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Scott SA. The Genetic Testing Reference Materials Coordination Program: Over 10 Years of Support for Pharmacogenomic Testing. J Mol Diagn 2023; 25:630-633. [PMID: 37481236 PMCID: PMC10488323 DOI: 10.1016/j.jmoldx.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/24/2023] Open
Affiliation(s)
- Stuart A Scott
- Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Laboratory, Stanford Medicine, Palo Alto, California.
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2
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Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
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Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
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3
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Abstract
Synthetic DNA is of increasing demand across many sectors of research and commercial activities. Engineering biology, therapy, data storage and nanotechnology are set for rapid developments if DNA can be provided at scale and low cost. Stimulated by successes in next generation sequencing and gene editing technologies, DNA synthesis is already a burgeoning industry. However, the synthesis of >200 bp sequences remains unaffordable. To overcome these limitations and start writing DNA as effectively as it is read, alternative technologies have been developed including molecular assembly and cloning methods, template-independent enzymatic synthesis, microarray and rolling circle amplification techniques. Here, we review the progress in developing and commercializing these technologies, which are exemplified by innovations from leading companies. We discuss pros and cons of each technology, the need for oversight and regulatory policies for DNA synthesis as a whole and give an overview of DNA synthesis business models.
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4
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An SI-traceable reference material for virus-like particles. iScience 2022; 25:104294. [PMID: 35573192 PMCID: PMC9095743 DOI: 10.1016/j.isci.2022.104294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
A reference material for virus-like particles traceable to the International System of Units (Système International d'Unités – the SI) is reported. The material addresses the need for developing reference standards to benchmark virus-like gene delivery systems and help harmonize measurement approaches for characterization and testing. The material is a major component of synthetic polypeptide virus-like particles produced by the state-of-the-art synthetic and analytical chemistry methods used to generate gene delivery systems. The purity profile of the material is evaluated to the highest metrological order demonstrating traceability to the SI. The material adds to the emerging toolkit of reference standards for quantitative biology. A reference material for virus-like particles with traceability to the SI The material is a major component of virus-like particles capable of gene delivery Purity profile of the material is evaluated to the highest metrological order The material allows comparability of physicochemical properties of virus-like systems
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5
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Carpenter RE, Tamrakar VK, Almas S, Brown E, Sharma R. COVIDSeq as Laboratory Developed Test (LDT) for Diagnosis of SARS-CoV-2 Variants of Concern (VOC). ARCHIVES OF CLINICAL AND BIOMEDICAL RESEARCH 2022; 6:954-970. [PMID: 36588916 PMCID: PMC9802674 DOI: 10.26502/acbr.50170309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the virus's transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, a U.S. Food and Drug Administration (FDA)-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVIDSeq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 (~15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVIDSeq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.
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Affiliation(s)
- Rob E Carpenter
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
- University of Texas at Tyler, 3900 University Boulevard, Tyler, Texas 75799, USA
- Scienetix, 10935 CR 159, Tyler, Texas 75703, USA
| | - Vaibhav K Tamrakar
- ICMR-National Institute of Research in Tribal Health, Jabalpur, MP 482003, INDIA
- RetroBioTech LLC, 838 Dalmalley Ln, Coppell, TX 75019, USA
| | - Sadia Almas
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
| | - Emily Brown
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
| | - Rahul Sharma
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
- RetroBioTech LLC, 838 Dalmalley Ln, Coppell, TX 75019, USA
- Scienetix, 10935 CR 159, Tyler, Texas 75703, USA
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6
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He X, Ding J, Xu Z, Li N, Yang J, Chen H, Lu D. Development of a new genetic reference material system based on Saccharomyces cerevisiae cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 20:473-482. [PMID: 33614823 PMCID: PMC7868937 DOI: 10.1016/j.omtm.2021.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/13/2021] [Indexed: 11/29/2022]
Abstract
As an important quality control link of molecular diagnosis, genetic reference materials (RMs) are widely used in various gene detection platforms such as mutation detection, gene quantification, and second generation sequencing. However, contamination, construction, and storage of existing genetic RMs still remain challenges. Here, we established a new genetic RM system based on Saccharomyces cerevisiae. We chose the non-small cell lung cancer (NSCLC) mutation hotspots in Kirsten rat sarcoma viral oncogene (KRAS) and epidermal growth factor receptor (EGFR), using clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas9) system-mediated gene editing technology, combined with the high homologous recombination efficiency of Saccharomyces cerevisiae. A single copy of the target gene was inserted into the yeast genome, and the inserted target gene was stably inherited with the passage of yeast cells. The copy number calculation for the target gene can replays by cell counting. The RM system was evaluated by sequence, copy number, stability, and homogeneity. In summary, the recombinant yeast cell line has ease of construction and screening, stable genetic characteristics, accurate copy number calculation, and convenient culture and preservation. Our findings may provide new ideas and directions for the research and industrialization of genetic RMs.
