ArticlePloS one2007
The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?
Article in PloS one, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
161 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Forensic analysis of formalin-fixed non-paraffin-embedded tissues: a comparative study of STR and mtDNA profiling.Forensic science, medicine, and pathology · 2026Article
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- High-quality histochemistry, immunohistochemistry, and immunofluorescence on xylene- and formalin-free paraffin-embedded tissues.PloS one · 2026Article
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- Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.Journal of translational medicine · 2025Article
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- Comprehensive Diagnosis, Treatment, and Outcome ofPathogens (Basel, Switzerland) · 2024Article
- Single nucleotide polymorphism within chromosome 8q24 is associated with prostate cancer development in Saudi Arabia.Asian journal of urology · 2024Article
- Comparison of diagnostic methods for detection of BRAFV600E mutation in ameloblastoma.Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology · 2024Article
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- Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros.Molecular biology and evolution · 2023Article
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
101 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
8 authors.
Funding
Abstract
Museums and pathology collections around the world represent an archive of genetic material to study populations and diseases. For preservation purposes, a large portion of these collections has been fixed in formalin-containing solutions, a treatment that results in cross-linking of biomolecules. Cross-linking not only complicates isolation of nucleic acid but also introduces polymerase "blocks" during PCR. A wide variety of methods exists for the recovery of DNA and RNA from archival tissues, and although a number of previous studies have qualitatively compared the relative merits of the different techniques, very few have undertaken wide scale quantitative comparisons. To help address this issue, we have undertaken a study that investigates the quality of nucleic acids recovered from a test panel of fixed specimens that have been manipulated following a number of the published protocols. These include methods of pre-treating the samples prior to extraction, extraction and nucleic acid purification methods themselves, and a post-extraction enzymatic repair technique. We find that although many of the published methods have distinct positive effects on some characteristics of the nucleic acids, the benefits often come at a cost. In addition, a number of the previously published techniques appear to have no effect at all. Our findings recommend that the extraction methodology adopted should be chosen carefully. Here we provide a quick reference table that can be used to determine appropriate protocols for particular aims.
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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.