ArticleThe Journal of molecular diagnostics : JMD2013
Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens.
Article in The Journal of molecular diagnostics : JMD, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers, 2 of them syntheses 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
101 citing papers in PubMed, 2 syntheses or guidelines 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
- Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues.Toxicological sciences : an official journal of the Society of Toxicology · 2015Pooled it
- Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers.PloS one · 2015Trial
- Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA.PloS one · 2015Trial
- Feasibility of Comprehensive Genomic Profiling for Biliary Tract Cancer Using Transpapillary Biopsy Samples: A Prospective Study.Journal of hepato-biliary-pancreatic sciences · 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
- Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.Genome biology · 2026Article
- Genomic landscape and molecular subtypes of primary central nervous system lymphoma.Blood cancer journal · 2025Article
- Capturing breast cancers' copy-number landscape in routine pathology: Exploiting low-resolution, genome-wide sequencing to identify HRD and beyond.British journal of cancer · 2025Article
- Article
- Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.Journal of translational medicine · 2025Article
- Tissue-based genomic profiling of 300,000 tumors highlights the detection of variants with low allele fraction.NPJ precision oncology · 2025Article
- Personalized High-Resolution Genetic Diagnostics of Prostate Adenocarcinoma Guided by Multiparametric Magnetic Resonance Imaging: Results of a Pilot Study.International journal of molecular sciences · 2025Article
- Cryo-X-Ray Phase Contrast Imaging Enables Combined 3D Structural Quantification and Nucleic Acid Analysis of Myocardial Biopsies.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- SSCI: Self-Supervised Deep Learning Improves Network Structure for Cancer Driver Gene Identification.International journal of molecular sciences · 2024Article
- DNA methylation profiling to determine the primary sites of metastatic cancers using formalin-fixed paraffin-embedded tissues.Nature communications · 2023Article
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Real-World Use of Highly Sensitive Liquid Biopsy Monitoring in Metastatic Breast Cancer Patients Treated with Endocrine Agents after Exposure to Aromatase Inhibitors.International journal of molecular sciences · 2023Article
- A Clinician's Guide to Bioinformatics for Next-Generation Sequencing.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2023Review
- Exploratory genomic analysis of high-grade neuroendocrine neoplasms across diverse primary sites.Endocrine-related cancer · 2022Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Next-generation sequencing (NGS) has emerged as a powerful technique for the detection of genetic variants in the clinical laboratory. NGS can be performed using DNA from FFPE tissue, but it is unknown whether such specimens are truly equivalent to unfixed tissue for NGS applications. To address this question, we performed hybridization-capture enrichment and multiplexed Illumina NGS for 27 cancer-related genes using DNA from 16 paired fresh-frozen and routine FFPE lung adenocarcinoma specimens and conducted extensive comparisons between the sequence data from each sample type. This analysis revealed small but detectable differences between FFPE and frozen samples. Compared with frozen samples, NGS data from FFPE samples had smaller library insert sizes, greater coverage variability, and an increase in C to T transitions that was most pronounced at CpG dinucleotides, suggesting interplay between DNA methylation and formalin-induced changes; however, the error rate, library complexity, enrichment performance, and coverage statistics were not significantly different. Comparison of base calls between paired samples demonstrated concordances of >99.99%, with 96.8% agreement in the single-nucleotide variants detected and >98% accuracy of NGS data when compared with genotypes from an orthogonal single-nucleotide polymorphism array platform. This study demonstrates that routine processing of FFPE samples has a detectable but negligible effect on NGS data and that these samples can be a reliable substrate for clinical NGS testing.
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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.