Diagnostic Targetd Sequencing Adjudication: Algorithms for Adjudicating Targeted Infectious Disease Next-Generation Sequencing Panels

Publication date: Available online 28 September 2018Source: The Journal of Molecular DiagnosticsAuthor(s): Turner A. Conrad, Chien-Chi Lo, Jeffrey W. Koehler, Amanda S. Graham, Christopher P. Stefan, Adrienne T. Hall, Christina E. Douglas, Patrick S.G. Chain, Timothy D. MinogueNext-generation sequencing (NGS) for infectious disease diagnostics is a relatively new and underdeveloped concept. If this technology is to become a regulatory-grade clinical diagnostic, standardization in the form of locked-down assays and firmly established underlying processes is necessary. Targeted sequencing, specifically by amplification of genomic signatures, has the potential to bridge the gap between PCR- and NGS-based diagnostics; however, existing NGS assay panels lack validated analytical techniques to adjudicate high background and error-prone NGS data. Herein, we present the Diagnostic targETEd seQuencing adjudicaTion (DETEQT) software, consisting of an intuitive bioinformatics pipeline entailing a set of algorithms to translate raw sequencing data into positive, negative, and indeterminate diagnostic determinations. After basic read filtering and mapping, the software compares abundance and quality metrics against heuristic and fixed thresholds. A novel generalized quality function provides an amalgamated quality score for the match between sequence reads of an assay and panel targets, rather than considering each component factor independently. When evaluated against numerous assay samp...
Source: The Journal of Molecular Diagnostics - Category: Pathology Source Type: research