ArticleNucleic acids research2014
Integrated RNA and DNA sequencing improves mutation detection in low purity tumors.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 84 citations in OpenAlex.
- Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Trial
- Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer.The Journal of clinical investigation · 2018Trial
- Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations.NPJ precision oncology · 2025Article
- Review
- A Genomic Analysis of Esophageal Squamous Cell Carcinoma in Eastern Africa.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2023Article
- Article
- Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways.Cell reports. Medicine · 2022Article
- Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant.NPJ breast cancer · 2022Article
- Organocatalyst treatment improves variant calling and mutant detection in archival clinical samples.Scientific reports · 2022Article
- Intratumor genetic heterogeneity and clonal evolution to decode endometrial cancer progression.Oncogene · 2022Article
- DETexT: An SNV detection enhancement for low read depth by integrating mutational signatures into TextCNN.Frontiers in genetics · 2022Article
- RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data.Frontiers in genetics · 2022Article
- Detecting Medium and Large Insertions and Deletions with transIndel.Methods in molecular biology (Clifton, N.J.) · 2022Article
- UNMASC: tumor-only variant calling with unmatched normal controls.NAR cancer · 2021Article
- Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures.DNA repair · 2021Review
- Multi-omics approaches in cancer research with applications in tumor subtyping, prognosis, and diagnosis.Computational and structural biotechnology journal · 2021Review
- The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome.EMBO molecular medicine · 2020Article
- Article
- Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations.Biomolecules · 2020Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
Identifying somatic mutations is critical for cancer genome characterization and for prioritizing patient treatment. DNA whole exome sequencing (DNA-WES) is currently the most popular technology; however, this yields low sensitivity in low purity tumors. RNA sequencing (RNA-seq) covers the expressed exome with depth proportional to expression. We hypothesized that integrating DNA-WES and RNA-seq would enable superior mutation detection versus DNA-WES alone. We developed a first-of-its-kind method, called UNCeqR, that detects somatic mutations by integrating patient-matched RNA-seq and DNA-WES. In simulation, the integrated DNA and RNA model outperformed the DNA-WES only model. Validation by patient-matched whole genome sequencing demonstrated superior performance of the integrated model over DNA-WES only models, including a published method and published mutation profiles. Genome-wide mutational analysis of breast and lung cancer cohorts (n = 871) revealed remarkable tumor genomics properties. Low purity tumors experienced the largest gains in mutation detection by integrating RNA-seq and DNA-WES. RNA provided greater mutation signal than DNA in expressed mutations. Compared to earlier studies on this cohort, UNCeqR increased mutation rates of driver and therapeutically targeted genes (e.g. PIK3CA, ERBB2 and FGFR2). In summary, integrating RNA-seq with DNA-WES increases mutation detection performance, especially for low purity tumors.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.