ArticleThe Journal of molecular diagnostics : JMD2014
cDNA hybrid capture improves transcriptome analysis on low-input and archived samples.
Article in The Journal of molecular diagnostics : JMD, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed, 47 citations in OpenAlex.
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- Description of two cases of follicular dendritic cell sarcoma, including next-generation sequencing analysis.Diagnostic pathology · 2025Article
- Transcriptomics and epigenomics datasets of primary brain cancers in formalin-fixed paraffin embedded format.Scientific data · 2025Article
- Solving Missing Heritability in Patients With Familial Adenomatous Polyposis With DNA-RNA Paired Testing.JCO precision oncology · 2024Article
- Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis.NAR cancer · 2023Article
- RNA-seq RNAaccess identified as the preferred method for gene expression analysis of low quality FFPE samples.PloS one · 2023Article
- From bulk, single-cell to spatial RNA sequencing.International journal of oral science · 2021Review
- Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples.RNA biology · 2020Article
- pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens.Cancer immunology research · 2020Article
- Changing Technologies of RNA Sequencing and Their Applications in Clinical Oncology.Frontiers in oncology · 2020Review
- A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples.BMC genomics · 2019Article
- Cancer transcriptome profiling at the juncture of clinical translation.Nature reviews. Genetics · 2018Review
- Robust transcriptional signatures for low-input RNA samples based on relative expression orderings.BMC genomics · 2017Article
- Exome-capture RNA sequencing of decade-old breast cancers and matched decalcified bone metastases.JCI insight · 2017Article
- Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors.The Journal of molecular diagnostics : JMD · 2017Article
- Neoantigens in immunotherapy and personalized vaccines: Implications for head and neck squamous cell carcinoma.Oral oncology · 2017Review
- Breast Cancer Neoantigens Can Induce CD8Cancer immunology research · 2017Article
- Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations.Journal of visualized experiments : JoVE · 2016Article
- Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.Nucleic acids research · 2016Review
- Gut microbiota, metabolites and host immunity.Nature reviews. Immunology · 2016Review
Corrections and comments
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Authors and funding
15 authors at 1 institution in 1 country.
Funding
Abstract
The use of massively parallel sequencing for studying RNA expression has greatly enhanced our understanding of the transcriptome through the myriad ways these data can be characterized. In particular, clinical samples provide important insights about RNA expression in health and disease, yet these studies can be complicated by RNA degradation that results from the use of formalin as a clinical preservative and by the limited amounts of RNA often available from these precious samples. In this study we describe the combined use of RNA sequencing with an exome capture selection step to enhance the yield of on-exon sequencing read data when compared with RNA sequencing alone. In particular, the exome capture step preserves the dynamic range of expression, permitting differential comparisons and validation of expressed mutations from limited and FFPE preserved samples, while reducing the data generation requirement. We conclude that cDNA hybrid capture has the potential to significantly improve transcriptome analysis from low-yield FFPE material.
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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.