ArticleGenome research2015
The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers.
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Who cites it
111 citing papers in PubMed, 187 citations in OpenAlex.
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- Evaluating Immune Checkpoint Blockade in Metastatic Castration-Resistant Prostate Cancers with Deleterious CDK12 Alterations in the Phase 2 IMPACT Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Trial
- Randomized phase II study of the Bruton tyrosine kinase inhibitor acalabrutinib, alone or with pembrolizumab in patients with advanced pancreatic cancer.Journal for immunotherapy of cancer · 2020Trial
- FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026Article
- Messenger RNA From Canine Cytology Lymph Node Specimens Can Be Utilised for Gene Expression Profiling Using Digital RNA Counting.Veterinary and comparative oncology · 2026Article
- Genomic Determinants of Lethality and Therapeutic Vulnerability in Castration-Resistant Prostate Cancer.bioRxiv : the preprint server for biology · 2026Article
- Transcriptome predictors of second breast events in ductal carcinoma in situ: a case‒control study including Black and White women.Breast cancer research : BCR · 2026Article
- Prolonged Sample Storage Reshapes the mInternational journal of molecular sciences · 2026Article
- Diagnostic whole transcriptome sequencing in a series of 1233 FFPE solid tumor samples.British journal of cancer · 2026Article
- Molecular profiling of primary versus paired asynchronous metastatic clear cell renal cell carcinoma reveals heterogeneity in tumor immune microenvironment.Scientific reports · 2026Article
- Molecular Profiling of Primary versus Paired Asynchronous Metastatic Clear Cell Renal Cell Carcinoma Reveals Heterogeneity in Tumor Immune Microenvironment.Research square · 2025Article
- Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- Clinical Implementation of Expanded Solid Tumor Fusion Detection With Whole-Transcriptome Sequencing at an Academic Cancer Center.JCO precision oncology · 2025Article
- Androgen receptor-regulated lncRNA PRCAT71 promotes AR signaling through the interaction with KHSRP in prostate cancer.Science advances · 2025Article
- Transcriptomics and epigenomics datasets of primary brain cancers in formalin-fixed paraffin embedded format.Scientific data · 2025Article
- Laser-capture microdissection for spatial transcriptomics of immunohistochemically detected neurons.The Journal of biological chemistry · 2025Article
- Robust Cluster Prediction Across Data Types Validates Association of Sex and Therapy Response in GBM.Cancers · 2025Article
- Analysis of the Pattern of RNA Expression in the Skin of TR-Deficient Mice By RNA-seq.Methods in molecular biology (Clifton, N.J.) · 2025Article
51 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
Abstract
RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and clinical samples, especially when specimens are formalin-fixed. To facilitate the use of RNA sequencing beyond cell lines and in the clinical setting, we developed an exome-capture transcriptome protocol with greatly improved performance on degraded RNA. Capture transcriptome libraries enable measuring absolute and differential gene expression, calling genetic variants, and detecting gene fusions. Through validation against gold-standard poly(A) and Ribo-Zero libraries from intact RNA, we show that capture RNA-seq provides accurate and unbiased estimates of RNA abundance, uniform transcript coverage, and broad dynamic range. Unlike poly(A) selection and Ribo-Zero depletion, capture libraries retain these qualities regardless of RNA quality and provide excellent data from clinical specimens including formalin-fixed paraffin-embedded (FFPE) blocks. Systematic improvements across key applications of RNA-seq are shown on a cohort of prostate cancer patients and a set of clinical FFPE samples. Further, we demonstrate the utility of capture RNA-seq libraries in a patient with a highly malignant solitary fibrous tumor (SFT) enrolled in our clinical sequencing program called MI-ONCOSEQ. Capture transcriptome profiling from FFPE revealed two oncogenic fusions: the pathognomonic NAB2-STAT6 inversion and a therapeutically actionable BRAF fusion, which may drive this specific cancer's aggressive phenotype.
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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.