Clinical Validation of Targeted Next-Generation Sequencing for Inherited Disorders

Yohe, Sophia; Hauge, Adam; Bunjer, Kari; Kemmer, Teresa; Bower, Matthew; Schomaker, Matthew; Onsongo, Getiria; Wilson, Jon D.; Erdmann, Jesse; Zhou, Yi; Deshpande, Archana; Spears, Michael D.; Beckman, Kenneth B.; Silverstein, Kevin A.T.; Thyagarajan, Bharat

doi:10.5858/arpa.2013-0625-oa

Cited by 45 publications

(41 citation statements)

References 22 publications

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“…It covers 614 genes, including the vast majority of genes currently known to cause neurometabolic disease, hence sharing similarities with WES approaches but with the added advantage of more optimal coverage of targeted areas (Kammermeier et al , 2014). Indeed, coverage of targeted areas was similar or superior to that reported in other gene panels despite the large number of genes covered (Nemeth et al , 2013; Yohe et al , 2015). Moreover, the diagnosis rate in our study was comparable to, or higher than, that reported in similar approaches recently applied in other patient groups exhibiting phenotypic heterogeneity (Kammermeier et al , 2014; Sommen et al , 2016; Trump et al , 2016).…”

Section: Discussionsupporting

confidence: 70%

Advantages and pitfalls of an extended gene panel for investigating complex neurometabolic phenotypes

Reid

Papandreou

Drury

et al. 2016

Brain

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Section: Discussionsupporting

confidence: 70%

Advantages and pitfalls of an extended gene panel for investigating complex neurometabolic phenotypes

Reid

Papandreou

Drury

et al. 2016

Brain

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“…While targeted enrichment is becoming widely used to screen for polymorphisms within human genomic loci associated with cancers and inherited disorders (7–9), its uses for multiplex pathogen characterization are still not widespread and, to our knowledge, have never been applied to veterinary pathogens. Wylie et al (10) recently reported the development of a comprehensive probe library for pathogen diagnostics and discovery that holds tremendous potential.…”

Section: Discussionmentioning

confidence: 99%

Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species

et al. 2017

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Traditional diagnostic assays often lack sensitivity and can be difficult to multiplex across many pathogens. Next-generation sequencing (NGS) can overcome some of these problems but has limited application in the detection of low-copy-number pathogens in complex samples. Targeted genome capture (TGC) utilizes oligonucleotide probes to enrich specific nucleic acids in heterogeneous extracts and can therefore increase the proportion of NGS reads for low-abundance targets. While earlier studies have demonstrated the utility of this technology for detection of novel pathogens in human clinical samples, the capacity and practicality of TGC-NGS in a veterinary diagnostic setting have not yet been evaluated. Here we report the use of TGC-NGS assays for the detection and characterization of diverse feline pathogen taxa. We detected 31 pathogens comprising nine pathogen taxa in 28 felid samples analyzed. This included 20 pathogens detected via traditional PCR and 11 additional pathogens that had not been previously detected in the same samples. Most of the pathogens detected were sequenced at sufficient breadth and depth to confidently classify them at the species or subspecies level. Target nucleic acids were enriched from a low of 58-fold to 56 million-fold relative to host nucleic acids. Despite the promising performance of these assays, a number of pathogens detected by conventional PCR or serology were not isolated by TGC-NGS, suggesting that further validation is required before this technology can be used in lieu of quality-controlled standard assays. We conclude that TGC-NGS offers great potential as a broad multiplex pathogen characterization assay in veterinary diagnostic and research settings.

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“…Although the majority of functionally critical and disease-causing mutations occur in protein-coding regions, most of the genome is noncoding and may contain overlooked pathogenic variants. Besides, the TNGS assay is insensitive to detection of copy number variation (CNV) and other structural variants [28,31]. In our study, 9 out of 11 high-risk cases were identified as having a recessive carrier mutation with concordant association, among which 2 even have confirmatory TMS results.…”

Section: Limitationmentioning

confidence: 73%

“…Furthermore, as far as the TAT of TNGS assay was concerned, we can now achieve a throughput for 20 samples in 5 days, comprising 2-day sample preparation, 2-day sequencing and analysis, and 1 day of confirmation and validation [28]. Because the primary screening rate is about 1:200, a maximum daily TMS screening throughput of 4000 could be processed in accordance with the TNGS assay.…”

Section: Proposition Of Screening-diagnosis Workflowmentioning

confidence: 99%

Applying targeted next generation sequencing to dried blood spot specimens from suspicious cases identified by tandem mass spectrometry-based newborn screening

Qian

Wang

Liu

et al. 2017

Journal of Pediatric Endocrinology and Metabolism

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Background: Tandem mass spectrometry (TMS)-based newborn screening has been proven successful as one of the public healthcare programs, although the practicability has not yet been specifically addressed. Methods: Sixty residual dried blood spot (DBS) specimens from confirmation/diagnosis-insufficient cases discovered by TMS screening were analyzed by targeted next generation sequencing (TNGS) assay. Results: In total, 26, 11, 9, and 14 cases were diagnosed as positive, high risk, low risk, and negative, respectively. Conclusions: Applying the DBS-based TNGS assay for the accurate and rapid diagnosis of inborn errors of metabolism (IEMs) is feasible, competent, and advantageous, enabling a simplified TMS screening-based, TNGS assay-integrated newborn screening scheme highlighting an efficient, executable, and one-step screening-to-diagnosis workflow.

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Clinical Validation of Targeted Next-Generation Sequencing for Inherited Disorders

Abstract: We have successfully demonstrated the feasibility of using the NGS platform to multiplex genetic tests for several rare diseases and the use of cloud computing for bioinformatics analysis as a relatively low-cost solution for implementing NGS in clinical laboratories.

Cited by 45 publications

References 22 publications

Advantages and pitfalls of an extended gene panel for investigating complex neurometabolic phenotypes

Advantages and pitfalls of an extended gene panel for investigating complex neurometabolic phenotypes

Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species

Applying targeted next generation sequencing to dried blood spot specimens from suspicious cases identified by tandem mass spectrometry-based newborn screening

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