GRCh38 · COSMIC v92

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
Impact of splicing factor mutations on clinical features in patients with myelodysplastic syndromes.
Paper ID
COSP47580
Authors
Shingai N, Harada Y, Iizuka H, Ogata Y, Doki N, Ohashi K, Hagihara M, Komatsu N and Harada H
Affiliation
Department of Hematology, Juntendo University School of Medicine, Tokyo, Japan.
Journal
International journal of hematology, 2018;108(6):598-606
ISSN: 1865-3774
PMID: 30353274 (view at PubMed or Europe PMC)
Abstract
Splicing factor gene mutations are found in 60-70% of patients with myelodysplastic syndromes (MDS). We investigated the effects of splicing factor gene mutations on the diagnosis, patient characteristics, and prognosis of MDS. A total of 106 patients with MDS were included. The percentage of patients with MDS with ring sideroblasts (14.15%) as per the 2017 WHO classification was significantly higher than that of patients with refractory anemia with ring sideroblasts (2.88%) as per the 2008 WHO classification (P = 0.005). Splicing factor mutations were detected in 32 patients (13 SF3B1, 8 U2AF1, and 11 SRSF2), and the mutations were mutually exclusive. Significant differences were observed in the mean corpuscular volume, platelet count, bone marrow myeloid:erythroid ratio, and megakaryocyte count in patients with different mutations. SRSF2 mutations were associated with a high cumulative incidence of red blood cell transfusion dependence, while SF3B1 mutations were associated with a low cumulative incidence of platelet concentrate transfusion dependence. Presence of SF3B1 mutation was a significant univariate predictor of overall survival, but become nonsignificant in the multivariate model. Although many factors also could affect survival, these results suggest that splicing factor mutations contribute to distinct MDS phenotypes, including patient characteristics and clinical courses.
Paper Status
Curated
Genes Analysed
11
Mutated Samples
32
Total No. of Samples
106

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)