1
|
Guha S, Reddi HV, Aarabi M, DiStefano M, Wakeling E, Dungan JS, Gregg AR. Laboratory testing for preconception/prenatal carrier screening: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024; 26:101137. [PMID: 38814327 DOI: 10.1016/j.gim.2024.101137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 05/31/2024] Open
Abstract
Carrier screening has historically assessed a relatively small number of autosomal recessive and X-linked conditions selected based on frequency in a specific subpopulation and association with severe morbidity or mortality. Advances in genomic technologies enable simultaneous screening of individuals for several conditions. The American College of Medical Genetics and Genomics recently published a clinical practice resource that presents a framework when offering screening for autosomal recessive and X-linked conditions during pregnancy and preconception and recommends a tier-based approach when considering the number of conditions to screen for and their frequency within the US population in general. This laboratory technical standard aims to complement the practice resource and to put forth considerations for clinical laboratories and clinicians who offer preconception/prenatal carrier screening.
Collapse
Affiliation(s)
| | - Honey V Reddi
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Mahmoud Aarabi
- UPMC Medical Genetics and Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA; Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | - Jeffrey S Dungan
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
| |
Collapse
|
2
|
Mighton C, Noor A, Watkins N, Di Gioacchino V, Lerner-Ellis J, Wong A, Mukharryamova E, Anggala N, Chitayat D, Greenfeld E. Validation of low-pass genome sequencing for prenatal diagnosis. Prenat Diagn 2024; 44:443-453. [PMID: 38279846 DOI: 10.1002/pd.6525] [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: 08/11/2023] [Revised: 12/11/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024]
Abstract
OBJECTIVE Chromosomal microarray (CMA), while considered the gold standard for detecting copy number variants (CNVs) in prenatal diagnostics, has its limitations, including the necessity to replace aging microarray equipment, low throughput, a static design, and an inefficient multi-day workflow. This study evaluates the feasibility of low-pass genome sequencing (LP-GS) as a potential replacement for CMA in prenatal diagnostics. METHODS We comprehensively compared LP-GS at 10x and 5x average depths with CMA in a prenatal laboratory. We examined parameters, including concordance, sensitivity, specificity, workflow efficiency, and cost-effectiveness. RESULTS We found a high degree of agreement between LP-GS and CMA for detecting CNVs and absence of heterozygosity. Furthermore, compared to CMA, LP-GS increased workflow efficiency and proved to be cost-neutral at 10x and cost-effective at 5x. CONCLUSION Our study suggests that LP-GS is a promising alternative to CMA in prenatal diagnostics, offering advantages, including a more efficient workflow and scalability for larger testing volumes. Importantly, for clinical laboratories that have adopted next-generation sequencing in a separate capacity, LP-GS facilitates a unified NGS-centric approach, enabling workflow consolidation. By offering a single, streamlined platform for detecting a broad range of genetic variants, LP-GS may represent a critical step toward enhancing the diagnostic capabilities of prenatal laboratories.
Collapse
Affiliation(s)
- Chloe Mighton
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Institute of Health Policy Management, and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Abdul Noor
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Watkins
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Wong
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elvira Mukharryamova
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nina Anggala
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elena Greenfeld
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
3
|
Kerkhof J, Rastin C, Schenkel L, Lin H, Sadikovic B. Clinical validation of a single NGS targeted panel pipeline using the KAPA HyperChoice system for detection of germline, somatic and mitochondrial sequence and copy number variants. Expert Rev Mol Diagn 2023; 23:827-841. [PMID: 37542410 DOI: 10.1080/14737159.2023.2245747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Comprehensive molecular diagnostics are highly dependent on the technical performance of next-generation sequencing (NGS) pipelines, which are assessed by data quality, cost, turnaround time, and accuracy of detecting a range of sequence and copy number variants. METHODS A dataset of 285 clinically validated cases (205 retrospective and 80 prospective), carrying complex sequence and copy number variants and thousands of genetic polymorphisms underwent a clinical validation of the KAPA HyperChoice target enrichment system with parallel sample fidelity assessment across a number of NGS panels. The analysis included assessment of peripheral blood, urine, muscle and FFPE tissues. RESULTS High-quality and exceptionally uniform data with 100% coverage of all targeted panels were obtained, resulting in complete sensitivity and specificity for all variant types across nearly all panels and tissue types. Overall reduction in cost and turnaround times was obtained with the implementation of a parallel genotyping sample fidelity system. CONCLUSION Results of the laboratory quality improvement study focused on a single NGS pipeline that includes both nuclear and mitochondrial genomes demonstrated utility in the clinical setting to assess a range of referral reasons, necessary due to the complex molecular etiology of human genetic disorders, while reducing costs and turnaround times.
