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Lyon E, Temple-Smolkin RL, Hegde M, Gastier-Foster JM, Palomaki GE, Richards CS. An Educational Assessment of Evidence Used for Variant Classification: A Report of the Association for Molecular Pathology. J Mol Diagn 2022; 24:555-565. [PMID: 35429647 DOI: 10.1016/j.jmoldx.2021.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/12/2021] [Accepted: 12/10/2021] [Indexed: 11/25/2022] Open
Abstract
The Association for Molecular Pathology Variant Interpretation Testing Among Laboratories (VITAL) Working Group convened to evaluate the Standards and Guidelines for the Interpretation of Sequence Variants implementation into clinical practice, identify problematic classification rules, and define implementation challenges. Variants and associated clinical information were provided to volunteer respondents. Participant variant classifications were compared with intended consensus-derived classifications of the Working Group. The 24 variant challenges received 1379 responses; 1119 agreed with the intended response (81%; 95% CI, 79% to 83%). Agreement ranged from 44% to 100%, with 16 challenges (67%; 47% to 82%) reaching consensus (≥80% agreement). Participant classifications were also compared to a calculated interpretation of the ACMG Guidelines using the participant-reported criteria as input. The 24 variant challenges had 1368 responses with specific evidence provided and 1121 (82%; 80% to 84%) agreed with the calculated interpretation. Agreement for challenges ranged from 63% to 98%; 15 (63%; 43% to 79%) reaching consensus. Among 81 individual participants, 32 (40%; 30% to 50%) reached agreement with at least 80% of the intended classifications and 42 (52%; 41% to 62%) with the calculated classifications. This study demonstrated that although variant classification remains challenging, published guidelines are being utilized and adapted to improve variant calling consensus. This study identified situations where clarifications are warranted and provides a model for competency assessment.
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Affiliation(s)
- Elaine Lyon
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Madhuri Hegde
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Global Genetics Laboratory, PerkinElmer Genomics, Pittsburgh, Pennsylvania
| | - Julie M Gastier-Foster
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Departments of Pediatrics and Pathology/Immunology, Baylor College of Medicine, Houston, Texas; Pathology Department, Texas Children's Hospital, Houston, Texas; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Glenn E Palomaki
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and Laboratory Medicine, Women & Infants Hospital and the Alpert Medical School at Brown University, Providence, Rhode Island
| | - C Sue Richards
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Molecular and Medical Genetics and Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon.
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2
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Tayeh MK, Gaedigk A, Goetz MP, Klein TE, Lyon E, McMillin GA, Rentas S, Shinawi M, Pratt VM, Scott SA. Clinical pharmacogenomic testing and reporting: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:759-768. [PMID: 35177334 DOI: 10.1016/j.gim.2021.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pharmacogenomic testing interrogates germline sequence variants implicated in interindividual drug response variability to infer a drug response phenotype and to guide medication management for certain drugs. Specifically, discrete aspects of pharmacokinetics, such as drug metabolism, and pharmacodynamics, as well as drug sensitivity, can be predicted by genes that code for proteins involved in these pathways. Pharmacogenomics is unique and differs from inherited disease genetics because the drug response phenotype can be drug-dependent and is often unrecognized until an unexpected drug reaction occurs or a patient fails to respond to a medication. Genes and variants with sufficiently high levels of evidence and consensus may be included in a clinical pharmacogenomic test; however, result interpretation and phenotype prediction can be challenging for some genes and medications. This document provides a resource for laboratories to develop and implement clinical pharmacogenomic testing by summarizing publicly available resources and detailing best practices for pharmacogenomic nomenclature, testing, result interpretation, and reporting.
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Affiliation(s)
- Marwan K Tayeh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO; Department of Pediatrics, UMKC School of Medicine, University of Missouri-Kansas City, Kansas City, MO
| | - Matthew P Goetz
- Department of Pharmacology and Oncology, Mayo Clinic, Rochester, MN
| | - Teri E Klein
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, CA
| | - Elaine Lyon
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | - Stefan Rentas
- Department of Pathology, Duke University School of Medicine, Durham, NC
| | - Marwan Shinawi
- Division of Genetics & Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, CA; Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, CA
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3
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Giles HH, Hegde MR, Lyon E, Stanley CM, Kerr ID, Garlapow ME, Eggington JM. The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy. Annu Rev Genomics Hum Genet 2021; 22:285-307. [PMID: 33900788 DOI: 10.1146/annurev-genom-121620-082709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clinical genetic variant classification science is a growing subspecialty of clinical genetics and genomics. The field's continued improvement is essential for the success of precision medicine in both germline (hereditary) and somatic (oncology) contexts. This review focuses on variant classification for DNA next-generation sequencing tests. We first summarize current limitations in variant discovery and definition, and then describe the current five- and four-tier classification systems outlined in dominant standards and guideline publications for germline and somatic tests, respectively. We then discuss measures of variant classification discordance and the field's bias for positive results, as well as considerations for panel size and population screening in the context of estimates of positive predictive value thatincorporate estimated variant classification imperfections. Finally, we share opinions on the current state of variant classification from some of the authors of the most widely used standards and guideline publications and from other domain experts.
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Affiliation(s)
- Hunter H Giles
- Center for Genomic Interpretation, Sandy, Utah 84092, USA; , ,
| | - Madhuri R Hegde
- PerkinElmer Genomics, Waltham, Massachusetts 02450, USA; .,Department of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Elaine Lyon
- HudsonAlpha Clinical Services Lab, Huntsville, Alabama 35806, USA;
| | - Christine M Stanley
- C2i Genomics, Cambridge, Massachusetts 02139, USA.,Variantyx, Framingham, Massachusetts 01701, USA;
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4
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Hamad L, Kreidieh K, Nakouzi G, Lyon E, Yazbek S. Recommended measures for the efficient care of patients with genetic disorders during the COVID-19 pandemic in low and middle income countries. Am J Med Genet A 2020; 182:2841-2846. [PMID: 33067931 DOI: 10.1002/ajmg.a.61879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
The coronavirus disease 2019 (COVID-19) emerged in early 2020 and since, has brought about tremendous cost to economies and healthcare systems universally. Reports of pediatric patients with inherited conditions and COVID-19 infections are emerging. Specific risks for morbidity and mortality that this pandemic carries for different categories of genetic disorders are still mostly unknown. Thus, there are no specific recommendations for the diagnosis, management, and treatment of patients with genetic disorders during the COVID-19 or other pandemics. Emerging publications, from Upper-Middle Income countries (UMIC), discuss the recent experiences of genetic centers in the continuity of care for patients with genetic disorders in the context of this pandemic. Many measures to facilitate the plan to continuous genetic care in a well-developed health system, may not be applicable in Low and Middle Income countries (LMIC). With poorly structured health systems and with the lack of established genetic services, the COVID-19 pandemic will easily exacerbate the access to care for patients with genetic disease in these countries. This article focuses on the unique challenges of providing genetic healthcare services during emergency situations in LMIC countries and provides practical preparations for this and other pandemic situations.
