GEO series

Mutational landscape of splicing genes and functional consequences across 33 cancer types

GSE100530 Homo sapiens Expression profiling by high throughput sequencing; Other 6 samples Submitted 2017/12/20 Platform GPL16791

Summary

Hotspot mutations in the spliceosome component genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of this pathway in cancer. However, a comprehensive survey of splicing factor mutations across tumor types has not yet been performed. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA) in order to discover recurrent mutations in spliceosome components, identifying 119 genes with significant non-silent mutation patterns, including mutation overrepresentation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). We used RNA sequencing data to identify altered splicing events associated with these spliceosome mutations. In addition, we were able to discover common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of the splicing pathway is common in solid tumors and may represent an underappreciated hallmark of tumorigenesis.

This dataset

Open GSE100530 in finder → Find more human RNA-seq datasets →

Download

Direct links to NCBI, no account and no request form: the whole study as GSE100530_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA392042 and SRA study SRP110582. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 29617667) ↗

Samples in this study

The sample list for this study is not cached yet. Press Sort into groups and it will be fetched from NCBI.

+ 6 more — browse all 6 samples with per-sample file links →

Similar datasets

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.