ArticlePloS one2017
Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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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
12 citing papers in PubMed, 27 citations in OpenAlex.
- Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.BioTechniques · 2025Article
- The ideal reporting ofPathologica · 2023Review
- Relapse timing is associated with distinct evolutionary dynamics in DLBCL.medRxiv : the preprint server for health sciences · 2023Article
- Results of the phase I CCTG IND.231 trial of CX-5461 in patients with advanced solid tumors enriched for DNA-repair deficiencies.Nature communications · 2022Article
- Enhancing Tumor Content through Tumor Macrodissection.Journal of visualized experiments : JoVE · 2022Article
- Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data.Frontiers in genetics · 2022Article
- Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data.NAR genomics and bioinformatics · 2021Article
- Integrative Analysis of miRNAs Identifies Clinically Relevant Epithelial and Stromal Subtypes of Head and Neck Squamous Cell Carcinoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells.Frontiers in genetics · 2021Article
- Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples.Nucleic acids research · 2019Article
- Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA.PloS one · 2019Article
- Epigenetic biomarkers: Current strategies and future challenges for their use in the clinical laboratory.Critical reviews in clinical laboratory sciencesReview
Corrections and comments
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Authors and funding
24 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification. These limitations and a number of other issues that span multiple steps from nucleic acid purification to library construction are addressed here. We optimized and automated a 96-well magnetic bead-based extraction protocol that can be scaled to large cohorts and is compatible with automation. Using sets of 32 and 91 individual FFPE samples respectively, we generated libraries from 100 ng of total RNA and DNA starting amounts with 95-100% success rate. The use of the resulting RNA in micro-RNA sequencing was also demonstrated. In addition to offering the potential of scalability and rapid throughput, the yield obtained with lower input requirements makes these methods applicable to clinical samples where tissue abundance is limiting.
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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.