This poster (#1737W) will be presented at the 62nd Annual Meeting of the American Society of Human Genetics by Scott Topper, assistant director of UCGS, Wednesday November 7: 2:15pm-3:15pm. Stop by and learn more
The diagnosis of many genetic conditions is complicated by extensive genetic heterogeneity. Phenotypically indistinguishable forms of Intellectual Disability, for example, can be caused by mutations in any one of about 100 known genes, each one of which accounts for a very small percentage of patient cases. In many cases a highly parallelized sequencing approach is a more effective and efficient diagnostic strategy than serial single gene sequencing. But handling the large amount of data generated, while maintaining the essential clinical standards developed in low-throughput tests, can present substantial challenges for the diagnostic lab. Here we present an enumeration of those standards as applied to large-panel, next-generation sequencing (NGS) diagnostic testing, a web-based tool to assist in meeting those standards, and data from validation samples for a set of diagnostic tests. These principles are intended to ensure reliable test results that can be successfully integrated into a diagnostic strategy, especially in the likely case of a negative result, an outcome that is still expected in more than 50% of patient samples. The principles are: 1)Data must be processed and evaluated efficiently and reproducibly; 2)Target regions of essential genes must be evaluated completely; 3)Identified mutations must be confirmed by an orthogonal technology; and 4)Pathogenicity of each identified variant must be evaluated independently and in the context of the patient’s entire data set. To ensure that these standards are met we developed a database and web-based interface to facilitate a teamwork approach to sample tracking, variant interpretation, annotated data storage, and integrating NGS and Sanger data. In this tool, an ‘Overview’ module presents data quality statistics, a summary of missed regions in the target genes, and sample tracking information. A ‘Confirmation’ module consists of an interface for coordinating Sanger sequencing of NGS data gaps, variants that must be confirmed, and provides a method for integrating Sanger data into the data set. An ‘Interpretation’ module provides an interface for presenting annotation information, tracking variant review status, maintaining notes, and linking to the data sets of other patients with the same sequence change. Using this system we have evaluated data from 50 validation samples, in some cases identifying pathogenic mutations in samples for which no molecular diagnosis had previously been found.