Collapse
Affiliation(s)
- Jennifer Kerkhof
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cassandra Rastin
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| |
Collapse
|
4
|
Zhang K, Lin G, Han Y, Peng R, Li J. Analysis of Clinical Laboratory Detecting Challenging Variants from Exome Sequencing Using Simulated Patient-Parent Trio Sample: Pilot Study for Neurodevelopmental Disorder de Novo Variants. J Mol Diagn 2023; 25:378-387. [PMID: 37208049 DOI: 10.1016/j.jmoldx.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 05/21/2023] Open
Abstract
To date, there has been no systematic analysis for the clinical laboratory in detecting technically challenging variants using the trio-based exome sequencing (ES) approach. Here, we present an interlaboratory pilot proficiency testing study that used synthetic patient-parent specimens to assess the detection of challenging variants with de novo dominant inheritance modes for neurodevelopmental disorders using various trio-based ES. In total, 27 clinical laboratories that performed diagnostic exome analyses participated in the survey. One of the 26 challenging variants was identified by all laboratories, whereas all 26 variants were identified by only nine laboratories. The lack of identification of mosaic variants was often due to the bioinformatics analysis that excluded the variant. For missing intended heterozygous variants, probable root causes were related to the technical bioinformatics pipeline and variant interpretation and reporting. For each missing variant, there may be more than one probable reason from the different laboratories. There was considerable variation in interlaboratory performance for detecting challenging variants using trio-based ES. This finding may have important implications for the design and validation of tests for different variant types in clinical laboratories, especially for technically challenging variants, and necessary workflow modification can potentially improve trio-based ES performance.
Collapse
Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.
| |
Collapse
|
5
|
Hassan S, Bahar R, Johan MF, Mohamed Hashim EK, Abdullah WZ, Esa E, Abdul Hamid FS, Zulkafli Z. Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) for the Diagnosis of Thalassemia. Diagnostics (Basel) 2023; 13:diagnostics13030373. [PMID: 36766477 PMCID: PMC9914462 DOI: 10.3390/diagnostics13030373] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Thalassemia is one of the most heterogeneous diseases, with more than a thousand mutation types recorded worldwide. Molecular diagnosis of thalassemia by conventional PCR-based DNA analysis is time- and resource-consuming owing to the phenotype variability, disease complexity, and molecular diagnostic test limitations. Moreover, genetic counseling must be backed-up by an extensive diagnosis of the thalassemia-causing phenotype and the possible genetic modifiers. Data coming from advanced molecular techniques such as targeted sequencing by next-generation sequencing (NGS) and third-generation sequencing (TGS) are more appropriate and valuable for DNA analysis of thalassemia. While NGS is superior at variant calling to TGS thanks to its lower error rates, the longer reads nature of the TGS permits haplotype-phasing that is superior for variant discovery on the homologous genes and CNV calling. The emergence of many cutting-edge machine learning-based bioinformatics tools has improved the accuracy of variant and CNV calling. Constant improvement of these sequencing and bioinformatics will enable precise thalassemia detections, especially for the CNV and the homologous HBA and HBG genes. In conclusion, laboratory transiting from conventional DNA analysis to NGS or TGS and following the guidelines towards a single assay will contribute to a better diagnostics approach of thalassemia.
