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Recommendations for Clinical CYP2C9 Genotyping Allele Selection: A Joint Recommendation of the Association for Molecular Pathology and College of American Pathologists.

ABSTRACT: The goals of the Association for Molecular Pathology Pharmacogenomics (PGx) Working Group of the Association for Molecular Pathology Clinical Practice Committee are to define the key attributes of PGx alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document provides recommendations for a minimum panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories when designing assays for CYP2C9 testing. The Working Group considered the functional impact of the variants, allele frequencies in different populations and ethnicities, the availability of reference materials, and other technical considerations for PGx testing when developing these recommendations. Our goal is to promote standardization of testing PGx genes and alleles across clinical laboratories. These recommendations are not to be interpreted as restrictive but to provide a reference guide. The current document will focus on CYP2C9 testing that can be applied to all CYP2C9-related medications. A separate recommendation on warfarin PGx testing is being developed to include recommendations on CYP2C9 alleles and additional warfarin sensitivity-associated genes and alleles.

SUBMITTER: Pratt VM

PROVIDER: S-EPMC7057225 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Recommendations for Clinical CYP2C9 Genotyping Allele Selection: A Joint Recommendation of the Association for Molecular Pathology and College of American Pathologists.

Pratt Victoria M VM Cavallari Larisa H LH Del Tredici Andria L AL Hachad Houda H Ji Yuan Y Moyer Ann M AM Scott Stuart A SA Whirl-Carrillo Michelle M Weck Karen E KE

The Journal of molecular diagnostics : JMD 20190508 5

The goals of the Association for Molecular Pathology Pharmacogenomics (PGx) Working Group of the Association for Molecular Pathology Clinical Practice Committee are to define the key attributes of PGx alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document provides recommendations for a minimum panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laborator ...[more]

PMID: 31075510

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Project description:CONTEXT:There is increasing interest in using whole slide imaging (WSI) for diagnostic purposes (primary and/or consultation). An important consideration is whether WSI can safely replace conventional light microscopy as the method by which pathologists review histologic sections, cytology slides, and/or hematology slides to render diagnoses. Validation of WSI is crucial to ensure that diagnostic performance based on digitized slides is at least equivalent to that of glass slides and light microscopy. Currently, there are no standard guidelines regarding validation of WSI for diagnostic use. OBJECTIVE:To recommend validation requirements for WSI systems to be used for diagnostic purposes. DESIGN:The College of American Pathologists Pathology and Laboratory Quality Center convened a nonvendor panel from North America with expertise in digital pathology to develop these validation recommendations. A literature review was performed in which 767 international publications that met search term requirements were identified. Studies outside the scope of this effort and those related solely to technical elements, education, and image analysis were excluded. A total of 27 publications were graded and underwent data extraction for evidence evaluation. Recommendations were derived from the strength of evidence determined from 23 of these published studies, open comment feedback, and expert panel consensus. RESULTS:Twelve guideline statements were established to help pathology laboratories validate their own WSI systems intended for clinical use. Validation of the entire WSI system, involving pathologists trained to use the system, should be performed in a manner that emulates the laboratory's actual clinical environment. It is recommended that such a validation study include at least 60 routine cases per application, comparing intraobserver diagnostic concordance between digitized and glass slides viewed at least 2 weeks apart. It is important that the validation process confirm that all material present on a glass slide to be scanned is included in the digital image. CONCLUSIONS:Validation should demonstrate that the WSI system under review produces acceptable digital slides for diagnostic interpretation. The intention of validating WSI systems is to permit the clinical use of this technology in a manner that does not compromise patient care.

Project description:The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes, and epigenetic assays for genetic disorders. By virtue of increased complexity, this shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context the ACMG convened a workgroup in 2013 comprising representatives from the ACMG, the Association for Molecular Pathology (AMP), and the College of American Pathologists to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP, and College of American Pathologists stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories, including genotyping, single genes, panels, exomes, and genomes. This report recommends the use of specific standard terminology-"pathogenic," "likely pathogenic," "uncertain significance," "likely benign," and "benign"-to describe variants identified in genes that cause Mendelian disorders. Moreover, this recommendation describes a process for classifying variants into these five categories based on criteria using typical types of variant evidence (e.g., population data, computational data, functional data, segregation data). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a Clinical Laboratory Improvement Amendments-approved laboratory, with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or the equivalent.

Project description:Little is known regarding the durability of clinical practice guideline recommendations over time.To characterize variations in the durability of class I ("procedure/treatment should be performed/administered") American College of Cardiology/American Heart Association (ACC/AHA) guideline recommendations.Textual analysis by 4 independent reviewers of 11 guidelines published between 1998 and 2007 and revised between 2006 and 2013.We abstracted all class I recommendations from the first of the 2 most recent versions of each guideline and identified corresponding recommendations in the subsequent version. We classified recommendations replaced by less determinate or contrary recommendations as having been downgraded or reversed; we classified recommendations for which no corresponding item could be identified as having been omitted. We tested for differences in the durability of recommendations according to guideline topic and underlying level of evidence using bivariable hypothesis tests and conditional logistic regression.Of 619 index recommendations, 495 (80.0%; 95% CI, 76.6%-83.1%) were retained in the subsequent guideline version, 57 (9.2%; 95% CI, 7.0%-11.8%) were downgraded or reversed, and 67 (10.8%; 95% CI, 8.4%-13.3%) were omitted. The percentage of recommendations retained varied across guidelines from 15.4% (95% CI, 1.9%-45.4%) to 94.1% (95% CI, 80.3%-99.3%; P?<?.001). Among recommendations with available information on level of evidence, 90.5% (95% CI, 83.2%-95.3%) of recommendations supported by multiple randomized studies were retained, vs 81.0% (95% CI, 74.8%-86.3%) of recommendations supported by 1 randomized trial or observational data and 73.7% (95% CI, 65.8%-80.5%) of recommendations supported by opinion (P?=?.001). After accounting for guideline-level factors, the probability of being downgraded, reversed, or omitted was greater for recommendations based on opinion (odds ratio, 3.14; 95% CI, 1.69-5.85; P?<?.001) or on 1 trial or observational data (odds ratio, 3.49; 95% CI, 1.45-8.41; P?=?.005) vs recommendations based on multiple trials.The durability of class I cardiology guideline recommendations for procedures and treatments promulgated by the ACC/AHA varied across individual guidelines and levels of evidence. Downgrades, reversals, and omissions were most common among recommendations not supported by multiple randomized studies.

Dataset Information

Recommendations for Clinical CYP2C9 Genotyping Allele Selection: A Joint Recommendation of the Association for Molecular Pathology and College of American Pathologists.

Publications

Recommendations for Clinical CYP2C9 Genotyping Allele Selection: A Joint Recommendation of the Association for Molecular Pathology and College of American Pathologists.

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