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Laboratory testing for fragile X, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)

Genetics in Medicine (2021)Cite this article

Abstract

Molecular genetic testing of the FMR1 gene is commonly performed in clinical laboratories. Pathogenic variants in the FMR1 gene are associated with fragile X syndrome, fragile X–associated tremor ataxia syndrome (FXTAS), and fragile X–associated primary ovarian insufficiency (FXPOI). This document provides updated information regarding FMR1 pathogenic variants, including prevalence, genotype–phenotype correlations, and variant nomenclature. Methodological considerations are provided for Southern blot analysis and polymerase chain reaction (PCR) amplification of FMR1, including triplet repeat–primed and methylation-specific PCR.

The American College of Medical Genetics and Genomics (ACMG) Laboratory Quality Assurance Committee has the mission of maintaining high technical standards for the performance and interpretation of genetic tests. In part, this is accomplished by the publication of the document ACMG Technical Standards for Clinical Genetics Laboratories, which is now maintained online (http://www.acmg.net). This subcommittee also reviews the outcome of national proficiency testing in the genetics area and may choose to focus on specific diseases or methodologies in response to those results. Accordingly, the subcommittee selected fragile X syndrome to be the first topic in a series of supplemental sections, recognizing that it is one of the most frequently ordered genetic tests and that it has many alternative methods with different strengths and weaknesses. This document is the fourth update to the original standards and guidelines for fragile X testing that were published in 2001, with revisions in 2005 and 2013, respectively.

This version

Clarifies the clinical features associated with different FMRI variants (Section 2.3)

Discusses important reporting considerations (Section 3.3.1.3)

Provides updates on technology (Section 4.1)

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Fig. 1: Southern blot using EcoRI and EagI digestion, probed with StB12.3, using extended electrophoresis to illustrate several subtle specimen types.
Fig. 2: Triplet repeat primed PCR results.

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Affiliations

  1. Clinical Genetics and Metabolism, University of Colorado, School of Medicine, Aurora, CO, USA

    Elaine Spector

  2. Precision Diagnostics Laboratory, Children’s Hospital Colorado, Aurora, CO, USA

    Elaine Spector & Kathryn Kronquist

  3. PerkinElmer Genomics, Duluth, GA, USA

    Andrea Behlmann

  4. Department of Obstetrics and Gynecology, Adjunct, University of Utah Health Sciences Center, Salt Lake City, UT, USA

    Nancy C. Rose

  5. Clinical Services Lab, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA

    Elaine Lyon

  6. Department of Pathology and Laboratory Medicine and Surgery, Medical College of Wisconsin, Milwaukee, WI, USA

    Honey V. Reddi

  7. Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA

    Honey V. Reddi

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  1. Elaine Spector
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ACMG Laboratory Quality Assurance Committee

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Competing interests

E.S., A.B., K.K., and H.V.R. direct or work in laboratories that offer clinical molecular genetic testing for fragile X syndrome. N.C.R. and E.L. declare no competing interests.

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Disclaimer

This technical standard is designed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to this technical standard is voluntary and does not necessarily assure a successful medical outcome. This technical standard 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 this technical standard. They also are advised to take notice of the date any particular technical standard 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.

Note

This document supersedes the Technical Standards and Guidelines for Fragile X Testing: The First of a Series of Disease-Specific Supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics and Genomics (2001),1 the Technical 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 (2005)2 and the 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 (2013).3 It is designed for genetic testing professionals who are already familiar with the disease and the methods of analysis.

The Board of Directors of the American College of Medical Genetics and Genomics approved this technical standard on 14 December 2020.

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Spector, E., Behlmann, A., Kronquist, K. et al. Laboratory testing for fragile X, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med (2021). https://doi.org/10.1038/s41436-021-01115-y

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