ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers
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.
Authors
- Lars Feuerbach (ORCID: https://orcid.org/0000-0003-1503-437X)
- Romina Royo (ORCID: https://orcid.org/0000-0003-3493-0874)
- Montserrat Puiggròs (ORCID: https://orcid.org/0000-0001-5034-7924)
- Tom Gutman
- Frédéric Jarlier (ORCID: https://orcid.org/0000-0002-8690-7898)
- Asier González (ORCID: https://orcid.org/0000-0002-9409-513X)
- Lucía Igual Estellés
- Philippe Hupé (ORCID: https://orcid.org/0000-0001-8468-3424)
- Marc Arbonés
- Benedikt Brors (ORCID: https://orcid.org/0000-0001-5940-3101)
- Henri de Soyres
- Salvador Capella-Gutiérrez (ORCID: https://orcid.org/0000-0002-0309-604X)
- Marta Gut
- David Torrents (ORCID: https://orcid.org/0000-0002-6086-9037)
- Nicolás Gaitán (ORCID: https://orcid.org/0009-0009-2979-2703)
- Lincoln D. Stein
- Alvaro Ferriz
- Rodrigo Martín (ORCID: https://orcid.org/0000-0002-2128-1329)
Institutions
- Ontario Institute for Cancer Research (CA)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Centre National de la Recherche Scientifique (FR)
- German Cancer Research Center (DE)
- Heidelberg University (DE)
- Université Paris Sciences et Lettres (FR)
- Barcelona Supercomputing Center (ES)
- Centro Nacional de Análisis Genómico (ES)
- Biologie cellulaire et Cancer (FR)
- Universitat Politècnica de Catalunya (ES)
Publication Details
- Journal
- Cell Genomics
- Published
- 2024-08-30
- DOI
- https://doi.org/10.1016/j.xgen.2024.100639
- Citations
- 1
- Primary Topic
- Cancer Genomics and Diagnostics
- Type
- article
- Field-Weighted Citation Impact
- 0.29
Funders
- Deutsches Krebsforschungszentrum
- Generalitat de Catalunya
- Conseil Régional, Île-de-France
- Sveučilište Josipa Jurja Strossmayera u Osijeku
- Canadian Institutes of Health Research
- Instituto de Salud Carlos III
- Agencia Estatal de Investigación