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Affiliation(s)
- Lina Hamad
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Khalil Kreidieh
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghunwa Nakouzi
- HudsonAlpha Clinical Services Lab, LLC, Huntsville, Alabama, USA
| | - Elaine Lyon
- HudsonAlpha Clinical Services Lab, LLC, Huntsville, Alabama, USA
| | - Soha Yazbek
- Medical Laboratory Sciences Program, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
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Affiliation(s)
- Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | | | - James M Holt
- HudsonAlpha Clinical Services Lab, Huntsville, AL
| | - Elaine Lyon
- HudsonAlpha Clinical Services Lab, Huntsville, AL
| | - David Bick
- HudsonAlpha Clinical Services Lab, Huntsville, AL
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6
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McGlaughon JL, Pasquali M, Wallace K, Ross J, Senol-Cosar O, Shen W, Weaver MA, Feigenbaum A, Lyon E, Enns GM, Mao R, Baudet HG. Assessing the strength of evidence for genes implicated in fatty acid oxidation disorders using the ClinGen clinical validity framework. Mol Genet Metab 2019; 128:122-128. [PMID: 31399326 DOI: 10.1016/j.ymgme.2019.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 12/30/2022]
Abstract
Newborn screening is an incredibly useful tool for the early identification of many metabolic disorders, including fatty acid oxidation (FAO) disorders. In many cases, molecular tests are necessary to reach a final diagnosis, highlighting the need for a thorough evaluation of genes implicated in FAO disorders. Using the ClinGen (Clinical Genome Resource) clinical validity framework, thirty genes were analyzed for the strength of evidence supporting their association with FAO disorders. Evidence was gathered from the literature by biocurators and presented to disease experts for review in order to assign a clinical validity classification of Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Reported Evidence. Of the gene-disease relationships evaluated, 22/30 were classified as Definitive, three as Moderate, one as Limited, three as No Reported Evidence and one as Disputed. Gene-disease relationships with a Limited, Disputed, and No Reported Evidence were found on two, six, and up to four panels out of 30 FAO disorder-specific panels, respectively, in the National Institute of Health Genetic Testing Registry, while over 70% of the genes on panels are definitively associated with an FAO disorder. These results highlight the need to systematically assess the clinical relevance of genes implicated in fatty acid oxidation disorders in order to improve the interpretation of genetic testing results and diagnosis of patients with these disorders.
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Affiliation(s)
- Jennifer L McGlaughon
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Marzia Pasquali
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Kathleen Wallace
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Justyne Ross
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Ozlem Senol-Cosar
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA; Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, MA, USA
| | - Wei Shen
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, MD, USA
| | - Annette Feigenbaum
- Department of Pediatrics, University of California San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Elaine Lyon
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Gregory M Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Stanford, CA, USA
| | - Rong Mao
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Heather G Baudet
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, NC, USA.
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7
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Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter-Konecki U, Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ, Mao R. Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene. Hum Mutat 2019; 39:1569-1580. [PMID: 30311390 DOI: 10.1002/humu.23649] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/28/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022]
Abstract
The ClinGen Inborn Errors of Metabolism Working Group was tasked with creating a comprehensive, standardized knowledge base of genes and variants for metabolic diseases. Phenylalanine hydroxylase (PAH) deficiency was chosen to pilot development of the Working Group's standards and guidelines. A PAH variant curation expert panel (VCEP) was created to facilitate this process. Following ACMG-AMP variant interpretation guidelines, we present the development of these standards in the context of PAH variant curation and interpretation. Existing ACMG-AMP rules were adjusted based on disease (6) or strength (5) or both (2). Disease adjustments include allele frequency thresholds, functional assay thresholds, and phenotype-specific guidelines. Our validation of PAH-specific variant interpretation guidelines is presented using 85 variants. The PAH VCEP interpretations were concordant with existing interpretations in ClinVar for 69 variants (81%). Development of biocurator tools and standards are also described. Using the PAH-specific ACMG-AMP guidelines, 714 PAH variants have been curated and will be submitted to ClinVar. We also discuss strategies and challenges in applying ACMG-AMP guidelines to autosomal recessive metabolic disease, and the curation of variants in these genes.
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Affiliation(s)
- Diane B Zastrow
- Palo Alto Medical Foundation, Palo Alto, California.,Stanford University, Stanford, California
| | - Heather Baudet
- University of North Carolina, Chapel Hill, North Carolina
| | - Wei Shen
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Amanda Thomas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Yue Si
- GeneDx, Gaithersburg, Maryland
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Angela M Lager
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Jixia Liu
- Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | | | | | | | | | | | | | - Annette Feigenbaum
- Rady Children's Hospital and University of California, San Diego, California
| | - Uta Lichter-Konecki
- Children's Hospital of Pittsburg of UPMC, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Elaine Lyon
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Marzia Pasquali
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Michael Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Nenad Blau
- Dietmar-Hopp Metabolic Center, University Children's Hospital, Department of General Pediatrics, Heidelberg, Germany
| | - Robert D Steiner
- Marshfield Clinic Research Institute, Marshfield, Wisconsin.,University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | | | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
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Melis R, Mohamed J, Ha Y, Lyon E, McMillin G. Postmortem CYP2D6 Genotyping and Copy Number Determinations Using DNA Extracted from Archived FTA Bloodstains. J Anal Toxicol 2019; 43:411-414. [DOI: 10.1093/jat/bkz008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/07/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Roberta Melis
- ARUP Institute for Clinical and Experimental Pathology, Department of Research and Development, 500 Chipeta Way, Salt Lake City, UT, USA
| | - Jama Mohamed
- ARUP Institute for Clinical and Experimental Pathology, Department of Research and Development, 500 Chipeta Way, Salt Lake City, UT, USA
| | - Youna Ha
- ARUP Institute for Clinical and Experimental Pathology, Department of Research and Development, 500 Chipeta Way, Salt Lake City, UT, USA
| | - Elaine Lyon
- Department of Pathology, University of Utah School of Medicine—Pathology, Salt Lake City, UT, USA
| | - Gwendolyn McMillin
- ARUP Institute for Clinical and Experimental Pathology, Department of Research and Development, 500 Chipeta Way, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine—Pathology, Salt Lake City, UT, USA
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9
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Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter‐Konecki U, Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ, Mao R. Cover Image, Volume 39, Issue 11. Hum Mutat 2018. [DOI: 10.1002/humu.23662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Ji Y, Si Y, McMillin GA, Lyon E. Clinical pharmacogenomics testing in the era of next generation sequencing: challenges and opportunities for precision medicine. Expert Rev Mol Diagn 2018; 18:411-421. [PMID: 29634383 DOI: 10.1080/14737159.2018.1461561] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION The rapid development and dramatic decrease in cost of sequencing techniques have ushered the implementation of genomic testing in patient care. Next generation DNA sequencing (NGS) techniques have been used increasingly in clinical laboratories to scan the whole or part of the human genome in order to facilitate diagnosis and/or prognostics of genetic disease. Despite many hurdles and debates, pharmacogenomics (PGx) is believed to be an area of genomic medicine where precision medicine could have immediate impact in the near future. Areas covered: This review focuses on lessons learned through early attempts of clinically implementing PGx testing; the challenges and opportunities that PGx testing brings to precision medicine in the era of NGS. Expert commentary: Replacing targeted analysis approach with NGS for PGx testing is neither technically feasible nor necessary currently due to several technical limitations and uncertainty involved in interpreting variants of uncertain significance for PGx variants. However, reporting PGx variants out of clinical whole exome or whole genome sequencing (WES/WGS) might represent additional benefits for patients who are tested by WES/WGS.
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Affiliation(s)
- Yuan Ji
- a ARUP Laboratories and Department of Pathology , University of Utah School of Medicine , Salt Lake City , UT , USA
| | - Yue Si
- a ARUP Laboratories and Department of Pathology , University of Utah School of Medicine , Salt Lake City , UT , USA
| | - Gwendolyn A McMillin
- a ARUP Laboratories and Department of Pathology , University of Utah School of Medicine , Salt Lake City , UT , USA
| | - Elaine Lyon
- a ARUP Laboratories and Department of Pathology , University of Utah School of Medicine , Salt Lake City , UT , USA
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11
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Kaul KL, Sabatini LM, Tsongalis GJ, Caliendo AM, Olsen RJ, Ashwood ER, Bale S, Benirschke R, Carlow D, Funke BH, Grody WW, Hayden RT, Hegde M, Lyon E, Murata K, Pessin M, Press RD, Thomson RB. The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care. Acad Pathol 2017; 4:2374289517708309. [PMID: 28815200 PMCID: PMC5528950 DOI: 10.1177/2374289517708309] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 12/16/2022] Open
Abstract
An explosion of knowledge and technology is revolutionizing medicine and patient care. Novel testing must be brought to the clinic with safety and accuracy, but also in a timely and cost-effective manner, so that patients can benefit and laboratories can offer testing consistent with current guidelines. Under the oversight provided by the Clinical Laboratory Improvement Amendments, laboratories have been able to develop and optimize laboratory procedures for use in-house. Quality improvement programs, interlaboratory comparisons, and the ability of laboratories to adjust assays as needed to improve results, utilize new sample types, or incorporate new mutations, information, or technologies are positive aspects of Clinical Laboratory Improvement Amendments oversight of laboratory-developed procedures. Laboratories have a long history of successful service to patients operating under Clinical Laboratory Improvement Amendments. A series of detailed clinical examples illustrating the quality and positive impact of laboratory-developed procedures on patient care is provided. These examples also demonstrate how Clinical Laboratory Improvement Amendments oversight ensures accurate, reliable, and reproducible testing in clinical laboratories.
