2019
DOI: 10.1016/j.ymgmr.2019.100464
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Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory

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 var… Show more

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Cited by 41 publications
(43 citation statements)
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“…Chromosomal microarray analysis (CMA), either comparative genomic hybridization (CGH) or SNP arrays, has long been the first-tier test used to identify copy number variants (CNVs) in individuals with intellectual disability and neurodevelopmental disorders [1012]. In recent years, MPS-based assays have been increasingly used in rare disease diagnostics, because of their high throughput and cost effectiveness in screening multi-gene panels for hereditary disorders [13]. Whole-exome sequencing (WES) is more and more widely used in clinical labs as a first-tier test, allowing detection of SNVs, INDELs, and CNVs covering multiple exons (typically > 2) [1416].…”
Section: Introductionmentioning
confidence: 99%
“…Chromosomal microarray analysis (CMA), either comparative genomic hybridization (CGH) or SNP arrays, has long been the first-tier test used to identify copy number variants (CNVs) in individuals with intellectual disability and neurodevelopmental disorders [1012]. In recent years, MPS-based assays have been increasingly used in rare disease diagnostics, because of their high throughput and cost effectiveness in screening multi-gene panels for hereditary disorders [13]. Whole-exome sequencing (WES) is more and more widely used in clinical labs as a first-tier test, allowing detection of SNVs, INDELs, and CNVs covering multiple exons (typically > 2) [1416].…”
Section: Introductionmentioning
confidence: 99%
“…The filtration and annotation of genetic variants include multiple components, and the diagnostic decision depends on the data resources used. Recent studies recommended NGS coverage of at least 20× for diagnostic purposes [ 41 ]. Despite the high coverage obtained using gene panels, Sanger technology should be used to confirm all variants included in a genetic report and to discard false positives, especially concerning insertions/deletions (indels).…”
Section: Technical Datamentioning
confidence: 99%
“…As of April 2020, 466 BAP1 germline variants of uncertain significance (VUS) have been reported on ClinVar, with 447 of them having single nucleotide variations and 404 of them resulting in missense mutations 22 . More of such BAP1 variants are expected to be discovered as clinical laboratories have increasingly adopted next-generation sequencing to diagnose hereditary disorders due to its costeffectiveness, high throughput and accuracy 23 . Given the increased risks and aggressiveness of cancer development and progression in patients with BAP1 germline variants, understanding how variants in BAP1 affect function will aid interpretation of uncertain variants.…”
Section: Introductionmentioning
confidence: 99%