Characterizing reduced coverage regions through comparison of exome and genome sequencing data across ten centers

PURPOSE: As massively parallel sequencing is increasingly being used for clinical decision-making, it has become critical to understand parameters that affect sequencing quality and to establish methods for measuring and reporting clinical sequencing standards. In this report, we propose a definition for reduced coverage regions and have established a set of standards for variant calling in clinical sequencing applications. METHODS: To enable sequencing centers to assess the regions of poor sequencing quality in their own data, we optimized and used a tool (ExCid) to identify reduced coverage loci within genes or regions of particular interest. We used this framework to examine sequencing data from 500 patients generated in ten projects from sequencing centers in the NHGRI/NCI Clinical Sequencing Exploratory Research (CSER) Consortium. RESULTS: This approach identified reduced coverage regions in clinically relevant genes, including known clinically relevant loci that were uniquely missed at individual centers, in multiple centers, and in all centers. CONCLUSIONS: This report provides a process roadmap for clinical sequencing centers looking to perform similar analyses on their data.