Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics ... View Full Text


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Article Info

DATE

2015-03-05

AUTHORS

Sue 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

ABSTRACT

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. More... »

PAGES

405-423

References to SciGraph publications

  • 2013-12-22. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database in NATURE GENETICS
  • 2013-11-21. In silico tools for splicing defect prediction: a survey from the viewpoint of end users in GENETICS IN MEDICINE
  • 2010-08. MutationTaster evaluates disease-causing potential of sequence alterations in NATURE METHODS
  • 2013-07-25. ACMG clinical laboratory standards for next-generation sequencing in GENETICS IN MEDICINE
  • 1999-06. Prospects for whole-genome linkage disequilibrium mapping of common disease genes in NATURE GENETICS
  • 2014-02-02. A general framework for estimating the relative pathogenicity of human genetic variants in NATURE GENETICS
  • 2013-08-25. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene in NATURE GENETICS
  • 2011-06-15. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants in GENETICS IN MEDICINE
  • 2009-06-25. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm in NATURE PROTOCOLS
  • 2014-04-23. Guidelines for investigating causality of sequence variants in human disease in NATURE
  • 2012-04-05. Communicating new knowledge on previously reported genetic variants in GENETICS IN MEDICINE
  • 2014-03-13. The impact of chromosomal microarray on clinical management: a retrospective analysis in GENETICS IN MEDICINE
  • 2010-04. A method and server for predicting damaging missense mutations in NATURE METHODS
  • Journal

    TITLE

    Genetics in Medicine

    ISSUE

    5

    VOLUME

    17

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/gim.2015.30

    DOI

    http://dx.doi.org/10.1038/gim.2015.30

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1022229472

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25741868


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