CACSV: a computational web-sever that provides classification for cancer somatic genetic variants from different tissues

Abstract

Abstract Background Understanding the role and function of genetic variants is extremely important when analyzing and interpreting a myriad of human disease processes. For cancer in general, cell-specific genetic variants are ubiquitous and distinct tissues have significantly heterogenic genetic profiles. In clinical practice, only a few genetic variants have identifiable clinical utility. Finding clinically relevant genetic variants constitute a challenging process. In addition, there had been no reference protocol to provide guidance for cancer somatic genetic variants classification and interpretation. In 2017, the first version of a reference protocol was published by the Association for Molecular Pathology, the American Society of Clinical Oncology, and the College of American Pathologists. Previously, we incorporated the reference protocol into a computational method to expedite the process of identification of clinically relevant genetic variants. In this work, we developed a computational web-server to increase the accessibility and availability of clinically relevant genetic variants. Results Our work provides the clinical classification for ~ 3 million cancer genetic variants that are now publicly available in a shareable database on GitHub. We have developed a graphical user interface for the database to enhance the accessibility and ease-of-use. Conclusion CACSV provides an open-source for about 3 million cancer tissue-specific genetic variants with their assigned clinical annotations.