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Affiliation(s)
- Karen L Kaul
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Linda M Sabatini
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Gregory J Tsongalis
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA.,Laboratory Medicine, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Angela M Caliendo
- Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | | | - Sherri Bale
- Department of Pathology, University of Colorado, Aurora, CO, USA
| | - Robert Benirschke
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Dean Carlow
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Birgit H Funke
- Laboratory for Molecular Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Wayne W Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics and Human Genetics, UCLA School of Medicine, Los Angeles, CA, USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Elaine Lyon
- Pathology Department, University of Utah School of Medicine/ARUP Laboratories, Salt Lake City, UT, USA
| | - Kazunori Murata
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard D Press
- Department of Pathology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Richard B Thomson
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
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12
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Joseph L, Cankovic M, Caughron S, Chandra P, Emmadi R, Hagenkord J, Hallam S, Jewell KE, Klein RD, Pratt VM, Rothberg PG, Temple-Smolkin RL, Lyon E. The Spectrum of Clinical Utilities in Molecular Pathology Testing Procedures for Inherited Conditions and Cancer: A Report of the Association for Molecular Pathology. J Mol Diagn 2016; 18:605-619. [PMID: 27542512 DOI: 10.1016/j.jmoldx.2016.05.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 05/18/2016] [Accepted: 05/26/2016] [Indexed: 12/24/2022] Open
Abstract
Clinical utility describes the benefits of each laboratory test for that patient. Many stakeholders have adopted narrow definitions for the clinical utility of molecular testing as applied to targeted pharmacotherapy in oncology, regardless of the population tested or the purpose of the testing. This definition does not address all of the important applications of molecular diagnostic testing. Definitions consistent with a patient-centered approach emphasize and recognize that a clinical test result's utility depends on the context in which it is used and are particularly relevant to molecular diagnostic testing because of the nature of the information they provide. Debates surrounding levels and types of evidence needed to properly evaluate the clinical value of molecular diagnostics are increasingly important because the growing body of knowledge, stemming from the increase of genomic medicine, provides many new opportunities for molecular testing to improve health care. We address the challenges in defining the clinical utility of molecular diagnostics for inherited diseases or cancer and provide assessment recommendations. Starting with a modified analytic validity, clinical validity, clinical utility, and ethical, legal, and social implications model for addressing clinical utility of molecular diagnostics with a variety of testing purposes, we recommend promotion of patient-centered definitions of clinical utility that appropriately recognize the valuable contribution of molecular diagnostic testing to improve patient care.
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Affiliation(s)
- Loren Joseph
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Milena Cankovic
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Samuel Caughron
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; MAWD Pathology Group, PA, North Kansas City, Missouri
| | - Pranil Chandra
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; PathGroup, LLC, Brentwood, Tennessee
| | - Rajyasree Emmadi
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Jill Hagenkord
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; 23andMe, Inc., Mountain View, California
| | - Stephanie Hallam
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Good Start Genetics, Inc., Cambridge, Massachusetts
| | - Kay E Jewell
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Tara Center, LLC, Stevens Point, Wisconsin
| | - Roger D Klein
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Department of Molecular Pathology, Cleveland Clinic, Cleveland, Ohio
| | - Victoria M Pratt
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, Indiana
| | - Paul G Rothberg
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, New York
| | | | - Elaine Lyon
- Association for Molecular Pathology's Framework for the Evidence Needed to Demonstrate Clinical Utility Task Force, Bethesda, Maryland; Department of Pathology, University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah.
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Powers JL, Buys SS, Fletcher D, Melis R, Johnson-Davis KL, Lyon E, Malmberg EM, McMillin GA. Multigene and Drug Interaction Approach for Tamoxifen Metabolite Patterns Reveals Possible Involvement of CYP2C9, CYP2C19, and ABCB1. J Clin Pharmacol 2016; 56:1570-1581. [PMID: 27198207 DOI: 10.1002/jcph.771] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 11/11/2022]
Abstract
Tamoxifen is metabolically activated to 4-hydroxytamoxifen and endoxifen by cytochrome P450 (CYP). CYP phenotypes have been correlated to tamoxifen outcomes, but few have considered drug interactions or combinations of genes. Fewer still have considered ABCB1, which encodes P-glycoprotein and transports active tamoxifen metabolites. We compared the concentrations of tamoxifen and metabolites in 116 breast cancer patients with predicted phenotypes for CYP2D6, CYP3A4, CYP3A5, CYP2C9, CYP2C19, and ABCB1 genotypes. A significant correlation between CYP2D6 phenotypes and tamoxifen metabolites was seen, strongest for endoxifen (P < .0001). Statistical fit of the data improved when using gene activity scores adjusted for known drug interactions. Concentration of tamoxifen was significantly higher (P = .02) for patients taking a CYP2C19 inhibitor. No significant relationships were found for other genes unless patients were subgrouped according to CYP2D6 phenotypes or ABCB1 genotypes. Lower concentrations of endoxifen and endoxifen/4-hydroxytamoxifen ratios were seen with impaired CYP2C9 (P = .05 and P = .03, respectively) if patients had the same CYP2D6 phenotype and were not taking a CYP2D6 or CYP2C19 inhibitor. Lower concentrations of 4-hydroxytamoxifen were seen for impaired CYP2C19 when ABCB1 SNP3435 was nonvariant (P = .04). With 3 impaired CYP phenotypes, endoxifen concentrations were lower than if only CYP2D6 was impaired (P = .05). When CYP2D6 was impaired, ABCB1 3435 CC (rs1045642) was associated with significantly higher endoxifen (P = .03). Thus, impairment in CYP2C9, CYP2C19, or ABCB1 contributes to a lower steady-state endoxifen concentration at the dose studied. These studies represent an improved way of examining relationships between pharmacogenetics, drug concentrations, and clinical outcomes and warrants study in larger populations.
