ArticlePloS one2018
Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits.Journal of translational medicine · 2025Article
- Comparing RNA extraction protocols from formalin-fixed paraffin-embedded microcore samples.PloS one · 2025Article
- Reliable RNA-seq analysis from FFPE specimens as a means to accelerate cancer-related health disparities research.PloS one · 2025Article
- Comparison of RNA-Sequencing Methods for Degraded RNA.International journal of molecular sciences · 2024Article
- A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- RNA-seq RNAaccess identified as the preferred method for gene expression analysis of low quality FFPE samples.PloS one · 2023Article
- The role of single nucleotide polymorphisms related to iron homeostasis in mesothelioma susceptibility after asbestos exposure: a genetic study on autoptic samples.Frontiers in public health · 2023Article
- A somatic hypermutation-based machine learning model stratifies individuals with Crohn's disease and controls.Genome research · 2023Article
- A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits.Molecular biology reports · 2022Article
- An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections.Biology methods & protocols · 2022Article
- Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.NPJ breast cancer · 2021Article
- Diagnostic utility of one-stop fusion gene panel to detect TFE3/TFEB gene rearrangement and amplification in renal cell carcinomas.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2021Article
- Molecular Mechanism of EGFR-TKI Resistance inCancers · 2021Review
- Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions.Genes · 2021Review
- Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation.BMC medical genomics · 2021Article
- Targeted Sequencing of Pancreatic Adenocarcinomas from Patients with Metachronous Pulmonary Metastases.Genes · 2020Article
- High yield gold nanoparticle-based DNA isolation method for human papillomaviruses genotypes from cervical cancer tissue samples.IET nanobiotechnology · 2020Article
- Protoblock - A biological standard for formalin fixed samples.Microbiome · 2020Article
- Evaluation of Extraction Methods for Clinical Metagenomic Assay.Microorganisms · 2020Article
- Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review.Diagnostics (Basel, Switzerland) · 2020Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.
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