ArticlePloS one2015
Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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
64 citing papers in PubMed, 108 citations in OpenAlex.
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- Exploring the somatic mutational landscape of ovarian cancer in Estonia.Acta oncologica (Stockholm, Sweden) · 2026Article
- The Molecular Landscape of CASTLE: A Rare Thymus-like Head and Neck Cancer.International journal of molecular sciences · 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
- Influence of pre-analytical factors on the success rates of smMIP and MLPA analyses in epithelial ovarian cancer.Virchows Archiv : an international journal of pathology · 2025Article
- Molecular diagnosis of suspected intestinal schistosomiasis in a non-endemic area of Yunnan Province, China.Infectious diseases of poverty · 2025Article
- High Prevalence of Human Papillomavirus in Vulvar Cancer Among Vietnamese Women: Implications for Vaccination Strategies.Cancer medicine · 2025Article
- Article
- Real-world application of targeted next-generation sequencing for identifying molecular variants in Asian non-small-cell lung cancer.BMC cancer · 2025Article
- Identification of Malignancy in Peritumoral Edema in Soft Tissue Sarcoma: A Novel Targeted Molecular Approach.Annals of surgical oncology · 2025Article
- Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis.Oncology letters · 2024Article
- Pathology Laboratory Archives: Conservation Quality of Nucleic Acids and Proteins for NSCLC Molecular Testing.Journal of personalized medicine · 2024Article
- Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation.NAR genomics and bioinformatics · 2024Article
- Next-Generation-Sequencing on fine needle aspirates in neck recurrence of thyroid cancers.European thyroid journal · 2024Article
- Validation of Modaplex POLE mutation assay in endometrial carcinoma.Virchows Archiv : an international journal of pathology · 2023Article
- Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels.Scientific reports · 2023Article
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies.International journal of legal medicine · 2023Article
- Exploratory genomic analysis of high-grade neuroendocrine neoplasms across diverse primary sites.Endocrine-related cancer · 2022Article
- Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens.Epidemiologia (Basel, Switzerland) · 2022Review
4 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
20 authors at 6 institutions in 1 country.
Funding
Abstract
Next Generation Sequencing (NGS) technologies are used to detect somatic mutations in tumors and study germ line variation. Most NGS studies use DNA isolated from whole blood or fresh frozen tissue. However, formalin-fixed paraffin-embedded (FFPE) tissues are one of the most widely available clinical specimens. Their potential utility as a source of DNA for NGS would greatly enhance population-based cancer studies. While preliminary studies suggest FFPE tissue may be used for NGS, the feasibility of using archived FFPE specimens in population based studies and the effect of storage time on these specimens needs to be determined. We conducted a study to determine whether DNA in archived FFPE high-grade ovarian serous adenocarcinomas from Surveillance, Epidemiology and End Results (SEER) registries Residual Tissue Repositories (RTR) was present in sufficient quantity and quality for NGS assays. Fifty-nine FFPE tissues, stored from 3 to 32 years, were obtained from three SEER RTR sites. DNA was extracted, quantified, quality assessed, and subjected to whole exome sequencing (WES). Following DNA extraction, 58 of 59 specimens (98%) yielded DNA and moved on to the library generation step followed by WES. Specimens stored for longer periods of time had significantly lower coverage of the target region (6% lower per 10 years, 95% CI: 3-10%) and lower average read depth (40x lower per 10 years, 95% CI: 18-60), although sufficient quality and quantity of WES data was obtained for data mining. Overall, 90% (53/59) of specimens provided usable NGS data regardless of storage time. This feasibility study demonstrates FFPE specimens acquired from SEER registries after varying lengths of storage time and under varying storage conditions are a promising source of DNA for NGS.
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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.