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Protocols

CGI specifications

Information


Unique identifier OMICS_15412
Name CGI
Alternative name Cancer Genome Interpreter
Interface Web user interface, Application programming interface
Restrictions to use None
Input data The list of genomic alterations detected in a tumor sample.
Output data An interactive report.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline CGI Team

Publication for Cancer Genome Interpreter

CGI citations

 (6)
library_books

New additions to the cancer precision medicine toolkit

2018
Genome Med
PMCID: 5899382
PMID: 29653583
DOI: 10.1186/s13073-018-0540-7

[…] y by two different groups but aimed at the same goals. Each tool has unique aspects that may indeed facilitate the interpretation bottleneck of NGS-based cancer diagnostics. One article describes the Cancer Genome Interpreter (CGI) tool [] developed under the leadership of Nuria Lopez-Bigas, whose group has previously contributed important tools that predict cancer variant functionality [] and ide […]

library_books

DGIdb 3.0: a redesign and expansion of the drug–gene interaction database

2017
Nucleic Acids Res
PMCID: 5888642
PMID: 29156001
DOI: 10.1093/nar/gkx1143

[…] ed databases of clinically actionable variants similar to the CIViC and Clearity Foundation sources, already included in the DGIdb () (). These include the Precision Oncology Knowledge Base (OncoKB), cancer genome interpreter (CGI) and The Jackson Laboratory Clinical Knowledgebase (CKB) () (,). From these three new sources, 2822 new interaction claims were added. These sources were added as anti-n […]

library_books

Resources for Interpreting Variants in Precision Genomic Oncology Applications

2017
PMCID: 5610688
PMID: 28975082
DOI: 10.3389/fonc.2017.00214

[…] of variants.The myvariant.info database is one of the newest and attempts to provide a “one-stop-shop” for variants. It is included in this section because it has recently incorporated the CIViC and Cancer Genome Interpreter databases. In addition, it provides annotations for SNVs from multiple other data sources (a growing list, so see the site for updates) and aggregates functional annotations […]

call_split

MediSyn: uncertainty aware visualization of multiple biomedical datasets to support drug treatment selection

2017
BMC Bioinformatics
PMCID: 5606218
PMID: 28929971
DOI: 10.1186/s12859-017-1785-7
call_split See protocol

[…] Two manually curated datasets of drug-target relations are synthesized (Fig. ). One is cancer treatment biomarkers from the Cancer Genome Interpreter (CGI) [], and the other is drug-target bioactivities from Drug Target Commons (DTC) []. The CGI contains drug responses such as responsiveness and resistance to various mutat […]

library_books

Integrating genomic alterations in diffuse large B cell lymphoma identifies new relevant pathways and potential therapeutic targets

2017
Leukemia
PMCID: 5843901
PMID: 28804123
DOI: 10.1038/leu.2017.251

[…] Genomic-guided potential therapeutic opportunities for each DLBCL patient were identified in silico by using the Cancer Genome Interpreter modified from our previous described pipeline (https://www.cancergenomeinterpreter.org/). The platform matches the genomic alterations of a tumor with an expert manually cura […]

library_books

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

2017
Nat Genet
PMCID: 5367263
PMID: 28138153
DOI: 10.1038/ng.3774

[…] cribed by this work is available at http://www.civicdb.org/. Personalized Cancer Therapy Knowledgebase, https://pct.mdanderson.org/; Precision Medicine Knowledgebase, https://pmkb.weill.cornell.edu/; Cancer Genome Interpreter, https://www.cancergenomeinterpreter.org/; OncoKB, http://oncokb.org/; GitHub, https://github.com/; GA4GH Variant Interpretation for Cancer Consortium (VICC), http://ga4gh.or […]

Citations

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CGI institution(s)
Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical, Research Institute and Pompeu Fabra University, Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Charité – Universitätsmedizin Berlin, Germany; Vall d´Hebron Institute of Oncology, Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain; Medical Oncology Service, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain; Autonomous University of Barcelona, Barcelona, Spain; Developmental Tumor Biology Laboratory, Institut de Recerca Pediàtrica- Hospital Sant Joan de Déu Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
CGI funding source(s)
Supported by Fundació La Marató de TV3, the European Union’s Horizon 2020 research and innovation programme 2014-2020 under Grant Agreement No 634143, the European Research Council (Consolidator Grant 682398), IRB Barcelona is a recipient of a Severo Ochoa Centre of Excellence Award from the Spanish Ministry of Economy and Competitiveness (MINECO) (Government of Spain), CERCA (Generalitat de Catalunya), project SAF2015-74072- JIN funded by the Agencia Estatal de Investigacion (AEI) and Fondo Europeo de Desarrollo Regional (FEDER), FPI MINECO grant (BES-2013-063354) and a Ramon y Cajal fellowship (RYC-2013-14554).

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