Evidence map›Paper›PMID 33333623›Full record

ArticlePathology international2021

Evaluation of clinical formalin-fixed paraffin-embedded tissue quality for targeted-bisulfite sequencing.

Hideki Ohmomo, Shohei Komaki, Kanako Ono, Yoichi Sutoh, Tsuyoshi Hachiya, Eri Arai, Hiroyuki Fujimoto, Teruhiko Yoshida, Yae Kanai, Makoto Sasaki and 1 more

Open access · hybridAbstract readComparative StudyEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Pathology international, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.5field-weighted citation impact, top 36% of its field
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 7 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 4 institutions in 3 countries.

Hideki OhmomoIwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.ORCID https://orcid.org/0000-0002-3524-6524
Shohei KomakiIwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.
Kanako OnoIwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.
Yoichi SutohIwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.
Tsuyoshi HachiyaIwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.
Eri AraiDepartment of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.
Hiroyuki FujimotoDepartment of Urology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo, Tokyo, 104-0045, Japan.
Teruhiko YoshidaDepartment of Clinical Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo, Tokyo, 104-0045, Japan.
Yae KanaiDepartment of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.
Makoto SasakiIwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.
Atsushi ShimizuIwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.ORCID http://orcid.org/0000-0001-8307-2461
Iwate Medical University · JPKeio University Hospital · JPNational Cancer Centre Japan · JPNational Cancer Research Institute · GB

Funding

Japan Agency for Medical Research and Development JP17km0105004
6 · The paper itself

Abstract

Formalin-fixed paraffin-embedded (FFPE) tissues are promising biological resources for genetic research. Recent improvements in DNA extraction from FFPE samples allowed the use of these tissues for multiple sequencing methods. However, fundamental research addressing the application of FFPE-derived DNA for targeted-bisulfite sequencing (TB-seq) is lacking. Here, we evaluated the suitability of FFPE-derived DNA for TB-seq. We conducted TB-seq using FFPE-derived DNA and corresponding fresh frozen (FF) tissues of patients with kidney cancer and compared the quality of DNA, libraries, and TB-seq statistics between the two preservation methods. The approximately 600-bp average fragment size of the FFPE-derived DNA was significantly shorter than that of the FF-derived DNA. The sequencing libraries constructed using FFPE-derived DNA and the mapping ratio were approximately 10 times and 10% lower, respectively, than those constructed using FF-derived DNA. In the mapped data of FFPE-derived DNA, duplicated reads accounted for > 60% of the obtained sequence reads, with lower mean on-target coverage. Therefore, the standard TB-seq protocol is inadequate for obtaining high-quality data for epigenetic analysis from FFPE-derived DNA, and technical improvements are necessary for enabling the use of archived FFPE resources.

Indexed as

CryopreservationFixativesFormaldehydeCpG IslandsDNADNA MethylationEpigenesis, GeneticHumansKidney NeoplasmsOligonucleotide Array Sequence AnalysisParaffin EmbeddingSequence Analysis, DNASulfitesTissue FixationDNAFixativesFormaldehydehydrogen sulfiteSulfitesDNA methylationEpigeneticsFormalin-fixed paraffin-embedded tissueFresh frozen tissueTargeted-bisulfite sequencing

Identifiers

PMID33333623
PMCPMC7898333
OpenAlexW3110834639

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.