Collapse
Affiliation(s)
- Syahzuwan Hassan
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Institute for Medical Research, Shah Alam 40170, Malaysia
| | - Rosnah Bahar
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Muhammad Farid Johan
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | | | - Wan Zaidah Abdullah
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ezalia Esa
- Institute for Medical Research, Shah Alam 40170, Malaysia
| | | | - Zefarina Zulkafli
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Correspondence:
| |
Collapse
|
6
|
Blout Zawatsky CL, Bick D, Bier L, Funke B, Lebo M, Lewis KL, Orlova E, Qian E, Ryan L, Schwartz MLB, Soper ER. Elective genomic testing: Practice resource of the National Society of Genetic Counselors. J Genet Couns 2023; 32:281-299. [PMID: 36597794 DOI: 10.1002/jgc4.1654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 01/05/2023]
Abstract
Genetic counseling for patients who are pursuing genetic testing in the absence of a medical indication, referred to as elective genomic testing (EGT), is becoming more common. This type of testing has the potential to detect genetic conditions before there is a significant health impact permitting earlier management and/or treatment. Pre- and post-test counseling for EGT is similar to indication-based genetic testing. Both require a complete family and medical history when ordering a test or interpreting a result. However, EGT counseling has some special considerations including greater uncertainties around penetrance and clinical utility and a lack of published guidelines. While certain considerations in the selection of a high-quality genetic testing laboratory are universal, there are some considerations that are unique to the selection of a laboratory performing EGT. This practice resource intends to provide guidance for genetic counselors and other healthcare providers caring for adults seeking pre- or post-test counseling for EGT. Genetic counselors and other genetics trained healthcare providers are the ideal medical professionals to supply accurate information to individuals seeking counseling about EGT enabling them to make informed decisions about testing and follow-up.
Collapse
Affiliation(s)
- Carrie L Blout Zawatsky
- Genomes2People, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Ariadne Labs, Boston, Massachusetts, USA.,The MGH Institute of Health Professions, Boston, Massachusetts, USA
| | | | - Louise Bier
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Matthew Lebo
- Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Cambridge, Massachusetts, USA.,Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Boston, Massachusetts, USA
| | - Katie L Lewis
- Center for Precision Health Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Ekaterina Orlova
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily Qian
- Department of Genetics, Yale University, New Haven, Connecticut, USA
| | | | - Marci L B Schwartz
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Emily R Soper
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
7
|
Pfeifer JD, Loberg R, Lofton-Day C, Zehnbauer BA. Reference Samples to Compare Next-Generation Sequencing Test Performance for Oncology Therapeutics and Diagnostics. Am J Clin Pathol 2022; 157:628-638. [PMID: 34871357 DOI: 10.1093/ajcp/aqab164] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/24/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Diversity of laboratory-developed tests (LDTs) using next-generation sequencing (NGS) raises concerns about their accuracy for selection of targeted therapies. A working group developed a pilot study of traceable reference samples to measure NGS LDT performance among a cohort of clinical laboratories. METHODS Human cell lines were engineered via CRISPR/Cas9 and prepared as formalin-fixed, paraffin-embedded cell pellets ("wet" samples) to assess the entire NGS test cycle. In silico mutagenized NGS sequence files ("dry" samples) were used to assess the bioinformatics component of the NGS test cycle. Single and multinucleotide variants (n = 36) of KRAS and NRAS were tested at 5% or 15% variant allele fraction to determine eligibility for therapy with the EGFR inhibitor panitumumab in the setting of metastatic colorectal cancer. RESULTS Twenty-one (21/21) laboratories tested wet samples; 19 of 21 analyzed dry samples. Of the laboratories that tested both the wet and dry samples, 7 (37%) of 19 laboratories correctly reported all variants, 3 (16%) of 19 had fewer than five errors, and 9 (47%) of 19 had five or more errors. Most errors were false negatives. CONCLUSIONS Genetically engineered cell lines and mutagenized sequence files are complementary reference samples for evaluating NGS test performance among clinical laboratories using LDTs. Variable accuracy in detection of genetic variants among some LDTs may identify different patient populations for targeted therapy.
Collapse
Affiliation(s)
- John D Pfeifer
- Department of Pathology, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Loberg
- Clinical Biomarkers and Diagnostics, Thousand Oaks, CA, USA
| | | | - Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| |
Collapse
|
8
|
Corominas J, Smeekens SP, Nelen MR, Yntema HG, Kamsteeg EJ, Pfundt R, Gilissen C. Clinical exome sequencing - mistakes and caveats. Hum Mutat 2022; 43:1041-1055. [PMID: 35191116 PMCID: PMC9541396 DOI: 10.1002/humu.24360] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 01/11/2022] [Accepted: 02/18/2022] [Indexed: 11/30/2022]
Abstract
Massive parallel sequencing technology has become the predominant technique for genetic diagnostics and research. Many genetic laboratories have wrestled with the challenges of setting up genetic testing workflows based on a completely new technology. The learning curve we went through as a laboratory was accompanied by growing pains while we gained new knowledge and expertise. Here we discuss some important mistakes that have been made in our laboratory through 10 years of clinical exome sequencing but that have given us important new insights on how to adapt our working methods. We provide these examples and the lessons that we learned to help other laboratories avoid to make the same mistakes.
