Ontology type: schema:ScholarlyArticle Open Access: True
2015-03-05
AUTHORSSue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W. Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector, Karl Voelkerding, Heidi L. Rehm
ABSTRACTDisclaimer: These ACMG Standards and Guidelines were developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory services. Adherence to these standards and guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient’s record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these Standards and Guidelines. They also are advised to take notice of the date any particular guideline was adopted and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.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.Genet Med17 5, 405–423. More... »
PAGES405-423
http://scigraph.springernature.com/pub.10.1038/gim.2015.30
DOIhttp://dx.doi.org/10.1038/gim.2015.30
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27 | ″ | schema:description | Disclaimer: These ACMG Standards and Guidelines were developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory services. Adherence to these standards and guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient’s record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these Standards and Guidelines. They also are advised to take notice of the date any particular guideline was adopted and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.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.Genet Med17 5, 405–423. |
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361 | ″ | schema:name | Department of Human Genetics, Emory Genetics Laboratory, Emory University, Atlanta, Georgia, USA |
362 | ″ | rdf:type | schema:Organization |
363 | grid-institutes:grid.19006.3e | schema:alternateName | Department of Human Genetics, University of California Los Angeles School of Medicine, Los Angeles, California, USA |
364 | ″ | schema:name | Department of Human Genetics, University of California Los Angeles School of Medicine, Los Angeles, California, USA |
365 | ″ | ″ | Department of Pathology and Laboratory Medicine, University of California Los Angeles School of Medicine, Los Angeles, California, USA |
366 | ″ | ″ | Department of Pediatrics, University of California Los Angeles School of Medicine, Los Angeles, California, USA |
367 | ″ | rdf:type | schema:Organization |
368 | grid-institutes:grid.223827.e | schema:alternateName | Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, University of Utah, Salt Lake City, Utah, USA |
369 | ″ | schema:name | Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, University of Utah, Salt Lake City, Utah, USA |
370 | ″ | rdf:type | schema:Organization |
371 | grid-institutes:grid.240344.5 | schema:alternateName | Nationwide Children’s Hospital, Columbus, Ohio, USA |
372 | ″ | schema:name | Cytogenetics/Molecular Genetics Laboratory |
373 | ″ | ″ | Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, USA |
374 | ″ | ″ | Department of Pediatrics, Ohio State University College of Medicine, Columbus, Ohio, USA |
375 | ″ | ″ | Nationwide Children’s Hospital, Columbus, Ohio, USA |
376 | ″ | rdf:type | schema:Organization |
377 | grid-institutes:grid.30760.32 | schema:alternateName | Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA |
378 | ″ | schema:name | Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA |
379 | ″ | rdf:type | schema:Organization |
380 | grid-institutes:grid.38142.3c | schema:alternateName | Partners Laboratory for Molecular Medicine and Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA |
381 | ″ | schema:name | Partners Laboratory for Molecular Medicine and Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA |
382 | ″ | rdf:type | schema:Organization |
383 | grid-institutes:grid.413957.d | schema:alternateName | Department of Pediatrics, Molecular Genetics Laboratory, Children’s Hospital Colorado, University of Colorado Anschutz Medical School, Denver, Colorado, USA |
384 | ″ | schema:name | Department of Pediatrics, Molecular Genetics Laboratory, Children’s Hospital Colorado, University of Colorado Anschutz Medical School, Denver, Colorado, USA |
385 | ″ | rdf:type | schema:Organization |
386 | grid-institutes:grid.417276.1 | schema:alternateName | Current affiliation: Phoenix Children’s Hospital, Phoenix, Arizona, USA |
387 | ″ | schema:name | College of American Pathologists, Chicago, Illinois, USA |
388 | ″ | ″ | Current affiliation: Phoenix Children’s Hospital, Phoenix, Arizona, USA |
389 | ″ | rdf:type | schema:Organization |
390 | grid-institutes:grid.428467.b | schema:alternateName | GeneDx, Gaithersburg, Maryland, USA |
391 | ″ | schema:name | GeneDx, Gaithersburg, Maryland, USA |
392 | ″ | rdf:type | schema:Organization |
393 | grid-institutes:grid.5288.7 | schema:alternateName | Department of Molecular and Medical Genetics, Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon, USA |
394 | ″ | schema:name | Department of Molecular and Medical Genetics, Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon, USA |
395 | ″ | rdf:type | schema:Organization |