Enabling precision medicine with CancerKB and KBCommons informatics framework

Abstract

Precision Medicine is one of the most rapidly evolving areas within medicine, which allows utilization of patient's own genomic information in guiding personalized treatments and customized therapy. Applying the public data obtained from human genomic and cancer cell line studies in the diagnosis and treatment of diseases is a challenging task as these data are spread across different repositories with diverse formats and omics data types. There is an immediate need for platforms to make this integration and analysis seamless and readily accessible to researchers and clinicians. To achieve this, we have implemented Cancer Cell Line KB, a branch of the KBCommons for homoSapiens which focuses on automatically establishing a web-based resource for comprehensive multi-omics data access using our in-house developed KBCommons framework. It currently provides data for human genes / proteins, miRNA, and publicly available information for 1046 cancer cell lines and drug response datasets. Additionally, gene expression and de-identified clinical data from The Cancer Genome Atlas has also been added which includes 7706 patient samples for 20 cancer types, and 23368 genes expression as FPKM and FeatureCounts. Users can view these datasets using various analytical and graphical visualization tools in Cancer Cell Line KB and search by genes or cancer cell lines. We have also developed Principal Component Analysis (PCA) tool and patient clinical data browser to provide access to patient's genomic tests information and gene expression. In the future, heatmap will be developed to analysis the microarray gene expression data with hierarchical clustering method and more de-identified clinical data from cBioportal can be imported through WEB-API. We also plan to implement a tool to show how the patient's own genomic tests information compares with the population based datasets for that disease traits.