Clinical Knowledgebase
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Clinical Knowledgebase
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
JAX-CKB
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Names
More detailed information about this field from each metasource.
Clinical Knowledgebase
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
JAX-CKB
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Names
More detailed information about this field from each metasource.
Clinical Knowledgebase
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
JAX-CKB
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Jackson Laboratory Clinical Knowledgebase (CKB) is a semi-automated/manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and clinical trials related to oncology. CKB not only contains current information on the protein effect of somatic gene variants, but also connects the variant to targeted therapies through an efficacy evidence annotation. In addition, CKB captures clinical trial patient eligibility criteria that include genomic alterations (genotype-specific). The public access version of CKB encompasses 82 commonly known driver genes. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials. The web-based version of CKB is designed to interrogate the knowledgebase for specific data attributes while also enabling a robust browse like feature when the desired content is unknown.
Description
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The Jackson Laboratory Clinical Knowledgebase (CKB) is a semi-automated/manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and clinical trials related to oncology. CKB not only contains current information on the protein effect of somatic gene variants, but also connects the variant to targeted therapies through an efficacy evidence annotation. In addition, CKB captures clinical trial patient eligibility criteria that include genomic alterations (genotype-specific). The public access version of CKB encompasses 82 commonly known driver genes. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials. The web-based version of CKB is designed to interrogate the knowledgebase for specific data attributes while also enabling a robust browse like feature when the desired content is unknown.
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Webpage:
https://jax.org/ckbWebpage
More detailed information about this field from each metasource.
https://jax.org/ckb
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies
PMID: 26772741
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications
More detailed information about this field from each metasource.
The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies
PMID: 26772741
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
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The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies
PubMed citations: 52.
52 articles citing: The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies
Hematopoietic differentiation persists in human iPSCs defective in de novo DNA methylation. PMID:35705990
CancerVar: An artificial intelligence-empowered platform for clinical interpretation of somatic mutations in cancer. PMID:35544644
Liquid Biopsy and Artificial Intelligence as Tools to Detect Signatures of Colorectal Malignancies: A Modern Approach in Patient's Stratification. PMID:35356214
Comprehensive characterization of PTEN mutational profile in a series of 34,129 colorectal cancers. PMID:35338148
The Architecture of a Precision Oncology Platform. PMID:35230680
A platform for oncogenomic reporting and interpretation. PMID:35140225
Discovery through clinical sequencing in oncology. PMID:35122052
JCGA: the Japanese version of the Cancer Genome Atlas and its contribution to the interpretation of gene alterations detected in clinical cancer genome sequencing. PMID:34588443
MUSTARD-a comprehensive resource of mutation-specific therapies in cancer. PMID:34309639
Criteria-based curation of a therapy-focused compendium to support treatment recommendations in precision oncology. PMID:34162978
Therapeutic Implications of Germline Testing in Patients With Advanced Cancers. PMID:34133209
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
Clinical cancer genomic profiling. PMID:33762738
Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology. PMID:33737716
Comparison of Open-access Databases for Clinical Variant Interpretation in Cancer: A Case Study of MDS/AML. PMID:33608312
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts. PMID:33414553
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. PMID:33237278
Multicenter Comparison of Molecular Tumor Boards in The Netherlands: Definition, Composition, Methods, and Targeted Therapy Recommendations. PMID:33111480
The KDR (VEGFR-2) Genetic Polymorphism Q472H and c-KIT Polymorphism M541L Are Associated With More Aggressive Behaviour in Astrocytic Gliomas. PMID:33099473
Comparison of three commercial decision support platforms for matching of next-generation sequencing results with therapies in patients with cancer. PMID:32967919
Comparison of Annotation Services for Next-Generation Sequencing in a Large-Scale Precision Oncology Program. PMID:32923873
Global clinical trial mobilization for COVID-19: higher, faster, stronger. PMID:32777537
Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices. PMID:32644817
The My Cancer Genome clinical trial data model and trial curation workflow. PMID:32483629
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. PMID:32246132
A Novel System for Functional Determination of Variants of Uncertain Significance using Deep Convolutional Neural Networks. PMID:32144301
A Review of Precision Oncology Knowledgebases for Determining the Clinical Actionability of Genetic Variants. PMID:32117976
Requirements Analysis and Specification for a Molecular Tumor Board Platform Based on cBioPortal. PMID:32050609
Text-mining clinically relevant cancer biomarkers for curation into the CIViC database. PMID:31796060
Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes. PMID:31618044
Multilayered control of exon acquisition permits the emergence of novel forms of regulatory control. PMID:31315652
Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines. PMID:31262303
Conceptual Framework to Support Clinical Trial Optimization and End-to-End Enrollment Workflow. PMID:31225983
ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer. PMID:31169290
[Detection and interpretation of somatic variants in molecular pathology]. PMID:31037375
Utility of the JAX Clinical Knowledgebase in capture and assessment of complex genomic cancer data. PMID:30675517
Knowledge base toward understanding actionable alterations and realizing precision oncology. PMID:30542800
Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards. PMID:30311370
A Computational Approach for Prioritizing Selection of Therapies Targeting Drug Resistant Variation in Anaplastic Lymphoma Kinase. PMID:29888064
PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data. PMID:29848362
Disease Ontology: improving and unifying disease annotations across species. PMID:29590633
Personalized cancer therapy-leveraging a knowledge base for clinical decision-making. PMID:29212833
DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. PMID:29156001
OncoKB: A Precision Oncology Knowledge Base. PMID:28890946
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. PMID:28138153
A variant by any name: quantifying annotation discordance across tools and clinical databases. PMID:28122645
Genomics pipelines and data integration: challenges and opportunities in the research setting. PMID:28092471
How "precise" is precision medicine in hematology? PMID:28040787
Integrating cancer genomic data into electronic health records. PMID:27784327
Targeted Next-Generation Sequencing of Plasma DNA from Cancer Patients: Factors Influencing Consistency with Tumour DNA and Prospective Investigation of Its Utility for Diagnosis. PMID:27626278
mTOR Inhibitors in Castration-Resistant Prostate Cancer: A Systematic Review. PMID:27503005
Changing paradigm of cancer therapy: precision medicine by next-generation sequencing. PMID:27144059
Tags:
Tags
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cancer
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
dna structural variation
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
drug
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
drug report
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genotype
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
next generation dna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
somatic mutation
metasource: Fairsharing.org
version: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Tags
More detailed information about this field from each metasource.
cancer
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
dna structural variation
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
drug
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
drug report
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genotype
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
next generation dna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
somatic mutation
metasource: Fairsharing.orgversion: FAIRsharing.org: JAX-CKB; Clinical Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.e5y0j0; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
cancer dna structural variation drug drug report genotype next generation dna sequencing somatic mutation
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