Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

Abstract

Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects alternative splicing events and tumor variants by reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more alternative splicing events than normal samples. Association analysis of somatic variants with alternative splicing events confirmed known trans associations with variants in SF3B1 and U2AF1 and identified additional trans-acting variants (e.g., TADA1, PPP2R1A). Many tumors have thousands of alternative splicing events not detectable in normal samples; on average, we identified ≈930 exon-exon junctions ("neojunctions") in tumors not typically found in GTEx normals. From Clinical Proteomic Tumor Analysis Consortium data available for breast and ovarian tumor samples, we confirmed ≈1.7 neojunction- and ≈0.6 single nucleotide variant-derived peptides per tumor sample that are also predicted major histocompatibility complex-I binders ("putative neoantigens").

Hsa‐miR‐139‐5p is a prognostic thyroid cancer marker involved in HNRNPF‐mediated alternative splicing

“…It has been reported to mediate the alternative splicing of multiple genes involved in different cancer‐related processes, such as the epithelial to mesenchymal transition and resistance to therapy . Recent reports have shown that the activity of alternative splicing regulators is recurrently altered in cancer, and this affects transcripts balance of key genes involved in cancer‐related pathways …”

Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions

“…3,39,45,46 Additionally, tumor transcriptional and/or splicing profiles may differ from reference profiles, resulting in miscounts and impacting the TMB score reported. 47,48 To date, most of the published studies have assessed TMB in solid tumor samples; however, blood TMB assessment assays are increasingly being used to assess TMB association with response to immune checkpoint inhibitors ( Preanalytical Sample type FFPE samples may harbor artefactual deamination alterations that may impact mutation calling and TMB calculation 56,57 Tumor purity Infiltration of tumor with immune or TME cells may impact TMB score (lower tumor purity is associated with reduced sensitivity) 32 Sequencing parameters Genomic region covered TMB score will depend on panel size and genomic region covered. Greater panel sizes are associated with more precise TMB estimated values 4,[62][63][64][65][66][67][68][69] Genes included in panel Gene selection in panels is biased toward frequently mutated cancerassociated genes, and mutation patterns of these genes are often nonrandom.…”

“…How factors impact TMB score Alternative splicing patterns are dependent on tumor types, and some tumor types have higher TMB than others2,47 …”

Massive computational identification of somatic variants in exonic splicing enhancers using The Cancer Genome Atlas

“…Recently, several studies have reported the identification of splicing patterns using TCGA datasets. Kahles et al identified approximately 173 000 tumor‐specific alternative splicing events and 251 000 exon‐exon junctions using tumor datasets from 8705 patients . Shirley et al showed that 341 486 variants had a significant impact on mRNA splicing, and approximately 70% of these variants were not registered in the dbSNP database .…”

“…Kahles et al identified approximately 173 000 tumor-specific alternative splicing events and 251 000 exon-exon junctions using tumor datasets from 8705 patients. 42 Shirley et al showed that 341 486 variants had a significant impact on mRNA splicing, and approximately 70% of these variants were not registered in the dbSNP database. 43,44 Furthermore, these studies could analyze all genes and identify novel splicing variants because of integrated analyses using raw sequence data such as FASTQ or BAM files.…”