1、405 American College of Medical Genetics and Genomics ACMG St And ArdS And GuidelineS Submitted 28 January 2015; accepted 28 January 2015; advance online publication 5 March 2015. doi:10.1038/gim.2015.30 Genet Med 405 423 2015 Genetics in Medicine 10.1038/gim.2015.30 ACMG Standards and Guidelines 17
2、 5 28January2015 28January2015 American College of Medical Genetics and Genomics 5March2015 The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants. 1In the past decade, sequencing technology has evolved rapidly with the
3、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
4、 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 repre- sentatives from the ACMG, the Association for Molecular Pathology (AMP),
5、 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
6、 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 stan- dard terminology“pathogenic,” “likely pathoge
7、nic,” “uncertain sig- nificance, ” “likely benign, ” and “benign”to describe variants identified in genes that cause Mendelian disorders. Moreover, this recommenda- tion describes a process for classifying variants into these five categories based on criteria using typical types of variant evidence
8、(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 recom- mends that clinical molecular genetic testing should be performed in a Cli
9、nical Laboratory Improvement Amendmentsapproved laboratory, with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or the equivalent. Genet Med advance online publication 5 March 2015 Key Words: ACMG laboratory guideline; clinical genetic testing
10、; interpretation; reporting; sequence variant terminology; variant reporting 1 Department of Molecular and Medical Genetics, Knight Diagnostic Laboratories, Oregon Health 2 College of American Pathologists, Chicago, Illinois, USA; 3 GeneDx, Gaithersburg, Maryland, USA; 4 Department of Pediatrics, Se
11、ction of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; 5 Department of Human Genetics, Clinical Molecular Genetics Laboratory, The University of Chicago, Chicago, Illinois, USA; 6 Cytogenetics/Molecular Genetics Laboratory, Nationwide Children s Hospital, Columbus, Ohio, USA; 7
12、Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, USA; 8 Department of Pediatrics, Ohio State University College of Medicine, Columbus, Ohio, USA; 9 Department of Pathology and Laboratory Medicine, University of California Los Angeles School of Medicine, Los Angeles
13、, California, USA; 10 Department of Pediatrics, University of California Los Angeles School of Medicine, Los Angeles, California, USA; 11 Department of Human Genetics, University of California Los Angeles School of Medicine, Los Angeles, California, USA; 12 Department of Human Genetics, Emory Geneti
14、cs Laboratory, Emory University, Atlanta, Georgia, USA; 13 Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, University of Utah, Salt Lake City, Utah, USA; 14 Department of Pediatrics, Molecular Genetics Laboratory, Children s Hospital Colorado, University of Colorado
15、Anschutz Medical School, Denver, Colorado, USA; 15 Partners Laboratory for Molecular Medicine and Department of Pathology, Brigham 16 Current affiliation: Phoenix Children s Hospital, Phoenix, Arizona, USA. Correspondence: Sue Richards (richarsuohsu.edu) Approved by the ACMG Board of Directors on 15
16、 December 2014 and the AMP Board of Directors on 9 January 2015. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Sue Richards, PhD 1 , Nazneen A
17、ziz, PhD 2,16 , Sherri Bale, PhD 3 , David Bick, MD 4 , Soma Das, PhD 5 , Julie Gastier-Foster, PhD 6,7,8 , Wayne W. Grody, MD, PhD 9,10,11 , Madhuri Hegde, PhD 12 , Elaine Lyon, PhD 13 , Elaine Spector, PhD 14 , Karl Voelkerding, MD 13and Heidi L. Rehm, PhD 15 ; on behalf of the ACMG Laboratory Qua
18、lity Assurance Committee Disclaimer: These ACMG Standards and Guidelines were developed primarily as an educational resource for clinical laboratory geneticists to help them pro- vide quality clinical laboratory services. Adherence to these standards and guidelines is voluntary and does not necessar
19、ily 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 reason- ably directed to obtaining the same results. In determining the propriety of any specific procedur
20、e 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 patients record the rationale for the use of a particular p
21、rocedure or test, whether or not it is in conformance with these Standards and Guide- lines. 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 b
22、e prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures. GenetiCS in MediCine | Volume 17 | Number 5 | May 2015406 RICHARDS et al | Interpretation of sequence variants ACMG St And ArdS And GuidelineS intROdUCtiOn Clinical molec
23、ular laboratories are increasingly detecting novel sequence variants in the course of testing patient specimens for a rapidly increasing number of genes associated with genetic disorders. While some phenotypes are associated with a single gene, many are associated with multiple genes. Our understand
24、- ing of the clinical significance of any given sequence variant falls along a gradient, ranging from those in which the variant is almost certainly pathogenic for a disorder to those that are almost certainly benign. While the previous American College of Medical Genetics and Genomics (ACMG) recomm
25、endations provided interpretative categories of sequence variants and an algorithm for interpretation, the recommendations did not pro- vide defined terms or detailed variant classification guidance. 1This report describes updated standards and guidelines for the classification of sequence variants
26、using criteria informed by expert opinion and empirical data. MetHOdS In 2013 a workgroup consisting of ACMG, Association for Molecular Pathology (AMP), and College of American Pathologists members, representing clinical laboratory direc- tors and clinicians, was formed with the goal of developing a
27、 recommendation for the use of standard terminology for clas- sifying sequence variants using available evidence weighted according to a system developed through expert opinion, work- group consensus, and community input. To assess the views of the clinical laboratory community, surveys were sent to
28、 over 100 sequencing laboratories in the United States and Canada that were listed in GeneTests.org, requesting input on termi- nology preferences and evaluation of evidence for classifying variants. Laboratory testing experience included rare disease as well as pharmacogenomics and somatic cancer t
29、esting. The first survey, aimed at assessing terminology preferences, was sent in February 2013, and the results were presented in an open forum at the 2013 ACMG annual meeting including over 75 attendees. Survey respondents represented more than 45 laboratories in North America. The outcome of the
30、survey and open forum indicated that (i) a five-tier terminology system using the terms “pathogenic,” “likely pathogenic,” “uncertain significance,” “likely benign, ” and “benign” was preferred and already in use by a majority of laboratories, and (ii) the first effort of the work- group should focu
31、s on Mendelian and mitochondrial variants. In the first survey, laboratories also were asked to provide their protocols for variant assessment, and 11 shared their methods. By analyzing all the protocols submitted, the work- group developed a set of criteria to weight variant evidence and a set of r
32、ules for combining criteria to arrive at one of the five classification tiers. Workgroup members tested the scheme within their laboratories for several weeks using variants already classified in their laboratories and/or by the broader community. In addition, typical examples of variants harbor- in
33、g the most common types of evidence were tested for clas- sification assignment to ensure the system would classify those variants according to current approaches consistently applied by workgroup members. A second survey was sent in August 2013 to the same laboratories identified through GeneTests.