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Affiliation(s)
- Jennifer L Powers
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Deborah Fletcher
- Department of Pharmacy, Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Roberta Melis
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Kamisha L Johnson-Davis
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Elaine Lyon
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | | | - Gwendolyn A McMillin
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
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Millson A, Lewis T, Pesaran T, Salvador D, Gillespie K, Gau CL, Pont-Kingdon G, Lyon E, Bayrak-Toydemir P. Processed Pseudogene Confounding Deletion/Duplication Assays for SMAD4. J Mol Diagn 2015; 17:576-82. [DOI: 10.1016/j.jmoldx.2015.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/23/2015] [Accepted: 05/06/2015] [Indexed: 11/25/2022] Open
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Affiliation(s)
| | - Elaine Lyon
- Department of Pathology and ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | - George M Rodgers
- Department of Pathology and Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, UT; ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | - Mohamed A Jama
- ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | | | - Kristi J Smock
- Department of Pathology and ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT;
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Powers JL, Melis R, Malmberg E, Johnson-Davis K, Buys S, Lyon E, McMillin GA. 31: Impact of Multiple CYP Variants on Tamoxifen Metabolite Concentrations. Am J Clin Pathol 2015. [DOI: 10.1093/ajcp/143.suppl1.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | | | - Saundra Buys
- Internal Medicine, University of Utah, Salt Lake City, and
| | - Elaine Lyon
- Departments of Pathology and
- ARUP Laboratories, Salt Lake City, UT
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Lyon E, Cockerill FR, Bale SJ, Beadling C, Bry L, Hagenkord J, Kulkarni S, Press R, Palomaki GE. Next Generation Sequencing in Clinical Diagnostics: Experiences of Early Adopters. Clin Chem 2015; 61:41-9. [DOI: 10.1373/clinchem.2014.222687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Elaine Lyon
- Associate Professor of Pathology, University of Utah School of Medicine, Salt Lake City, UT
- Medical Director, Molecular Genetics, ARUP Laboratories, Salt Lake City, UT
| | - Franklin R Cockerill
- Professor and Chair, Department of Laboratory Medicine and Pathology and
- President and CEO, Mayo Medical Laboratories, Mayo Clinic, Rochester, MN
- Current affiliation: Quest Diagnostics (10/1/14)
| | | | - Carol Beadling
- Assistant Director, Pathology Translational Research Laboratory, Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon
| | - Lynn Bry
- Director, Center for Clinical and Translational Metagenomics, Brigham & Women's Hospital and Associate Professor of Pathology, Harvard Medical School, Boston, MA
| | | | - Shashikant Kulkarni
- Associate Professor, Pathology and Immunology, Pediatrics and Genetics, Director of Cytogenomics and Molecular Pathology, Washington University School of Medicine, St. Louis, MO
| | - Richard Press
- Department of Pathology & Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Glenn E Palomaki
- Department of Pathology and Laboratory Medicine. Women & Infants Hospital, Alpert Medical School at Brown University, Providence, RI
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Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PIW, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJH, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PMK, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol 2014; 15:R53. [PMID: 24667040 PMCID: PMC4073084 DOI: 10.1186/gb-2014-15-3-r53] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Background There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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Ramos EM, Din-Lovinescu C, Berg JS, Brooks LD, Duncanson A, Dunn M, Good P, Hubbard TJP, Jarvik GP, O'Donnell C, Sherry ST, Aronson N, Biesecker LG, Blumberg B, Calonge N, Colhoun HM, Epstein RS, Flicek P, Gordon ES, Green ED, Green RC, Hurles M, Kawamoto K, Knaus W, Ledbetter DH, Levy HP, Lyon E, Maglott D, McLeod HL, Rahman N, Randhawa G, Wicklund C, Manolio TA, Chisholm RL, Williams MS. Characterizing genetic variants for clinical action. Am J Med Genet C Semin Med Genet 2014; 166C:93-104. [PMID: 24634402 DOI: 10.1002/ajmg.c.31386] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genome-wide association studies, DNA sequencing studies, and other genomic studies are finding an increasing number of genetic variants associated with clinical phenotypes that may be useful in developing diagnostic, preventive, and treatment strategies for individual patients. However, few variants have been integrated into routine clinical practice. The reasons for this are several, but two of the most significant are limited evidence about the clinical implications of the variants and a lack of a comprehensive knowledge base that captures genetic variants, their phenotypic associations, and other pertinent phenotypic information that is openly accessible to clinical groups attempting to interpret sequencing data. As the field of medicine begins to incorporate genome-scale analysis into clinical care, approaches need to be developed for collecting and characterizing data on the clinical implications of variants, developing consensus on their actionability, and making this information available for clinical use. The National Human Genome Research Institute (NHGRI) and the Wellcome Trust thus convened a workshop to consider the processes and resources needed to: (1) identify clinically valid genetic variants; (2) decide whether they are actionable and what the action should be; and (3) provide this information for clinical use. This commentary outlines the key discussion points and recommendations from the workshop.
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Feldman GL, Schrijver I, Lyon E, Palomaki GE. Results of the College of American Pathology/American College of Medical Genetics and Genomics external proficiency testing from 2006 to 2013 for three conditions prevalent in the Ashkenazi Jewish population. Genet Med 2014; 16:695-702. [PMID: 24577267 DOI: 10.1038/gim.2014.14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/22/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE The purpose of this study was to determine analytic performance of laboratories offering molecular testing for conditions such as Tay-Sachs disease, Canavan disease, and familial dysautonomia, which are prevalent in the Ashkenazi Jewish population. METHODS The College of American Pathologists and the American College of Medical Genetics and Genomics cosponsor molecular proficiency testing for these disorders. Responses from 2006 to 2013 were analyzed for accuracy (genotyping and interpretations). RESULTS Between 11 and 36 laboratories participated in each Tay-Sachs disease distribution. Samples tested per month were constant (2,900) from 2006 to 2011 but recently increased. Participants reporting <10 samples tested per month had longer turnaround times (42 vs. 7%, longer than 14 days; P = 0.03). Analytic sensitivity and specificity for US participants were 97.2% (95% confidence interval: 94.7-98.7%) and 99.8% (95% confidence interval: 99.1-99.9%), respectively. Of 11 genotyping errors, 2 were due to sample mix-up. Analytic interpretations were correct in 99.3% of challenges (956/963; 95% confidence interval: 98.5-99.7%). Better performance was found for Canavan disease and familial dysautonomia. International laboratories performed equally well. CONCLUSION These results demonstrated high analytic sensitivity and specificity along with excellent analytic interpretation performance, confirming the genetics community impression that laboratories provide accurate test results in both diagnostic and screening settings. Proficiency testing can identify potential laboratory issues and helps document overall laboratory performance.
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Affiliation(s)
- Gerald L Feldman
- 1] Department of Pathology, Wayne State University School of Medicine and Detroit Medical Center, Detroit, Michigan, USA [2] Department of Pediatrics, Wayne State University School of Medicine and Detroit Medical Center, Detroit, Michigan, USA [3] Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Iris Schrijver
- 1] Department of Pathology, Stanford University School of Medicine, Stanford, California, USA [2] Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Elaine Lyon
- ARUP Laboratories and Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Glenn E Palomaki
- Department of Pathology and Laboratory Medicine, Women & Infants Hospital, Alpert School of Medicine at Brown University, Providence, Rhode Island, USA
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22
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Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013; 15:733-47. [PMID: 23887774 PMCID: PMC4098820 DOI: 10.1038/gim.2013.92] [Citation(s) in RCA: 619] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 05/30/2013] [Indexed: 01/01/2023] Open
Abstract
Next-generation sequencing technologies have been and continue to be deployed in clinical laboratories, enabling rapid transformations in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude, and continuous advances are being made. It is now feasible to analyze an individual's near-complete exome or genome to assist in the diagnosis of a wide array of clinical scenarios. Next-generation sequencing technologies are also facilitating further advances in therapeutic decision making and disease prediction for at-risk patients. However, with rapid advances come additional challenges involving the clinical validation and use of these constantly evolving technologies and platforms in clinical laboratories. To assist clinical laboratories with the validation of next-generation sequencing methods and platforms, the ongoing monitoring of next-generation sequencing testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics has developed the following professional standards and guidelines.
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Affiliation(s)
- Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.
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Tripp SR, Gedge FEH, Lyon E, Samowitz WS. Microsatellite Instability Testing by Immunohistochemistry: Initial Evaluation of Hereditary Nonpolyposis Colon Cancer and Potential Prognostic and Therapeutic Information. J Histotechnol 2013. [DOI: 10.1179/his.2004.27.3.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Monaghan KG, Lyon E, Spector EB. ACMG Standards and Guidelines for fragile X testing: a revision to the disease-specific supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics and Genomics. Genet Med 2013; 15:575-86. [PMID: 23765048 DOI: 10.1038/gim.2013.61] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 04/04/2013] [Indexed: 12/29/2022] Open
Abstract
Molecular genetic testing of the FMR1 gene is commonly performed in clinical laboratories. Mutations in the FMR1 gene are associated with fragile X syndrome, fragile X tremor ataxia syndrome, and premature ovarian insufficiency. This document provides updated information regarding FMR1 gene mutations, including prevalence, genotype-phenotype correlation, and mutation nomenclature. Methodological considerations are provided for Southern blot analysis and polymerase chain reaction amplification of the FMR1 gene, including triplet repeat-primed and methylation-specific polymerase chain reaction. In addition to report elements, examples of laboratory reports for various genotypes are also included.