Collapse
Affiliation(s)
- Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sanne P Smeekens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
9
|
Wilcox E, Harrison SM, Lockhart E, Voelkerding K, Lubin IM, Rehm HL, Kalman LV, Funke B. Creation of an Expert Curated Variant List for Clinical Genomic Test Development and Validation: A ClinGen and GeT-RM Collaborative Project. J Mol Diagn 2021; 23:1500-1505. [PMID: 34384894 PMCID: PMC8647424 DOI: 10.1016/j.jmoldx.2021.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/09/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022] Open
Abstract
Modern genomic sequencing tests often interrogate large numbers of genes. Identification of appropriate reference materials for development, validation studies, and quality assurance of these tests poses a significant challenge for laboratories. It is difficult to develop and maintain expert knowledge to identify all variants that must be validated to ensure analytic and clinical validity. Additionally, it is usually not possible to procure appropriate and characterized genomic DNA reference materials containing the number and scope of variants required. To address these challenges, the Centers for Disease Control and Prevention's Genetic Testing Reference Material Program (GeT-RM) has partnered with the Clinical Genome Resource (ClinGen) to develop a publicly available list of expert curated, clinically important variants. ClinGen Variant Curation Expert Panels nominated 546 variants found in 84 disease-associated genes, including common pathogenic and difficult-to-detect variants. Variant types nominated included 346 single nucleotide variants, 104 deletions, 37 copy number variants, 25 duplications, 18 deletion-insertions, 5 inversions, 4 insertions, 2 complex rearrangements, 3 difficult-to-sequence regions, and 2 fusions. This expert-curated variant list is a resource that provides a foundation for designing comprehensive validation studies and for creating in silico reference materials for clinical genomic test development and validation.
Collapse
Affiliation(s)
- Emma Wilcox
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Edward Lockhart
- Informatics and Data Science Branch, Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Ira M Lubin
- Quality and Safety Systems Branch, Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Lisa V Kalman
- Informatics and Data Science Branch, Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
| | - Birgit Funke
- Division of Genomic Health, Sema4, Stamford, Connecticut
| |
Collapse
|
10
|
Rosenbaum JN, Berry AB, Church AJ, Crooks K, Gagan JR, López-Terrada D, Pfeifer JD, Rennert H, Schrijver I, Snow AN, Wu D, Ewalt MD. A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee. J Mol Diagn 2021; 23:1218-1240. [PMID: 34245921 DOI: 10.1016/j.jmoldx.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Molecular genetic pathology (MGP) is a subspecialty of pathology and medical genetics and genomics. Genomic testing, which we define as that which generates large data sets and interrogates large segments of the genome in a single assay, is increasingly recognized as essential for optimal patient care through precision medicine. The most common genomic testing technologies in clinical laboratories are next-generation sequencing and microarray. It is essential to train in these methods and to consider the data generated in the context of the diagnosis, medical history, and other clinical findings of individual patients. Accordingly, updating the MGP fellowship curriculum to include genomics is timely, important, and challenging. At the completion of training, an MGP fellow should be capable of independently interpreting and signing out results of a wide range of genomic assays and, given the appropriate context and institutional support, of developing and validating new assays in compliance with applicable regulations. The Genomics Task Force of the MGP Program Directors, a working group of the Association for Molecular Pathology Training and Education Committee, has developed a genomics curriculum framework and recommendations specific to the MGP fellowship. These recommendations are presented for consideration and implementation by MGP fellowship programs with the understanding that MGP programs exist in a diversity of clinical practice environments with a spectrum of available resources.