34、 org as well as through AMPs listserv of 2,000 members, along with the proposed classification scheme and a detailed supple- ment describing how to use each of the criteria. Laboratories were asked to use the scheme and to provide feedback as to the suitability and relative weighting of each criteri
35、a, the ease of use of the classification system, and whether they would adopt such a system in their own laboratory. Responses from over 33 labo- ratories indicated majority support for the proposed approach, and feedback further guided the development of the proposed standards and guidelines. In No
36、vember 2013 the workgroup held a workshop at the AMP meeting with more than 50 attendees, presenting the revised classification criteria and two potential scoring systems. One system is consistent with the approach presented here and the other is a point system whereby each criterion is given a numb
37、er of points, assigning positive points for pathogenic criteria and negative points for benign criteria, with the total defining the variant class. With an audience-response system, the participants were asked how they would weight each cri- terion (as strong, moderate or supporting, or not used) du
38、r- ing evaluation of variant evidence. Again, the responses were incorporated into the classification system presented here. It should be noted that while the majority of respondents did favor a point system, the workgroup felt that the assignment of specific points for each criterion implied a quan
39、titative level of understanding of each criterion that is currently not supported scientifically and does not take into account the complexity of interpreting genetic evidence. The workgroup also evaluated the literature for recommen- dations from other professional societies and working groups that
40、 have developed variant classification guidelines for well- studied genes in breast cancer, colon cancer, and cystic fibro- sis and statistical analysis programs for quantitative evaluation of variants in select diseases. 25While those variant analysis guidelines are useful in a specific setting, it
41、 was difficult to apply their proposed criteria to all genes and in different laboratory settings. The variant classification approach described in this article is meant to be applicable to variants in all Mendelian genes, whether identified by single gene tests, multigene panels, exome sequencing,
42、or genome sequencing. We expect that this variant classification approach will evolve as technology and knowledge improve. We should also note that those working in specific disease groups should continue to develop more focused guidance regarding the classification of variants in spe- cific genes g
43、iven that the applicability and weight assigned to certain criteria may vary by gene and disease. GeneRAL COnSideRA tiOnS terminology A mutation is defined as a permanent change in the nucleo- tide sequence, whereas a polymorphism is defined as a vari- ant with a frequency above 1%. The terms “mutat
44、ion” and “polymorphism,” however, which have been used widely, Volume 17 | Number 5 | May 2015 | GenetiCS in MediCine407 Interpretation of sequence variants | RICHARDS et al ACMG St And ArdS And GuidelineS often lead to confusion because of incorrect assumptions of pathogenic and benign effects, res
45、pectively. Thus, it is recom- mended that both terms be replaced by the term “variant” with the following modifiers: (i) pathogenic, (ii) likely pathogenic, (iii) uncertain significance, (iv) likely benign, or (v) benign. Although these modifiers may not address all human phe- notypes, they comprise
46、 a five-tier system of classification for variants relevant to Mendelian disease as addressed in this guidance. It is recommended that all assertions of pathogenic- ity (including “likely pathogenic”) be reported with respect to a condition and inheritance pattern (e.g., c.1521_1523delCTT (p.Phe508d
47、el), pathogenic, cystic fibrosis, autosomal recessive). It should be noted that some laboratories may choose to have additional tiers (e.g., subclassification of variants of uncertain significance, particularly for internal use), and this practice is not considered inconsistent with these recommenda
48、tions. It should also be noted that the terms recommended here differ somewhat from the current recommendations for classifying copy-number variants detected by cytogenetic microarray. 6The schema recommended for copy-number variants, while also including five tiers, uses “uncertain clinical signifi
49、cance likely pathogenic” and “uncertain clinical significancelikely benign.” The majority of the workgroup was not supportive of using “uncertain significance” to modify the terms “likely pathogenic” or “likely benign” given that it was felt that the criteria presented here to classify variants into the “likely” categories included stronger evidence than outlined in the copy-number variant guideline and that combining these two categories would create confusion for the health-care provid- ers and individuals receiving clinical reports. However, it was felt that the use of the
