ArticleThe Journal of surgical research2017
Formalin-fixed paraffin-embedded sample conditions for deep next generation sequencing.
Article in The Journal of surgical research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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.
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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
33 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
- Prevalence of human papillomavirus detection in ovarian cancer: a meta-analysis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2021Pooled it
- Perspectives From an Expert-Guided Discussion on Maximizing the Research Potential of Small Biopsy Tissue.JCO precision oncology · 2026Article
- Detection of TERT Promoter Mutations in Papillary Thyroid Carcinoma Using Droplet Digital PCR and Their Association with Aggressive Tumor Features.International journal of molecular sciences · 2026Article
- Tissue gene expression analysis approach in a context of high technical and biological heterogeneity.BMC research notes · 2025Article
- Protein Expression, Amplification, and Mutation ofAnimals : an open access journal from MDPI · 2024Article
- Article
- Evaluation of pancreatic cancer specimens for comprehensive genomic profiling.Pathology international · 2024Article
- Pathology Laboratory Archives: Conservation Quality of Nucleic Acids and Proteins for NSCLC Molecular Testing.Journal of personalized medicine · 2024Article
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Copy number alteration is an independent prognostic biomarker in triple-negative breast cancer patients.Breast cancer (Tokyo, Japan) · 2023Article
- A Genetic and Immunohistochemical Analysis of Helicobacter pylori Phenotypes and p27 Expression in Adenocarcinoma Patients in Jordan.Journal of epidemiology and global health · 2023Article
- Areas of Crush Nuclear Streaming Should Be Included as Tumor Content in the Era of Molecular Diagnostics.Cancers · 2023Article
- Validation of p53 Immunohistochemistry (PAb240 Clone) in Canine Tumors with Next-Generation Sequencing (NGS) Analysis.Animals : an open access journal from MDPI · 2023Article
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2022Article
- A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits.Molecular biology reports · 2022Article
- Delivering precision oncology to patients with cancer.Nature medicine · 2022Review
- Article
- Epitachophoresis is a novel versatile total nucleic acid extraction method.Scientific reports · 2021Article
- Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer.BMC microbiology · 2021Article
- Validation of an NGS Panel Designed for Detection of Actionable Mutations in Tumors Common in Latin America.Journal of personalized medicine · 2021Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 2 countries.
Funding
Abstract
introductionPrecision medicine is only possible in oncology practice if targetable genes in fragmented DNA, such as DNA from formalin-fixed paraffin-embedded (FFPE) samples, can be sequenced using next generation sequencing (NGS). The aim of this study was to examine the quality and quantity of DNA from FFPE cancerous tissue samples from surgically resected and biopsy specimens.
methodsDNA was extracted from unstained FFPE tissue sections prepared from surgically resected specimens of breast, colorectal and gastric cancer, and biopsy specimens of breast cancer. A total quantity of DNA ≥60 ng from a sample was considered adequate for NGS. The DNA quality was assessed by Q-ratios, with a Q-ratio >0.1 considered sufficient for NGS.
resultsThe Q-ratio for DNA from FFPE tissue processed with neutral-buffered formalin was significantly better than that processed with unbuffered formalin. All Q-ratios for DNA from breast, colorectal and gastric cancer samples indicated DNA levels sufficient for NGS. DNA extracted from gastric cancer FFPE samples prepared within the last 7 years is suitable for NGS analysis, whereas those older than 7 years may not be suitable. Our data suggested that adequate amounts of DNA can be extracted from FFPE samples, not only of surgically resected tissue but also of biopsy specimens.
conclusionsThe type of formalin used for fixation and the time since FFPE sample preparation affect DNA quality. Sufficient amounts of DNA can be extracted from FFPE samples of both surgically resected and biopsy tissue, thus expanding the potential diagnostic uses of NGS in a clinical setting.
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