Collapse
Affiliation(s)
- Jason N Rosenbaum
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna B Berry
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Swedish Cancer Institute and Institute of Systems Biology, Seattle, Washington
| | - Alanna J Church
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Kristy Crooks
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jeffrey R Gagan
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Dolores López-Terrada
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Baylor College of Medicine, Houston, Texas
| | - John D Pfeifer
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Hanna Rennert
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Iris Schrijver
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anthony N Snow
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - David Wu
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Mark D Ewalt
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
11
|
Genetic testing for inherited colorectal cancer and polyposis, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1807-1817. [PMID: 34140662 DOI: 10.1038/s41436-021-01207-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the fourth most frequently diagnosed cancer and 30% of all cases of CRC are believed to have a familial component and up to one-third of these (10%) are hereditary. Pathogenic germline variants in multiple genes have been associated with predisposition to hereditary CRC or polyposis. Lynch syndrome (LS) is the most common hereditary CRC syndrome, caused by variants in the mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2 and is inherited in a dominant manner. Heritable conditions associated with colonic polyposis include familial adenomatous polyposis (FAP) associated with APC pathogenic variants, MUTYH-associated polyposis (MAP) caused by biallelic MUTYH pathogenic variants, and polymerase proofreading-associated polyposis (PPAP) caused by POLE or POLD1 pathogenic variants. Given the overlapping phenotypes of the cancer syndromes along with the limited sensitivity of using clinical criteria alone, a multigene panel testing approach to diagnose these conditions using next-generation sequencing (NGS) is effective and efficient. This technical standard is not recommended for use in the clinic for patient evaluation. Please refer to National Comprehensive Cancer Network (NCCN) clinical practice guidelines to determine an appropriate testing strategy and guide medical screening and management. This 2021 edition of the American College of Medical Genetics and Genomics (ACMG) technical standard supersedes the 2013 edition on this topic.
Collapse
|
12
|
One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation. Genet Med 2021; 23:1673-1680. [PMID: 34007000 PMCID: PMC8460443 DOI: 10.1038/s41436-021-01187-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions. METHODS An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)-based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients. RESULTS In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests. CONCLUSION The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.
Collapse
|
13
|
Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM. Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1399-1415. [PMID: 33927380 DOI: 10.1038/s41436-021-01139-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
Collapse
Affiliation(s)
| | - Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Julianne O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Lisa M Vincent
- Division of Pathology & Laboratory Medicine, Children's National Health System, Washington, DC, USA.,Departments of Pathology and Pediatrics, George Washington University, Washington, DC, USA
| | | |
Collapse
|
14
|
Zehnbauer BA. The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice. J Mol Diagn 2019; 21:938-942. [PMID: 31635797 DOI: 10.1016/j.jmoldx.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023] Open
Abstract
This editorial highlights 20 years of JMD defining professional practice.
Collapse
Affiliation(s)
- Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia (Editor-in-Chief).
| |
Collapse
|
15
|
One byte at a time: evidencing the quality of clinical service next-generation sequencing for germline and somatic variants. Eur J Hum Genet 2019; 28:202-212. [PMID: 31570784 PMCID: PMC6974611 DOI: 10.1038/s41431-019-0515-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/03/2019] [Accepted: 08/29/2019] [Indexed: 12/16/2022] Open
Abstract
Next-generation sequencing (NGS) is replacing other molecular techniques to become the de facto gene diagnostics approach, transforming the speed of diagnosis for patients and expanding opportunities for precision medicine. Consequently, for accredited laboratories as well as those seeking accreditation, both objective measures of quality and external review of laboratory processes are required. External quality assessment (EQA), or Proficiency Testing (PT), can assess a laboratory’s service through an independent external agency, the EQA provider. The analysis of a growing number of genes and whole exome and genomes is now routine; therefore, an EQA must be delivered to enable all testing laboratories to participate. In this paper, we describe the development of a unique platform and gene target independent EQA scheme for NGS, designed to scale from current to future requirements of clinical diagnostic laboratories testing for germline and somatic variants. The EQA results from three annual rounds indicate that clinical diagnostic laboratories are providing an increasingly high-quality NGS service and variant calling abilities are improving. From an EQA provider perspective, challenges remain regarding delivery and performance criteria, as well as in analysing similar NGS approaches between cohorts with meaningful metrics, sample sourcing and data formats.
Collapse
|