ArticlePloS one2019
Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.Scientific reports · 2024Pooled it
- Archived medical specimens as antemortem DNA references for disaster victim identification, optimization study following the October 7 massacre.International journal of legal medicine · 2026Article
- Pre-Analytical and Analytical Challenges in Whole-Exome Sequencing of Formalin-Fixed Paraffin-Embedded Breast and Prostate Cancer Tissue: A Real-World Multicenter Study.Diagnostics (Basel, Switzerland) · 2026Article
- Enhanced recovery of high-quality DNA from limited FFPE tissue for advancing cancer genomics.Scientific reports · 2026Article
- An Initial Indonesian Genome-Wide SNP-Array Study with Functional Variant Prioritization Reveals NASP and GPR78 Candidate SNVs in Hepatocellular Carcinoma.Biomedicines · 2026Article
- Cell-Free DNA-Based Theranostics for Inflammatory Disorders.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- New Candidate Reference Measurement Procedures for MET CNV Detection and Quantification Using Digital PCR.Biological procedures online · 2026Article
- Molecular diagnosis of suspected intestinal schistosomiasis in a non-endemic area of Yunnan Province, China.Infectious diseases of poverty · 2025Article
- Evaluation of the HumanMethylationEPIC v2.0 Bead Chip Using Low Quality and Quantity DNA Samples.Biological procedures online · 2025Article
- Assessing the suitability of formalin-fixed paraffin-embedded (FFPE) tissue for genome-wide association studies (GWAS).BMC research notes · 2025Article
- Sudden Cardiac Death: The Role of Molecular Autopsy with Next-Generation Sequencing.Diagnostics (Basel, Switzerland) · 2025Review
- Extraction, Purification, and Next-Generation Sequencing (NGS) Analysis of DNA and RNA from Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Genetic screening of FFPE breast cancer biopsies for theRevista panamericana de salud publica = Pan American journal of public health · 2025Article
- InDEL instability in two different tumoral tissues and its forensic significance.Forensic science, medicine, and pathology · 2024Article
- Somatic Molecular Heterogeneity in Bilateral Macronodular Adrenocortical Disease (BMAD) Differs Among the Pathological Subgroups.Endocrine pathology · 2024Article
- A pilot study on the detection of microsatellite instability using long mononucleotide repeats in solid tumors.Oncology letters · 2024Article
- Single-Cell Sequencing: High-Resolution Analysis of Cellular Heterogeneity in Autoimmune Diseases.Clinical reviews in allergy & immunology · 2024Review
- Comprehensive Diagnosis, Treatment, and Outcome ofPathogens (Basel, Switzerland) · 2024Article
- Comparative Analyses of Targeted Myeloid Cancer Next-Generation Sequencing Panel in Fresh Blood, Bone Marrow and FFPE Material.International journal of molecular sciences · 2024Article
- Updates in Genetic Testing for Head and Neck Vascular Anomalies.Oral and maxillofacial surgery clinics of North America · 2024Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Archival tissues represent a rich resource for clinical genomic studies, particularly when coupled with comprehensive medical records. Use of these in next generation sequencing (NGS) is a priority. Nine formalin-fixed paraffin-embedded (FFPE) DNA extraction methods were evaluated using twelve FFPE samples of varying tissue types. Quality assessment included total yield, percent dsDNA, fragment analysis and multiplex PCR. After assessment, three tissue types from four FFPE DNA methods were selected for NGS downstream evaluation, targeted and whole exome sequencing. In addition, two low input library protocols were evaluated for WES. Analysis revealed average coverage across the target regions for WES was ~20-30X for all four FFPE DNA extraction methods. For the targeted panels, the highest molecular tag coverage was obtained with the Kingfisher FFPE extraction method. The genotype concordance was 99% for the commonly called variant positions between all four extraction methods with the targeted PCR NGS panel and 96% with WES. Assessing quality of extracted DNA aids in selecting the optimal NGS approach, and the choice of both DNA extraction and library preparation approaches can impact the performance of archival tissue in NGS.
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