Abstract
Clinical laboratories have adopted next generation sequencing (NGS) as a gold standard for the diagnosis of hereditary disorders because of its analytic accuracy, high throughput, and potential for cost-effectiveness. We describe the implementation of a single broad-based NGS sequencing assay to meet the genetic testing needs at the University of Minnesota. A single hybrid capture library preparation was used for each test ordered, data was informatically blinded to clinically-ordered genes, and identified variants were reviewed and classified by genetic counselors and molecular pathologists. We performed 2509 sequencing tests from August 2012 till December 2017. The diagnostic yield has remained steady at 25%, but the number of variants of uncertain significance (VUS) included in a patient report decreased over time with 50% of the patient reports including at least one VUS in 2012 and only 22% of the patient reports reporting a VUS in 2017 (p = .002). Among the various clinical specialties, the diagnostic yield was highest in dermatology (60% diagnostic yield) and ophthalmology (42% diagnostic yield) while the diagnostic yield was lowest in gastrointestinal diseases and pulmonary diseases (10% detection yield in both specialties). Deletion/duplication analysis was also implemented in a subset of panels ordered, with 9% of samples having a diagnostic finding using the deletion/duplication analysis. We have demonstrated the feasibility of this broad-based NGS platform to meet the needs of our academic institution by aggregating a sufficient sample volume from many individually rare tests and providing a flexible ordering for custom, patient-specific panels.
Highlights
Clinical laboratories have increasingly adopted generation sequencing (NGS) as a standard for the diagnosis of hereditary disorders.Depending upon the specific focus of the diagnostic laboratory, next generation sequencing (NGS) methods can be used to detect either germline or somatic mutations [2]
When accounting for the number of genes analyzed, the number of variants of uncertain significance (VUS) identified per gene analyzed has decreased over time (Fig. 2B) with an average of 0.19 VUS reported per gene analyzed in 2012 to 0.03 VUS reported per gene analyzed in 2017
A diagnostic finding was identified in 24.10% (24.08%–24.14%) of samples, a possible diagnostic finding was identified in 9.56% (9.54%–9.58%) of samples, and 66.33% (66.31%–66.36%) of samples were reported as negative
Summary
Clinical laboratories have increasingly adopted generation sequencing (NGS) as a standard for the diagnosis of hereditary disorders. Since single gene tests and multi-gene panels tend to be the first step in genetic diagnosis of specific clinical diseases. The initial evaluation of a patient suspected of having a hereditary disease may include a combination of both nonNGS based tests and NGS-based gene panels. If this initial targeted testing does not identify a diagnostic finding, whole exome sequencing is often considered [18]. At the final step of the bioinformatics pipeline, the data was restricted to the specific set of genes requested by the ordering physician This approach allowed our laboratory to offer a comprehensive sequencing menu utilizing a single wet-bench workflow and bioinformatics pipeline [13,20]. A detailed description of the specific genes offered is provided in Supplementary Table 1 and gene panels offered within each clinical specialty is provided in Supplementary Table 2
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