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Affiliation(s)
- Xin He
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jiaqi Ding
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Zhenhua Xu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Na Li
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jingmin Yang
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
| | - Hongyan Chen
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
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7
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Pranckeviciene E, Racacho L, Ghani M, Nfonsam L, Potter R, Sinclair-Bourque E, Mettler G, Smith A, Bronicki L, Huang L, Jarinova O. Interplay between probe design and test performance: overlap between genomic regions of interest, capture regions and high quality reference calls influence performance of WES-based assays. Hum Genet 2020; 140:289-297. [PMID: 32627054 DOI: 10.1007/s00439-020-02201-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/25/2020] [Indexed: 11/25/2022]
Abstract
Whole exome sequencing (WES)-based assays undergo rigorous validation before being implemented in diagnostic laboratories. This validation process generates experimental evidence that allows laboratories to predict the performance of the intended assay. The NA12878 Genome in a Bottle (GIAB) HapMap reference sample is commonly used for validation in diagnostic laboratories. We investigated what data points should be taken into consideration when validating WES-based assays using the GIAB reference in a diagnostic setting. We delineate specific factors that require special consideration and identify OMIM genes associated with diseases that may 'bypass' validation. Four replicates of the NA12878 sample were sequenced at the CHEO Genetics Diagnostic Laboratory on a NextSeq 500; the data were analyzed using the bcbio_nexgen v1.1.2 pipeline. The hap.py validation engine, Real Time Genomics vcfeval tool, and high confidence (HC) variant calls in HC regions available for the GIAB sample were used to validate the obtained variant calls. The same validation process was then used to evaluate variant calls obtained for the same sample by two other clinical diagnostic laboratories. We showed that variant calls in NA12878 can be confidently measured only in the regions that intersect between the GIAB HC regions and the target regions of exome capture. Of the 4139 (as of October 2019) OMIM genes associated with a phenotype and having a known molecular basis of disease, 84 were fully outside of the GIAB HC regions and many of the remaining OMIM genes were only partially covered by the HC regions. A significant proportion of variants identified in the NA12878 sample outside of the HC regions have unknown (UNK) status due to the absence of HC reference alleles. Verification of such calls is possible either by an alternative truth set or by orthogonal testing. Similarly, many variants outside of exome capture regions, if not accounted for, will be deemed false negatives due to insufficient probe coverage. Our results demonstrate the importance of the intersection between genomic regions of interest, capture regions, and the high confidence regions. If not considered, false and ambiguous variant calls could have a negative impact on diagnostic accuracy of the intended WES-based diagnostic assay and increase the need for confirmatory testing. To enable laboratories to identify 'problematic' regions and optimize validation efforts, we have made our VCF and BED files available in UCSC Genome Browser: NA12878 WES Benchmark. Relevant genes and genome annotations are evolving, we implemented a general purpose algorithm to cross-reference OMIM genes with the genomic regions of interest that can be applied to capture genes/regions outside HC regions (see repository of data material section).
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Affiliation(s)
- Erinija Pranckeviciene
- Department of Genetics, CHEO, Ottawa, ON, Canada.
- Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.
| | - Lemuel Racacho
- Department of Genetics, CHEO, Ottawa, ON, Canada
- Department of Newborn Screening, CHEO, Ottawa, ON, Canada
| | - Mahdi Ghani
- Department of Genetics, CHEO, Ottawa, ON, Canada
| | | | - Ryan Potter
- Department of Genetics, CHEO, Ottawa, ON, Canada
| | | | | | - Amanda Smith
- Department of Genetics, CHEO, Ottawa, ON, Canada
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Lucas Bronicki
- Department of Genetics, CHEO, Ottawa, ON, Canada
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Lijia Huang
- Department of Genetics, CHEO, Ottawa, ON, Canada
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Olga Jarinova
- Department of Genetics, CHEO, Ottawa, ON, Canada.