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Affiliation(s)
- Kristin G Monaghan
- Department of Medical Genetics, Henry Ford Health System, Detroit, Michigan, USA.
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Richards CS, Palomaki GE, Lacbawan FL, Lyon E, Feldman GL. Three-year experience of a CAP/ACMG methods-based external proficiency testing program for laboratories offering DNA sequencing for rare inherited disorders. Genet Med 2013; 16:25-32. [PMID: 23703682 DOI: 10.1038/gim.2013.65] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/15/2013] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Thousands of genetic tests are now offered clinically, but many are for rare disorders that are offered by only a few laboratories. The classic approach to disease-specific external proficiency testing programs is not feasible for such testing, yet calls have been made to provide external oversight. METHODS A methods-based Sequencing Educational Challenge Survey was launched in 2010, under joint administration of the College of American Pathologists and the American College of Medical Genetics and Genomics. Three sets of Sanger ABI sequence data were distributed twice per year. Participants were asked to identify, formally name, and interpret the sequence variant(s). RESULTS Between 2010 and 2012, 117 laboratories participated. Using a proposed assessment scheme (e.g., at least 10 of 12 components correct), 98.3% of the 67 US participants had acceptable performance (235 of 239 challenges; 95% confidence interval: 95.8-99.5%) as compared with 88.9% (136 of 153; 95% confidence interval: 82.8-93.4%) for the 50 international participants. CONCLUSION These data provide a high level of confidence that most US laboratories offering rare disease testing are providing consistent and reliable clinical interpretations. Methods-based proficiency testing programs may be one part of the solution to assessing genetic testing based on next-generation sequencing technology.
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Affiliation(s)
- C Sue Richards
- Department of Molecular and Medical Genetics, Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon, USA
| | - Glenn E Palomaki
- Department of Pathology, Women & Infants Hospital, Alpert School of Medicine at Brown University, Providence, Rhode Island, USA
| | - Felicitas L Lacbawan
- Department of Molecular Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Elaine Lyon
- Department of Pathology, University of Utah, and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Gerald L Feldman
- Detroit Medical Center and Departments of Pathology and Pediatrics and Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
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Furtado LV, Jama MA, Paxton CN, Wilson AA, Gardiner AE, Lyon E, Geiersbach KB. Aneuploidy detection in paraffin embedded tissue from products of conception by mini-STR genotyping. Fetal Pediatr Pathol 2013; 32:133-50. [PMID: 22607361 DOI: 10.3109/15513815.2012.681428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Autosomal trisomy is the most common genetic abnormality observed in pregnancy loss. We designed a panel of mini-short tandem repeats (mini-STRs) for aneuploidy detection in chromosomes 13, 16, 18 and 21 from fresh and formalin fixed, paraffin embedded (FFPE) samples from products of conception (POC). FFPE POCs with trisomy 13 (n = 6), trisomy 18 (n = 6), trisomy 21 (n = 12), 6 euploid for the chromosomes of interest and two trisomy 16 samples from fresh tissue were tested. Concordance between cytogenetics and genotyping was 100% for non-mosaic samples. Mini-STR genotyping is a viable method for targeted aneuploidy detection in low quality DNA samples.
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Affiliation(s)
- Larissa V Furtado
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
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Desai DS, Lyon E, Rodgers G, Jama M, Wallentine S, Smock K. Gene Sequencing Aids in Differentiation of von Willebrand Disease Type 2B from Platelet‐Type vWD. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.871.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - George Rodgers
- PathologyARUP LaboratoriesSalt Lake CityUT
- PathologyUniversity of Utah Health Sciences CenterSalt Lake CityUT
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Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin ELH, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmüller U, Gunselman SJ, Hegde MR, Johnson PLF, Kasarskis A, Kulkarni S, Lenk T, Liu CSJ, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 2013; 30:1033-6. [PMID: 23138292 DOI: 10.1038/nbt.2403] [Citation(s) in RCA: 381] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Furtado LV, Paxton CN, Jama MA, Tripp SR, Wilson AR, Lyon E, Jarboe EA, Thaker HM, Geiersbach KB. Diagnostic utility of microsatellite genotyping for molar pregnancy testing. Arch Pathol Lab Med 2013; 137:55-63. [PMID: 23276175 DOI: 10.5858/arpa.2012-0047-oa] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Molecular genotyping by analysis of DNA microsatellites, also known as short tandem repeats (STRs), is an established method for diagnosing and classifying hydatidiform mole. Distinction of both complete hydatidiform mole and partial hydatidiform mole from nonmolar specimens is relevant for clinical management owing to differences in risk for persistent gestational trophoblastic disease. OBJECTIVE To determine the technical performance of microsatellite genotyping by using a commercially available multiplex assay, and to describe the application of additional methods to confirm other genetic abnormalities detected by the genotyping assay. DESIGN Microsatellite genotyping data on 102 cases referred for molar pregnancy testing are presented. A separate panel of mini STR markers, flow cytometry, fluorescence in situ hybridization, and p57 immunohistochemistry were used to characterize cases with other incidental genetic abnormalities. RESULTS Forty-eight cases were classified as hydatidiform mole (31, complete hydatidiform mole; 17, partial hydatidiform mole). Genotyping also revealed 11 cases of suspected trisomy and 1 case of androgenetic/biparental mosaicism. Trisomy for selected chromosomes (13, 16, 18, and 21) was confirmed in all cases by using a panel of mini STR markers. CONCLUSIONS This series illustrates the utility of microsatellite genotyping as a stand-alone method for accurate classification of hydatidiform mole. Other genetic abnormalities may be detected by genotyping; confirmation of the suspected abnormality requires additional testing.
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Affiliation(s)
- Larissa V Furtado
- Department of Pathology, University of Utah School of Medicine, Salt Lake City 84108, USA
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Jama M, Millson A, Miller CE, Lyon E. Triplet repeat primed PCR simplifies testing for Huntington disease. J Mol Diagn 2013; 15:255-62. [PMID: 23414820 DOI: 10.1016/j.jmoldx.2012.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 09/18/2012] [Accepted: 09/26/2012] [Indexed: 12/14/2022] Open
Abstract
Diagnostic and predictive testing for Huntington disease (HD) requires an accurate determination of the number of CAG repeats in the Huntingtin (HHT) gene. Currently, when a sample appears to be homozygous for a normal allele, additional testing is required to confirm amplification from both alleles. If the sample still appears homozygous, Southern blot analysis is performed to rule out an undetected expanded HTT allele. Southern blot analysis is expensive, time-consuming, and labor intensive and requires high concentrations of DNA. We have developed a chimeric PCR process to help streamline workflow; true homozygous alleles are easily distinguished by this simplified method, and only very large expanded alleles still require Southern blot analysis. Two hundred forty-six HD samples, previously run with a different fragment analysis method, were analyzed with our new method. All samples were correctly genotyped, resulting in 100% concordance between the methods. The chimeric PCR assay was able to identify expanded alleles up to >150 CAG repeats. This method offers a simple strategy to differentiate normal from expanded CAG alleles, thereby reducing the number of samples reflexed to Southern blot analysis. It also provides assurance that expanded alleles are not routinely missed because of allele dropout.
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Affiliation(s)
- Mohamed Jama
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, USA.
