An integrated clinical and genomic information system for cancer precision medicine.

An integrated clinical and genomic information system for cancer precision medicine.

Publication date: Apr 20, 2018

Increasing affordability of next-generation sequencing (NGS) has created an opportunity for realizing genomically-informed personalized cancer therapy as a path to precision oncology. However, the complex nature of genomic information presents a huge challenge for clinicians in interpreting the patient’s genomic alterations and selecting the optimum approved or investigational therapy. An elaborate and practical information system is urgently needed to support clinical decision as well as to test clinical hypotheses quickly.

Here, we present an integrated clinical and genomic information system (CGIS) based on NGS data analyses. Major components include modules for handling clinical data, NGS data processing, variant annotation and prioritization, drug-target-pathway analysis, and population cohort explorer. We built a comprehensive knowledgebase of genes, variants, drugs by collecting annotated information from public and in-house resources. Structured reports for molecular pathology are generated using standardized terminology in order to help clinicians interpret genomic variants and utilize them for targeted cancer therapy. We also implemented many features useful for testing hypotheses to develop prognostic markers from mutation and gene expression data.

Our CGIS software is an attempt to provide useful information for both clinicians and scientists who want to explore genomic information for precision oncology.

Open Access PDF

Jang, Y., Choi, T., Kim, J., Park, J., Seo, J., Kim, S., Kwon, Y., Lee, S., and Lee, S. An integrated clinical and genomic information system for cancer precision medicine. 05536. 2018 BMC Med Genomics (11):Suppl 2.

Concepts Keywords
BMC Evidence-based medicine
Cohort Articles
Drug Target Systems biology
Explorer Health sciences
Mutation Investigational therapy
Oncology Precision medicine
Pathology Therapy
Precision Medicine
Sequencing
Targeted Therapy

Semantics

Type Source Name
pathway BSID Signal Transduction
gene UNIPROT CLOCK
gene UNIPROT MCU
gene UNIPROT EXOG
drug DRUGBANK Tamoxifen
gene UNIPROT TNIP1
gene UNIPROT SCN8A
gene UNIPROT TNFSF13
gene UNIPROT ANP32B
drug DRUGBANK Coenzyme M
gene UNIPROT TNFRSF19
gene UNIPROT CHL1
gene UNIPROT PPP3CA
gene UNIPROT PDF
gene UNIPROT GDF15
gene UNIPROT PPP1R14B
gene UNIPROT NAA11
gene UNIPROT SETD2
disease DOID adenocarcinoma
disease MESH adenocarcinoma
pathway BSID Breast cancer
disease DOID breast cancer
disease MESH breast cancer
pathway BSID Methylation
gene UNIPROT BTG3
gene UNIPROT ABCC8
gene UNIPROT ARR3
gene UNIPROT CXADR
gene UNIPROT CASR
gene UNIPROT NR1I3
gene UNIPROT SPG7
gene UNIPROT SLC35G1
gene UNIPROT DESI1
gene UNIPROT HIF1A
gene UNIPROT MDM2
gene UNIPROT RORC
gene UNIPROT NR1H4
gene UNIPROT BFAR
gene UNIPROT BRAF
gene UNIPROT LARGE1
gene UNIPROT FRZB
gene UNIPROT CCAR1
gene UNIPROT PRAC1
drug DRUGBANK Caffeine
disease MESH classi
gene UNIPROT EGFR
gene UNIPROT SGSM3
gene UNIPROT SMC3
drug DRUGBANK Nonoxynol-9
gene UNIPROT TP53
disease MESH smoker
disease MESH diagnosis
disease MESH risk factors
disease DOID lung adenocarcinoma
disease MESH lung adenocarcinoma
disease MESH glioblastoma
disease DOID carcinoma
disease MESH carcinoma
drug DRUGBANK Hyaluronic acid
gene UNIPROT EHD1
gene UNIPROT BPIFA4P
gene UNIPROT FNDC3A
disease MESH multi
gene UNIPROT SLC25A16
gene UNIPROT PTPN5
disease MESH varia
disease DOID WTS
gene UNIPROT DEPP1
gene UNIPROT GOPC
disease MESH development
gene UNIPROT TNMD
drug DRUGBANK Tretamine
gene UNIPROT GRASP
disease MESH tics
gene UNIPROT LITAF
gene UNIPROT HAVCR1
pathway BSID Gene Expression
disease DOID cancer
disease MESH cancer

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