ArticlePloS one2014
RADIA: RNA and DNA integrated analysis for somatic mutation detection.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 93 citations in OpenAlex.
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- Immune gene diversity and STING1 variants in shaping cancer immunity across different genetic ancestry populations.Cell reports · 2026Article
- MutAnt: mutation annotation tool predicts deleteriousness of missense mutations and improves mutation calling from transcriptomics.Human genetics · 2025Article
- Scaling for African Inclusion in High-Throughput Whole Cancer Genome Bioinformatic Workflows.Cancers · 2025Review
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- Insights into targeting LKB1 in tumorigenesis.Genes & diseases · 2025Review
- 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
- Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery.Journal for immunotherapy of cancer · 2023Review
- Control-independent mosaic single nucleotide variant detection with DeepMosaic.Nature biotechnology · 2023Article
- Validation of genetic variants from NGS data using deep convolutional neural networks.BMC bioinformatics · 2023Article
- Article
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- Integrated analysis of genes encoding ATP-dependent chromatin remodellers identifies CHD7 as a potential target for colorectal cancer therapy.Clinical and translational medicine · 2022Article
- Identification of neoantigens for individualized therapeutic cancer vaccines.Nature reviews. Drug discovery · 2022Review
- Systematic illumination of druggable genes in cancer genomes.Cell reports · 2022Article
- Detecting Medium and Large Insertions and Deletions with transIndel.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Somatic and Germline Variant Calling from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- PAK3 is a key signature gene of the glioma proneural subtype and affects its proliferation, differentiation and growth.Cellular oncology (Dordrecht, Netherlands) · 2021Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on comparing the normal and tumor genomes from the same individual. In recent years, it has become routine for projects like The Cancer Genome Atlas (TCGA) to also sequence the tumor RNA. Here we present RADIA (RNA and DNA Integrated Analysis), a novel computational method combining the patient-matched normal and tumor DNA with the tumor RNA to detect somatic mutations. The inclusion of the RNA increases the power to detect somatic mutations, especially at low DNA allelic frequencies. By integrating an individual's DNA and RNA, we are able to detect mutations that would otherwise be missed by traditional algorithms that examine only the DNA. We demonstrate high sensitivity (84%) and very high precision (98% and 99%) for RADIA in patient data from endometrial carcinoma and lung adenocarcinoma from TCGA. Mutations with both high DNA and RNA read support have the highest validation rate of over 99%. We also introduce a simulation package that spikes in artificial mutations to patient data, rather than simulating sequencing data from a reference genome. We evaluate sensitivity on the simulation data and demonstrate our ability to rescue back mutations at low DNA allelic frequencies by including the RNA. Finally, we highlight mutations in important cancer genes that were rescued due to the incorporation of the RNA.
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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.