ArticleGenome medicine2013
Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies.
Article in Genome medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Are pre-analytical factors fully considered in forensic FFPE molecular analyses? A systematic review reveals the need for standardised procedures.International journal of legal medicine · 2025Pooled it
- A predictive endocrine resistance index accurately stratifies luminal breast cancer treatment responders and nonresponders.The Journal of clinical investigation · 2025Trial
- Perspectives From an Expert-Guided Discussion on Maximizing the Research Potential of Small Biopsy Tissue.JCO precision oncology · 2026Article
- Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology.Nature communications · 2025Article
- scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.Nature communications · 2025Article
- μMap-FFPE: A High-Resolution Protein Proximity Labeling Platform for Formalin-Fixed Paraffin-Embedded Tissue Samples.Journal of the American Chemical Society · 2025Article
- Review
- Real-world data analysis for factors influencing the quality check status in FoundationOne CDx cancer genomic profiling tests.Scientific reports · 2025Article
- Comparing RNA extraction protocols from formalin-fixed paraffin-embedded microcore samples.PloS one · 2025Article
- Comparison between Fluorimetry (Qubit) and Spectrophotometry (NanoDrop) in the Quantification of DNA and RNA Extracted from Frozen and FFPE Tissues from Lung Cancer Patients: A Real-World Use of Genomic Tests.Medicina (Kaunas, Lithuania) · 2021Article
- A new method to accurately identify single nucleotide variants using small FFPE breast samples.Briefings in bioinformatics · 2021Article
- Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions.Genes · 2021Review
- Article
- A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples.iScience · 2021Article
- In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network.Journal of translational medicine · 2019Review
- Review
- An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer.Translational oncology · 2019Article
- Design, Optimization, and Multisite Evaluation of a Targeted Next-Generation Sequencing Assay System for Chimeric RNAs from Gene Fusions and Exon-Skipping Events in Non-Small Cell Lung Cancer.The Journal of molecular diagnostics : JMD · 2019Article
- Considerations and quality controls when analyzing cell-free tumor DNA.Biomolecular detection and quantification · 2019Article
- DNA extraction from FFPE tissue samples - a comparison of three procedures.Contemporary oncology (Poznan, Poland) · 2019Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay ('QFI-PCR') that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing.
Identifiers
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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.