Evidence map›Paper›PMID 33100132›Full record

ArticleEpigenetics2021

AmpliconDesign - an interactive web server for the design of high-throughput targeted DNA methylation assays.

Maximilian Schönung, Jana Hess, Pascal Bawidamann, Sina Stäble, Joschka Hey, Jens Langstein, Yassen Assenov, Dieter Weichenhan, Pavlo Lutsik, Daniel B Lipka

Abstract read
In one paragraph

Article in Epigenetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
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

2 citing papers in PubMed.

  1. Methods in DNA methylation array dataset analysis: A review.Computational and structural biotechnology journal · 2024
    Review
  2. Article
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

10 authors.

Maximilian SchönungSection Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.ORCID 0000-0002-9778-9698
Jana HessSaarland University, Saarbrücken, Germany.
Pascal BawidamannDepartment of Informatics, Technical University of Munich, Garching, Germany.
Sina StäbleSection Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.ORCID 0000-0002-5962-2440
Joschka HeyFaculty of Biosciences, Heidelberg University, Heidelberg, Germany.ORCID 0000-0003-2842-764X
Jens LangsteinSection Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.
Yassen AssenovDivision of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.ORCID 0000-0002-6992-2092
Dieter WeichenhanDivision of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Pavlo LutsikDivision of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Daniel B LipkaSection Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.ORCID 0000-0001-5081-7869

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Targeted analysis of DNA methylation patterns based on bisulfite-treated genomic DNA (BT-DNA) is considered as a gold-standard for epigenetic biomarker development. Existing software tools facilitate primer design, primer quality control or visualization of primer localization. However, high-throughput design of primers for BT-DNA amplification is hampered by limits in throughput and functionality of existing tools, requiring users to repeatedly perform specific tasks manually. Consequently, the design of PCR primers for BT-DNA remains a tedious and time-consuming process. To bridge this gap, we developed

Indexed as

DNA MethylationSulfitesEpigenomicsHigh-Throughput Nucleotide SequencingPolymerase Chain ReactionSequence Analysis, DNASoftwareSulfitesanalysis pipelinebisulfite sequencingDNA methylationepitypermassarrayprimer designtargeted sequencing

Identifiers

PMID33100132
PMCPMC8451469

What OpenQuestion holds

Textmetadata
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.