715169 (view at PubMed or Europe PMC)
Abstract
Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL), a newly included provisional entity in the 2016 revision of the World Health Organization classification, is a distinct form of CD30-positive T-cell non-Hodgkin lymphoma that arises in association with a breast implant after reconstructive or cosmetic surgery. In addition to its characteristic clinical presentation, recent studies using next-generation sequencing have revealed that BIA-ALCL has a unique pattern of genetic alterations. BIA-ALCL is consistently negative for ALCL-related gene rearrangements involving ALK, DUSP22, and TP63. However, the JAK-STAT3 pathway is constitutively activated in BIA-ALCL, which in some cases is associated with recurrent somatic mutations of JAK1 and/or STAT3. These activating mutations, which may be concurrent, are identified in 13% (3/23) and 26% (6/23) of BIA-ALCLs, respectively. Other genetic alterations include point mutations of DNMT3A and TP53. Although the number of examined cases has been limited, these findings suggest that BIA-ALCL shows more uniform molecular features than systemic and primary cutaneous ALCLs, which show considerable genetic heterogeneity. Targeted therapies inhibiting JAK-STAT signaling are being developed and may offer novel therapeutic options for patients with BIA-ALCL, especially those with advanced disease.
Paper Status
Listed
Genes Analysed
30
Mutated Samples
0
Total No. of Samples
0

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)