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Ridge PG, Miller C, Bayrak-Toydemir P, Best DH, Mao R, Swensen JJ, Lyon E, Voelkerding KV. Cystic fibrosis testing in a referral laboratory: results and lessons from a six-year period. J Clin Bioinforma 2013; 3:3. [PMID: 23343000 PMCID: PMC3563502 DOI: 10.1186/2043-9113-3-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 01/08/2013] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED BACKGROUND The recent introduction of high throughput sequencing technologies into clinical genetics has made it practical to simultaneously sequence many genes. In contrast, previous technologies limited sequencing based tests to only a handful of genes. While the ability to more accurately diagnose inherited diseases is a great benefit it introduces specific challenges. Interpretation of missense mutations continues to be challenging and the number of variants of uncertain significance continues to grow. RESULTS We leveraged the data available at ARUP Laboratories, a major reference laboratory, for the CFTR gene to explore specific challenges related to variant interpretation, including a focus on understanding ethnic-specific variants and an evaluation of existing databases for clinical interpretation of variants. In this study we analyzed 555 patients representing eight different ethnic groups. We observed 184 different variants, most of which were ethnic group specific. Eighty-five percent of these variants were present in the Cystic Fibrosis Mutation Database, whereas the Human Mutation Database and dbSNP/1000 Genomes had far fewer of the observed variants. Finally, 21 of the variants were novel and we report these variants and their clinical classifications. CONCLUSIONS Based on our analyses of data from six years of CFTR testing at ARUP Laboratories a more comprehensive, clinical grade database is needed for the accurate interpretation of observed variants. Furthermore, there is a particular need for more and better information regarding variants from individuals of non-Caucasian ethnicity.
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Affiliation(s)
- Perry G Ridge
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
- Department of Biology, Brigham Young University, Provo, UT, USA
- 500 W Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Christine Miller
- ARUP Laboratories, Salt Lake City, UT, USA
- 500 W Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Pinar Bayrak-Toydemir
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- 500 W Chipeta Way, Salt Lake City, UT, 84108, USA
| | - D Hunter Best
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- 500 W Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Rong Mao
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- 500 W Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Jeffrey J Swensen
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- 500 W Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Elaine Lyon
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- 500 W Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Karl V Voelkerding
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- 500 W Chipeta Way, Salt Lake City, UT, 84108, USA
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32
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Mao R, Bayrak-Toydemir P, Lyon E. Capillary electrophoresis for the detection of Fragile X expanded alleles. Methods Mol Biol 2012; 919:275-85. [PMID: 22976108 DOI: 10.1007/978-1-62703-029-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Capillary electrophoresis is an analytical technique that separates ions based on their electrophoresis mobility with the use of an applied voltage. Capillary electrophoresis is used most predominantly in nuclear acid fragment analysis as well as DNA sequencing because it gives faster results and provides high resolution separation. Here we describe an application using capillary electrophoreses for screening the Fragile X expanded alleles to demonstrate the application.
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Affiliation(s)
- Rong Mao
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT, USA.
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33
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Lyon E, Gastier Foster J, Palomaki GE, Pratt VM, Reynolds K, Sábato MF, Scott SA, Vitazka P. Laboratory testing of CYP2D6 alleles in relation to tamoxifen therapy. Genet Med 2012; 14:990-1000. [DOI: 10.1038/gim.2012.108] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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34
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Melis R, Lewis T, Millson A, Lyon E, McMillin GA, Slev PR, Swensen J. Copy number variation and incomplete linkage disequilibrium interfere with the HCP5 genotyping assay for abacavir hypersensitivity. Genet Test Mol Biomarkers 2012; 16:1111-4. [PMID: 22913531 DOI: 10.1089/gtmb.2012.0115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Carriers of HLA-B*57:01 are at risk for Abacavir hypersensitivity reaction (ABC-HSR). In Caucasians, a SNP (rs2395029) in the HCP5 gene is reported to be in linkage disequilibrium (LD) with HLA-B*57:01. Genotyping the HCP5 SNP has increasingly been adopted as a simple method to screen for susceptibility to ABC-HSR. We genotyped both the HCP5 SNP and HLA-B*57:01 in a set of 1888 samples and found a good correlation; significantly, however, one HLA-B*57:01-positive sample tested negative for the HCP5 SNP. In addition, HCP5 could not be amplified in two samples, both negative for HLA-B*57:01. Further investigation demonstrated both samples were homozygous for deletion of the HCP5 gene. The fact HCP5 occurs within a region of copy number variation and the fact LD is incomplete and may vary between ethnicities should be considered when using the HCP5 SNP as a surrogate marker for HLA-B*57:01.
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Affiliation(s)
- Roberta Melis
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, USA.
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35
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Anderson S, Botti C, Li B, Millonig JH, Lyon E, Millson A, Karabin SS, Brooks SS. Medium chain acyl-CoA dehydrogenase deficiency detected among Hispanics by New Jersey newborn screening. Am J Med Genet A 2012; 158A:2100-5. [DOI: 10.1002/ajmg.a.35448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 04/10/2012] [Indexed: 11/09/2022]
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36
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Crockett DK, Ridge PG, Wilson AR, Lyon E, Williams MS, Narus SP, Facelli JC, Mitchell JA. Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting. Genome Med 2012; 4:48. [PMID: 22640420 PMCID: PMC3506914 DOI: 10.1186/gm347] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 04/05/2012] [Accepted: 05/28/2012] [Indexed: 12/15/2022] Open
Abstract
Accurate interpretation of gene testing is a key component in customizing patient therapy. Where confirming evidence for a gene variant is lacking, computational prediction may be employed. A standardized framework, however, does not yet exist for quantitative evaluation of disease association for uncertain or novel gene variants in an objective manner. Here, complementary predictors for missense gene variants were incorporated into a weighted Consensus framework that includes calculated reference intervals from known disease outcomes. Data visualization for clinical reporting is also discussed.
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Affiliation(s)
- David K Crockett
- University of Utah School of Medicine, Biomedical Informatics, 26 South 2000 East, Salt Lake City, UT 84112, USA.
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37
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Pont-Kingdon G, Gedge F, Wooderchak-Donahue W, Schrijver I, Weck KE, Kant JA, Oglesbee D, Bayrak-Toydemir P, Lyon E. Design and analytical validation of clinical DNA sequencing assays. Arch Pathol Lab Med 2012; 136:41-6. [PMID: 22208486 DOI: 10.5858/arpa.2010-0623-oa] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT DNA sequencing is the method of choice for mutation detection in many genes. OBJECTIVES To demonstrate the analytical accuracy and reliability of DNA sequencing assays developed in clinical laboratories. Only general guidelines exist for the validation of these tests. We provide examples of assay validation strategies for DNA sequencing tests. DESIGN We discuss important design and validation considerations. RESULTS The validation examples include an accuracy study to evaluate concordance between results obtained by the newly designed assay and analyzed by another method or laboratory. Precision (reproducibility) studies are performed to determine the robustness of the assay. To assess the quality of sequencing assays, several sequence quality measures are available. In addition, assessing the ability of primers to specifically and robustly amplify target regions before sequencing is important. CONCLUSION Protocols for validation of laboratory-developed sequencing assays may vary between laboratories. An example summary of a validation is provided.
