Although next-generation sequencing (NGS) is widely used for sequencing analysis, it involves a fragmented workflow along with complex bioinformatic analysis and interpretation. In this study, the performance characteristics and workflow of the GeneReader NGS System (QIAGEN), including sequencing, were evaluated. For genetic testing, we conducted library preparation, emulsion PCR, and sequencing. QCI Analyze software was used for read alignment, quality control, variant calling, and clinical report generation. GeneReader and Sanger sequencing utilized 63 patients with breast or ovarian cancer for comparison. Reproducibility, precision, variant calling, turnaround time, and hands-on time were evaluated. The read percentage in the on-target regions was 90.5%. More than 99.99% of target regions showed read depths ≥100x. Variants generated from GeneReader showed 100% accuracy compared to the Sanger sequencing results. Annotation with GeneReader showed >99.8% concordance with HGVS nomenclature. Single-nucleotide variations and indel variants showed 100% calling reproducibility; the precision for variant frequency showed a 0.3-3.6% coefficient of variation. Most processes involved hands-off time (3714 min, 88.6% of total run time). The GeneReader NGS System for and testing showed good analytical performance and a short hands-on time. Because of its integrated sample preparation for bioinformatic interpretation, this system is practical for clinical laboratories.
© 2020 by the Association of Clinical Scientists, Inc.

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