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada.
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8
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Liu Z, Zhu L, Roberts R, Tong W. Toward Clinical Implementation of Next-Generation Sequencing-Based Genetic Testing in Rare Diseases: Where Are We? Trends Genet 2019; 35:852-867. [PMID: 31623871 DOI: 10.1016/j.tig.2019.08.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/08/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technologies have changed the landscape of genetic testing in rare diseases. However, the rapid evolution of NGS technologies has outpaced its clinical adoption. Here, we re-evaluate the critical steps in the clinical application of NGS-based genetic testing from an informatics perspective. We suggest a 'fit-for-purpose' triage of current NGS technologies. We also point out potential shortcomings in the clinical management of genetic variants and offer ideas for potential improvement. We specifically emphasize the importance of ensuring the accuracy and reproducibility of NGS-based genetic testing in the context of rare disease diagnosis. We highlight the role of artificial intelligence (AI) in enhancing understanding and prioritization of variance in the clinical setting and propose deep learning frameworks for further investigation.
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Affiliation(s)
- Zhichao Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Liyuan Zhu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Ruth Roberts
- ApconiX, Alderley Park, Alderley Edge, SK10 4TG, UK; University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
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9
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Lee SB, Wheeler MM, Thummel KE, Nickerson DA. Calling Star Alleles With Stargazer in 28 Pharmacogenes With Whole Genome Sequences. Clin Pharmacol Ther 2019; 106:1328-1337. [PMID: 31206625 PMCID: PMC6896231 DOI: 10.1002/cpt.1552] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/30/2019] [Indexed: 02/01/2023]
Abstract
Variation in the enzymatic activity of pharmacogenes is defined by star alleles (haplotypes) comprised of single-nucleotide variants, small insertion-deletions, and large structural variants. We recently developed Stargazer, a next-generation sequencing-based tool to call star alleles for the clinically important CYP2D6 gene. Here, we present the utility of extending Stargazer to call star alleles for 28 pharmacogenes using whole genome sequencing (WGS) data. We applied Stargazer to WGS data from 70 ethnically diverse samples from the Genetic Testing Reference Materials Coordination Program (GeT-RM). These reference samples were extensively characterized by GeT-RM using multiple pharmacogenetic testing assays. In all 28 genes, Stargazer recalled 100% of star alleles (N = 92) present in GeT-RM's consensus genotypes (N = 1,559). Stargazer also detected star alleles not previously reported by GeT-RM, including complex structural variants. Our results demonstrate that combining WGS data and Stargazer enables automated, accurate, and comprehensive genotyping of pharmacogenes in the human genome.
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Affiliation(s)
- Seung-Been Lee
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Marsha M Wheeler
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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10
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Quality assurance of genetic laboratories and the EBTNA practice certification, a simple standardization assurance system for a laboratory network. EUROBIOTECH JOURNAL 2018. [DOI: 10.2478/ebtj-2018-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Analytical laboratory results greatly influence medical diagnosis, about 70% of medical decisions are based on laboratory results. Quality assurance and quality control are designed to detect and correct errors in a laboratory’s analytical process to ensure both the reliability and accuracy of test results. Unreliable performance can result in misdiagnosis and delayed treatment. Furthermore, improved quality guarantees increased productivity at a lower cost. Quality assurance programmes include internal quality control, external quality assessment, proficiency surveillance and standardization. It is necessary to try to ensure compliance with the requirements of the standards at all levels of the process. The sources of these standards are the International Standards Organization (ISO), national standards bodies, guidelines from professional organisations, accreditation bodies and governmental regulations. Laboratory networks increase the performance of laboratories in support of diagnostic screening programme. It is essential that genetic laboratories of a network have procedures underpinned by a robust quality assurance system to minimize errors and to reassure the clinicians and the patients that international standards are being met. This article provides an overview of the bases of quality assurance and its importance in genetic tests and it reports the EBTNA quality assurance system which is a clear and simple system available for access to adequate standardization of a genetic laboratory’s network.
