CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.

Jake Lever,Martin R Jones,Steven J M Jones,Jasleen Grewal,Eric Y Zhao

doi:10.1038/s41592-019-0422-y

Abstract

Tumors from individuals with cancer are frequently genetically profiled for information about the driving forces behind the disease. We present the CancerMine resource, a text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. All data are available online ( http://bionlp.bcgsc.ca/cancermine ) and downloadable under a Creative Commons Zero license for ease of use.

Highlights

As sequencing technology becomes more widely integrated into clinical practice, genomic data from cancer samples is increasingly being used to support clinical decision making as part of precision medicine efforts
By filtering for a customized set of keywords, these sentences were enriched for those likely discussing the genes’ role and 1,500 randomly selected sentences were manually annotated by three expert annotators
An example of a simple relation that was annotated as “Tumor Suppressor” annotation is: “DBC2 is a tumor suppressor gene linked to breast and lung cancers” (PMID: 17023000)

Summary

Introduction

As sequencing technology becomes more widely integrated into clinical practice, genomic data from cancer samples is increasingly being used to support clinical decision making as part of precision medicine efforts. The importance of a particular mutation depends on the role of the associated gene and the specific cancer type. A deletion or loss-of-function mutation in a tumor suppressor gene associated with the cancer type of the sample is potentially an important event for this cancer. Amplifications and gain-of function mutations in oncogenes, and any somatic activity in known driver genes may be valuable information in understanding the mutational landscape of a given cancer sample. This knowledge can help select therapeutic options and improve our understanding of markers of resistance in the particular cancer type

Methods

Results

Conclusion