Building a Research-Quality Copy Number Variation Data Repository for Translational Research

Abstract

Copy number variation (CNV) has known associations with population diversities and disease conditions. However, research communities face great challenges in reusing the CNV data due to the heterogeneity of existing CNV data sources. The objective of the study is to design, develop and evaluate a scalable CNV data repository based on a proposed common data schema for facilitating research-quality CNV data integration and reuse. We created a proposal for a CNV common data schema through analyzing multiple existing CNV data sources. We designed a collection of the CNV quality metrics and demonstrated its usefulness using the CNV data from a study of ovarian cancer xenograft models. We implemented a CNV data repository using a MongoDB database backend and established the CNV genomic data services that enable reusing of the curated CNV data and answering CNV-relevant research questions. The critical issues and future plan for the system enhancement and community engagement were discussed.