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Affiliation(s)
- Genevieve Pont-Kingdon
- ARUP Laboratories, Institute of Clinical and Experimental Pathology, Salt Lake City, Utah, USA
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38
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Sumner K, Hubley L, Pont-Kingdon G, Mitchell S, Wayman T, Wilson A, Meadows C, Elenitoba-Johnson K, Pattison D, Dobrowolski S, Best H, Lyon E. Validation of an unlabeled probe melting analysis assay combined with high-throughput extractions for genotyping of the most common variants in HFE-associated hereditary hemochromatosis, C282Y, H63D, and S65C. Genet Test Mol Biomarkers 2012; 16:656-60. [PMID: 22364140 DOI: 10.1089/gtmb.2011.0204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hereditary hemochromatosis is an inherited disorder of iron metabolism, characterized by high absorption of iron by the gastrointestinal tract leading to a toxic accumulation of iron in various organs and impaired organ function. Three variants in the HFE gene (p.C282Y, p.H63D, and p.S65C) are commonly associated with the development of the disease. Of these, p.C282Y homozygotes are at the highest risk. Compound heterozygotes of p.C282Y along with p.H63D or p.S65C have reduced penetrance. Furthermore, p.H63D homozygotes are not at an increased risk and little is known about the risk associated with homozygocity for p.S65C. Our current clinical assay for the three common HFE variants utilizes the LightCycler platform and paired probes employing fluorescent resonance energy transfer. To increase throughput and decrease costs, we developed a method whereby automated extraction was combined with unlabeled probes and differential melt profiles to detect these variants using the LightCycler 480 instrument. Using this approach, 43 samples extracted with three different extraction platforms were correctly genotyped. These data demonstrate that the newly developed assay to genotype the HFE mutations p.C282Y, p.H63D, and p.S65C, combined with high-throughput extraction platforms, is accurate and reproducible and represents an alternative to previously described tests.
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Affiliation(s)
- Kelli Sumner
- ARUP Institute for Clinical and Experimental Pathology® , Salt Lake City, Utah 84108-1221, USA.
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Greene DN, Procter M, Krautscheid P, Mao R, Lyon E, Grenache DG. α1-Antitrypsin Deficiency in Fraternal Twins Born With Familial Spontaneous Pneumothorax. Chest 2012; 141:239-241. [DOI: 10.1378/chest.11-0104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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40
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Millson A, LaGrave D, Willis MJ, Rowe LR, Lyon E, South ST. Chromosomal loss of 3q26.3-3q26.32, involving a partial neuroligin 1 deletion, identified by genomic microarray in a child with microcephaly, seizure disorder, and severe intellectual disability. Am J Med Genet A 2011; 158A:159-65. [DOI: 10.1002/ajmg.a.34349] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 09/22/2011] [Indexed: 11/10/2022]
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41
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Crockett DK, Lyon E, Williams MS, Narus SP, Facelli JC, Mitchell JA. Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. J Am Med Inform Assoc 2011; 19:207-11. [PMID: 22037892 DOI: 10.1136/amiajnl-2011-000309] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The rapid advance of gene sequencing technologies has produced an unprecedented rate of discovery of genome variation in humans. A growing number of authoritative clinical repositories archive gene variants and disease phenotypes, yet there are currently many more gene variants that lack clear annotation or disease association. To date, there has been very limited coverage of gene-specific predictors in the literature. Here the evaluation is presented of "gene-specific" predictor models based on a naïve Bayesian classifier for 20 gene-disease datasets, containing 3986 variants with clinically characterized patient conditions. The utility of gene-specific prediction is then compared with "all-gene" generalized prediction and also with existing popular predictors. Gene-specific computational prediction models derived from clinically curated gene variant disease datasets often outperform established generalized algorithms for novel and uncertain gene variants.
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Affiliation(s)
- David K Crockett
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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42
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Melis R, Fauron C, McMillin G, Lyon E, Shirts B, Hubley LM, Slev PR. Simultaneous genotyping of rs12979860 and rs8099917 variants near the IL28B locus associated with HCV clearance and treatment response. J Mol Diagn 2011; 13:446-51. [PMID: 21704279 PMCID: PMC3123790 DOI: 10.1016/j.jmoldx.2011.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 02/16/2011] [Accepted: 03/22/2011] [Indexed: 01/01/2023] Open
Abstract
Recent genome-wide association studies have identified two host single-nucleotide polymorphisms (SNPs) near the IL28B gene (rs12979860 C/T and rs8099917 T/G) that are associated with sustained virological response in patients infected with the hepatitis C virus. Herein, we describe a rapid multiplexed dual-color fluorescence resonance energy transfer (FRET) probe assay that accurately genotypes for both SNPs simultaneously. A single-nucleotide extension assay was also developed for verification of genotypes. Agreement (100%) was observed in genotype calls between the FRET and single-nucleotide extension methods for both SNPs, yielding 100% analytical sensitivity and specificity. By using the FRET assay, 443 samples of varying ethnic backgrounds were genotyped and six different compound genotypes (rs12979860/rs8099917) were detected in whites, Asians, Middle Easterners, Hispanics, and African Americans, at the following frequencies: CC/TT (39.2%, 78.9%, 40.0%, 33.9%, and 16.8%), CT/TT (20.8%, 0%, 40%, 9.3%, and 37.0%), TT/TT (2.4%, 0%, 0%, 3.4%, and 35.3%), CT/TG (24.0%, 19.7%, 20%, 39.8%, and 3.4%), TT/TG (8.0%, 1.4%, 0%, 3.4%, and 5.9%), and TT/GG (5.6%, 0%, 0%, 10.2%, and 1.7%), respectively. The multiplexed FRET assay can be used to effectively genotype for both SNPs in a single tube, with high analytical sensitivity and specificity.
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Affiliation(s)
- Roberta Melis
- Associated Regional and University Pathologists (ARUP) Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108-1221, USA.
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43
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Wooderchak-Donahue W, Vaughn C, Chou LS, Lewis T, Sumner K, Procter M, Gedge F, Bayrak-Toydemir P, Lyon E, Pont-Kingdon G. Verification of multiplex ligation-dependent probe amplification probes in the absence of positive samples. Genet Test Mol Biomarkers 2011; 15:793-9. [PMID: 21689003 DOI: 10.1089/gtmb.2011.0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deletions and duplications of single or multiple exons in specific genes are associated with human diseases. Multiplex ligation-dependant probe amplification (MLPA), a technique recently introduced to clinical laboratories, can detect deletions or duplications at the exon level. MLPA kits have a high multiplexing capability containing mixtures of exon-specific probes that target the gene of interest and control probes that hybridize to other genomic areas before PCR amplification. To verify each probe set, known positive samples with a single-exon deletion or duplication and normal samples are ideally used. Often, positive samples do not exist for each exon and normal samples are not suited to verify the identity of each probe set. We designed a straightforward approach using mixes of exon-specific PCR products as template to unequivocally verify each probe set in MLPA kits. This method can be used to verify the identity of MLPA probes for exons when positive samples are unavailable. Exon-specific probes from 15 MLPA kits were shown to hybridize to the targeted exons of interest. In one kit, this method identified probes that also bind a pseudogene, making them unreliable for clinical analysis. Incorporating this methodology in the analytical validation process will help ensure that MLPA results are interpreted correctly.
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Chen B, Richards CS, Wilson JA, Lyon E. Quality Assurance and Quality Improvement in U.S. Clinical Molecular Genetic Laboratories. ACTA ACUST UNITED AC 2011; Chapter 9:Unit9.2. [DOI: 10.1002/0471142905.hg0902s69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bin Chen
- Centers for Disease Control and Prevention Atlanta Georgia
| | | | | | - Elaine Lyon
- University of Utah School of Medicine Salt Lake City Utah
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Crockett DK, Piccolo SR, Ridge PG, Margraf RL, Lyon E, Williams MS, Mitchell JA. Predicting phenotypic severity of uncertain gene variants in the RET proto-oncogene. PLoS One 2011; 6:e18380. [PMID: 21479187 PMCID: PMC3068179 DOI: 10.1371/journal.pone.0018380] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 03/04/2011] [Indexed: 02/02/2023] Open
Abstract
Although reported gene variants in the RET oncogene have been directly associated with multiple endocrine neoplasia type 2 and hereditary medullary thyroid carcinoma, other mutations are classified as variants of uncertain significance (VUS) until the associated clinical phenotype is made clear. Currently, some 46 non-synonymous VUS entries exist in curated archives. In the absence of a gold standard method for predicting phenotype outcomes, this follow up study applies feature selected amino acid physical and chemical properties feeding a Bayes classifier to predict disease association of uncertain gene variants into categories of benign and pathogenic. Algorithm performance and VUS predictions were compared to established phylogenetic based mutation prediction algorithms. Curated outcomes and unpublished RET gene variants with known disease association were used to benchmark predictor performance. Reliable classification of RET uncertain gene variants will augment current clinical information of RET mutations and assist in improving prediction algorithms as knowledge increases.
