Evidence map›Paper›PMID 29699497›Full record

ArticleBMC bioinformatics2018

Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data.

Jan Budczies, Nicole Pfarr, Eva Romanovsky, Volker Endris, Albrecht Stenzinger, Carsten Denkert

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022
    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

6 authors.

Jan BudcziesInstitute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany. jan.budczies@charite.de.ORCID 0000-0002-1959-2240
Nicole PfarrInstitute of Pathology, Technical University Munich (TUM), Munich, Germany.
Eva RomanovskyInstitute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.
Volker EndrisInstitute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
Albrecht StenzingerInstitute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
Carsten DenkertInstitute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.

Funding

Deutsche Krebshilfe TransLUMINAL-B
6 · The paper itself

Abstract

backgroundSomatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together with somatic mutations is highly desirable.

resultsIoncopy is a validated method and easy-to-use software for CNA calling from targeted NGS data. Copy number and significance of CNA are estimated for each gene in each sample. Copy number gains and losses are called after multiple testing corrections controlling FWER or FDR.

conclusionsIoncopy facilitates calling of CNAs in a cohort of tumors tissues with or without using normal (germline) DNA controls.

Indexed as

DNA Copy Number VariationsGenome, HumanSoftwareHigh-Throughput Nucleotide SequencingHumansNeoplasmsAmplicon sequencingCopy number alterationsNGSR Shiny

Identifiers

PMID29699497
PMCPMC5921540

What OpenQuestion holds

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LicenceCC BY
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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.