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11
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Beretta S, Patterson MD, Zaccaria S, Della Vedova G, Bonizzoni P. HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinformatics 2018; 19:252. [PMID: 29970002 PMCID: PMC6029272 DOI: 10.1186/s12859-018-2253-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/18/2018] [Indexed: 01/08/2023] Open
Abstract
Background Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays cheaper to produce and more widely available than ever before, have been used to reduce the fragmentation of the assembled haplotypes since their ability to span several variants along the genome. These long reads are also characterized by a high error rate, an issue which may be mitigated, however, with larger sets of reads, when this error rate is uniform across genome positions. Unfortunately, current state-of-the-art dynamic programming approaches designed for long reads deal only with limited coverages. Results Here, we propose a new method for assembling haplotypes which combines and extends the features of previous approaches to deal with long reads and higher coverages. In particular, our algorithm is able to dynamically adapt the estimated number of errors at each variant site, while minimizing the total number of error corrections necessary for finding a feasible solution. This allows our method to significantly reduce the required computational resources, allowing to consider datasets composed of higher coverages. The algorithm has been implemented in a freely available tool, HapCHAT: Haplotype Assembly Coverage Handling by Adapting Thresholds. An experimental analysis on sequencing reads with up to 60 × coverage reveals improvements in accuracy and recall achieved by considering a higher coverage with lower runtimes. Conclusions Our method leverages the long-range information of sequencing reads that allows to obtain assembled haplotypes fragmented in a lower number of unphased haplotype blocks. At the same time, our method is also able to deal with higher coverages to better correct the errors in the original reads and to obtain more accurate haplotypes as a result. Availability HapCHAT is available at http://hapchat.algolab.euunder the GNU Public License (GPL).
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Affiliation(s)
- Stefano Beretta
- Department of Informatics, Systems, and Communication, University of Milano-Bicocca, Milan, Italy
| | - Murray D Patterson
- Department of Informatics, Systems, and Communication, University of Milano-Bicocca, Milan, Italy.
| | - Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, New Jersey, USA
| | - Gianluca Della Vedova
- Department of Informatics, Systems, and Communication, University of Milano-Bicocca, Milan, Italy
| | - Paola Bonizzoni
- Department of Informatics, Systems, and Communication, University of Milano-Bicocca, Milan, Italy
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12
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Shum BO, Henner I, Belluoccio D, Hinchcliffe MJ. Utility of NIST Whole-Genome Reference Materials for the Technical Validation of a Multigene Next-Generation Sequencing Test. J Mol Diagn 2017; 19:602-612. [DOI: 10.1016/j.jmoldx.2017.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 01/04/2023] Open
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13
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Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory. J Clin Microbiol 2017; 55:2502-2520. [PMID: 28592550 PMCID: PMC5527429 DOI: 10.1128/jcm.00361-17] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/26/2017] [Indexed: 11/24/2022] Open
Abstract
Public health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. Here, we describe the validation of WGS on the Illumina platform for routine use in PHLs according to Clinical Laboratory Improvements Act (CLIA) guidelines for laboratory-developed tests (LDTs). We developed a validation panel comprising 10 Enterobacteriaceae isolates, 5 Gram-positive cocci, 5 Gram-negative nonfermenting species, 9 Mycobacterium tuberculosis isolates, and 5 miscellaneous bacteria. The genome coverage range was 15.71× to 216.4× (average, 79.72×; median, 71.55×); the limit of detection (LOD) for single nucleotide polymorphisms (SNPs) was 60×. The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from multilocus sequence typing (MLST) and genome-wide SNP-based phylogenetic assays were 100%. The following objectives were accomplished: (i) the establishment of the performance specifications for WGS applications in PHLs according to CLIA guidelines, (ii) the development of quality assurance and quality control measures, (iii) the development of a reporting format for end users with or without WGS expertise, (iv) the availability of a validation set of microorganisms, and (v) the creation of a modular template for the validation of WGS processes in PHLs. The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data. Additionally, the WGS performance specifications and modular template are adaptable for the validation of other platforms and reagent kits.
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14
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Considerations of developing an NGS assay for clinical applications in precision oncology: The NCI-MATCH NGS assay experience. Curr Probl Cancer 2017. [DOI: 10.1016/j.currproblcancer.2017.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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