ArticleCell reports2016
Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer.
Article in Cell reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 45 citations in OpenAlex.
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- Copy number alteration is an independent prognostic biomarker in triple-negative breast cancer patients.Breast cancer (Tokyo, Japan) · 2023Article
- Widespread hypertranscription in aggressive human cancers.Science advances · 2022Article
- Detecting Medium and Large Insertions and Deletions with transIndel.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The expressed mutational landscape of microsatellite stable colorectal cancers.Genome medicine · 2021Article
- Breast Cancer and the Other Non-Coding RNAs.International journal of molecular sciences · 2021Review
- Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts.Molecular therapy. Nucleic acids · 2020Article
- GeTallele: A Method for Analysis of DNA and RNA Allele Frequency Distributions.Frontiers in bioengineering and biotechnology · 2020Article
- Targeted-Gene Sequencing to Catch Triple Negative Breast Cancer Heterogeneity before and after Neoadjuvant Chemotherapy.Cancers · 2019Article
- Genomic and transcriptomic characterisation of undifferentiated pleomorphic sarcoma of bone.The Journal of pathology · 2019Article
- Overexpression of MUC1 predicts poor prognosis in patients with breast cancer.Oncology reports · 2019Article
- ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching.Journal of proteome research · 2018Article
- Network integration of multi-tumour omics data suggests novel targeting strategies.Nature communications · 2018Article
- Genetic Mechanisms of Immune Evasion in Colorectal Cancer.Cancer discovery · 2018Article
- Systematic pan-cancer analysis of somatic allele frequency.Scientific reports · 2018Article
- Indel detection from DNA and RNA sequencing data with transIndel.BMC genomics · 2018Article
- Pan-cancer analysis of somatic mutations and transcriptomes reveals common functional gene clusters shared by multiple cancer types.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
38 authors at 12 institutions in 7 countries.
Funding
Abstract
Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation.
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