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Affiliation(s)
- David K Crockett
- Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.
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46
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Aronson SJ, Clark EH, Babb LJ, Baxter S, Farwell LM, Funke BH, Hernandez AL, Joshi VA, Lyon E, Parthum AR, Russell FJ, Varugheese M, Venman TC, Rehm HL. The GeneInsight Suite: a platform to support laboratory and provider use of DNA-based genetic testing. Hum Mutat 2011; 32:532-6. [PMID: 21432942 DOI: 10.1002/humu.21470] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 01/31/2011] [Indexed: 11/10/2022]
Abstract
The future of personalized medicine will hinge on effective management of patient genetic profiles. Molecular diagnostic testing laboratories need to track knowledge surrounding an increasingly large number of genetic variants, incorporate this knowledge into interpretative reports, and keep ordering clinicians up to date as this knowledge evolves. Treating clinicians need to track which variants have been identified in each of their patients along with the significance of these variants. The GeneInsight(SM) Suite assists in these areas. The suite also provides a basis for interconnecting laboratories and clinicians in a manner that increases the scalability of personalized medicine processes.
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Affiliation(s)
- Samuel J Aronson
- Partners HealthCare Center for Personalized Genetic Medicine, Cambridge, Massachusetts 02139, USA.
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47
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Svensson AM, Chou LS, Meadows C, Miller CE, Palais R, Sumner K, Wayman TC, Mao R, Lyon E. Implementation of a cost-effective unlabeled probe high-resolution melt assay for genotyping of Factor V Leiden. Genet Test Mol Biomarkers 2011; 15:207-13. [PMID: 21254846 DOI: 10.1089/gtmb.2010.0137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Factor V Leiden mutation (FVL; c.1601G>A, p.Arg534Gln), the most common aberration underlying activated Protein C resistance, results in disruption of a major anticoagulation pathway and is a leading cause of inherited thrombophilia. A high-throughput assay for FVL mutation detection was developed using a single unlabeled probe on a high-resolution platform, the 96-well Roche 480 LightCycler (LC480) instrument. This method replaced the U.S. Food and Drug Administration-approved Roche Factor V Leiden kit assay on the LightCycler PCR instrument, decreasing total cost by 48%. The analytical sensitivity and specificity of the LC480 high-resolution assay approached 100% for the FVL mutation. Factor V mutations in proximity to the FVL locus may influence probe binding efficiency and melt characteristics. One out of three very rare variants tested in a separate study, 1600delC, was not distinguishable from FVL using the described high-resolution assay. However, a c.1598G>A variant, which changes the amino acid sequence from arginine to lysine at position 533, was detected by this high-resolution assay and confirmed by bidirectional sequencing. In the labeled probe LightCycler assay, the c.1598G>A variant was indistinguishable from the heterozygous FVL control. The c.1598G>A variant has not been described previously and its clinical significance is uncertain. In conclusion, the LC480 FVL assay is cost effective in a high-throughput setting, with capability to detect both previously described and novel FV variants.
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Affiliation(s)
- Annika M Svensson
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.
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48
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Abstract
Alport Syndrome is a progressive renal disease with cochlear and ocular involvement. The most common form ( approximately 80%) is inherited in an X-linked pattern. X-linked Alport Syndrome (XLAS) is caused by mutations in the type IV collagen alpha chain 5 (COL4A5). We have developed a curated disease-specific database containing reported sequence variants in COL4A5. Currently the database archives a total of 520 sequence variants, verified for their position within the COL4A5 gene and named following standard nomenclature. Sequence variants are reported with accompanying information on protein effect, classification of mutation vs. polymorphism, mutation type based on the first description in the literature, and links to pertinent publications. In addition, features of this database include disease information, relevant links for Alport syndrome literature, reference sequence information, and ability to query by various criteria. On-line submission for novel gene variants or updating information on existing database entries is also possible. This free online scientific resource was developed with the clinical laboratory in mind to serve as a reference and repository for COL4A5 variants.
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Affiliation(s)
- David K Crockett
- ARUP Laboratories, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
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49
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Pratt VM, Zehnbauer B, Wilson JA, Baak R, Babic N, Bettinotti M, Buller A, Butz K, Campbell M, Civalier C, El-Badry A, Farkas DH, Lyon E, Mandal S, McKinney J, Muralidharan K, Noll L, Sander T, Shabbeer J, Smith C, Telatar M, Toji L, Vairavan A, Vance C, Weck KE, Wu AHB, Yeo KTJ, Zeller M, Kalman L. Characterization of 107 genomic DNA reference materials for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1: a GeT-RM and Association for Molecular Pathology collaborative project. J Mol Diagn 2010; 12:835-46. [PMID: 20889555 DOI: 10.2353/jmoldx.2010.100090] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pharmacogenetic testing is becoming more common; however, very few quality control and other reference materials that cover alleles commonly included in such assays are currently available. To address these needs, the Centers for Disease Control and Prevention's Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing community and the Coriell Cell Repositories, have characterized a panel of 107 genomic DNA reference materials for five loci (CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1) that are commonly included in pharmacogenetic testing panels and proficiency testing surveys. Genomic DNA from publicly available cell lines was sent to volunteer laboratories for genotyping. Each sample was tested in three to six laboratories using a variety of commercially available or laboratory-developed platforms. The results were consistent among laboratories, with differences in allele assignments largely related to the manufacturer's assay design and variable nomenclature, especially for CYP2D6. The alleles included in the assay platforms varied, but most were identified in the set of 107 DNA samples. Nine additional pharmacogenetic loci (CYP4F2, EPHX1, ABCB1, HLAB, KIF6, CYP3A4, CYP3A5, TPMT, and DPD) were also tested. These samples are publicly available from Coriell and will be useful for quality assurance, proficiency testing, test development, and research.
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Vaughn CP, Robles J, Swensen JJ, Miller CE, Lyon E, Mao R, Bayrak-Toydemir P, Samowitz WS. Clinical analysis of PMS2: mutation detection and avoidance of pseudogenes. Hum Mutat 2010; 31:588-93. [PMID: 20205264 DOI: 10.1002/humu.21230] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Germline mutation detection in PMS2, one of four mismatch repair genes associated with Lynch syndrome, is greatly complicated by the presence of numerous pseudogenes. We used a modification of a long-range PCR method to evaluate PMS2 in 145 clinical samples. This modification avoids potential interference from the pseudogene PMS2CL by utilizing a long-range product spanning exons 11-15, with the forward primer anchored in exon 10, an exon not shared by PMS2CL. Large deletions were identified by MLPA. Pathogenic PMS2 mutations were identified in 22 of 59 patients whose tumors showed isolated loss of PMS2 by immunohistochemistry (IHC), the IHC profile most commonly associated with a germline PMS2 mutation. Three additional patients with pathogenic mutations were identified from 53 samples without IHC data. Thirty-seven percent of the identified mutations were large deletions encompassing one or more exons. In 27 patients whose tumors showed absence of either another protein or combination of proteins, no pathogenic mutations were identified. We conclude that modified long-range PCR can be used to preferentially amplify the PMS2 gene and avoid pseudogene interference, thus providing a clinically useful germline analysis of PMS2. Our data also support the use of IHC screening to direct germline testing of PMS2.
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Affiliation(s)
- Cecily P Vaughn
- ARUP Institute for Clinical and Experimental Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84108, USA
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