Evidence map›Paper›PMID 39216474›Full record

ArticleCell genomics2024

ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers.

Rodrigo Martín, Nicolás Gaitán, Frédéric Jarlier, Lars Feuerbach, Henri de Soyres, Marc Arbonés, Tom Gutman, Montserrat Puiggròs, Alvaro Ferriz, Asier Gonzalez and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2024. 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. 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

18 authors.

Rodrigo MartínLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Nicolás GaitánLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Frédéric JarlierInstitut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France.
Lars FeuerbachDivision of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Henri de SoyresInstitut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France.
Marc ArbonésLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Tom GutmanInstitut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France.
Montserrat PuiggròsLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Alvaro FerrizLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Asier GonzalezLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Lucía EstellesCentro Nacional de Análisis Genómico, Barcelona, Spain.
Ivo GutCentro Nacional de Análisis Genómico, Barcelona, Spain.
Salvador Capella-GutierrezLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Lincoln D SteinDepartment of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada.
Benedikt BrorsDivision of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany.
Romina RoyoLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
Philippe HupéInstitut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France; UMR144, CNRS, Paris, France.
David TorrentsLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. Electronic address: david.torrents@bsc.es.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.

Indexed as

GenomicsNeoplasmsGenome, HumanHumansINDEL MutationMedical OncologyPolymorphism, Single NucleotidePrecision MedicineSoftwarebenchmarkingbenchmarking databioinformaticscancer genomicsoncologysomatic variant calling

Identifiers

PMID39216474
PMCPMC11480849

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Registered trials

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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.