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Cited by 81Genomics and Rare DiseasesGenetic Associations and EpidemiologyBRCA gene mutations in cancer

Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation

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On behalf of the Brotman Baty Institute Mutational Scanning Working Group, Gelman, Hannah, Dines, Jennifer N., Berg, Jonathan, Berger, Alice H., Brnich, Sarah, Hisama, Fuki M., James, Richard G. +5 more·2019·Genome Medicine
DOI 10.1186/s13073-019-0698-7PMC PMC6925490
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Abstract

Variants of uncertain significance represent a massive challenge to medical genetics. Multiplexed functional assays, in which the functional effects of thousands of genomic variants are assessed simultaneously, are increasingly generating data that can be used as additional evidence for or against variant pathogenicity. Such assays have the potential to resolve variants of uncertain significance, thereby increasing the clinical utility of genomic testing. Existing standards from the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) and new guidelines from the Clinical Genome Resource (ClinGen) establish the role of functional data in variant interpretation, but do not address the specific challenges or advantages of using functional data derived from multiplexed assays. Here, we build on these existing guidelines to provide recommendations to experimentalists for the production and reporting of multiplexed functional data and to clinicians for the evaluation and use of such data. By following these recommendations, experimentalists can produce transparent, complete, and well-validated datasets that are primed for clinical uptake. Our recommendations to clinicians and diagnostic labs on how to evaluate the quality of multiplexed functional datasets, and how different datasets could be incorporated into the ACMG/AMP variant-interpretation framework, will hopefully clarify whether and how such data should be used. The recommendations that we provide are designed to enhance the quality and utility of multiplexed functional data, and to promote their judicious use.

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  • Rigorous functional studies are considered strong evidence (PS3/BS3) by the widely used American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) genetic diagnostic guidelines.

    “Rigorous functional studies are considered strong evidence (PS3/BS3) by the widely used American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) genetic diagnostic guidelines.”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [38]

    The Background identifies PS3/BS3 as the ACMG/AMP framework’s Pathogenic Strong and Benign Strong evidence levels for functional data. But the Germline variants section says evidence can reach *up to* PS3/BS3 depending on assay quality and the individual variant, and the Conclusions caution that not all functional data reach strong evidence. The claim omits that qualification. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • In the context of a Bayesian decision-making framework, rigorous functional studies can effectively play a deterministic role in classifying variants.

    “In the context of a Bayesian decision-making framework they can effectively play a deterministic role in classifying variants (25, 38, 39), thereby potentially making major inroads into the ‘VUS problem’.”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [38]

    The ‘Germline variants’ section says that functional data can be assigned Bayesian odds of pathogenicity and incorporated into variant-classification frameworks. It does not describe the data as deterministic: their evidentiary strength depends on the variant’s score and measurement error, as well as assay quality and predictive power. The ‘Multiplexed functional data as evidence for variant interpretation’ section says they are incorporated with existing clinical and in silico evidence. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • The second key design consideration is whether or not the functional readout of the chosen downstream assay is relevant to the clinical condition or phenotype being studied.

    “The second key design consideration is whether or not the functional readout of the chosen downstream assay is relevant to the clinical condition or phenotype being studied (38).”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [38]

  • Attempts to develop standards and a statistical framework for assessment of diagnostic performance of functional assays lagged behind efforts to curate and assess gene variants, but a rigorous approach has been proposed.

    “Attempts to develop standards, and a statistical framework, for assessment of the diagnostic performance of functional assays lagged somewhat behind efforts to curate and assess gene variants, but a rigorous approach to this has been proposed (38).”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [38]

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Authors
On behalf of the Brotman Baty Institute Mutational Scanning Working Group, Gelman, H., Dines, J. N., Berg, J., Berger, A. H., Brnich, S., Hisama, F. M., James, R. G., Rubin, A. F., Shendure, J., Shirts, B., Fowler, D. M., & Starita, L. M.
Affiliations
  • University of Washington (US)
  • University of North Carolina at Chapel Hill (US)
  • Fred Hutch Cancer Center (US)
  • The University of Melbourne (AU)
  • Howard Hughes Medical Institute (US)
Corresponding author
  • Fowler, Douglas M.
  • Starita, Lea M.
ORCID
Venue
Genome Medicine
Publisher
Springer Science and Business Media LLC
Published
2019-12
Volume
11
Issue
1
Pages
85-85
ISSN
1756-994X (ISSN-L)
DOI
10.1186/s13073-019-0698-7
PMC
PMC6925490
OpenAlex
W2995651968
Cited by
81
References
8
Citations by year
2026: 8 · 2025: 14 · 2024: 15 · 2023: 12 · 2022: 10 · 2021: 15 · 2020: 5 · 2019: 1 · 2018: 1
FWCI
4.61
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome Medicine (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
National Human Genome Research Institute (HG010461)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
Keywords
variants of uncertain significance, variant interpretation, ACMG/AMP guidelines, ClinGen, data quality assessment, clinical genomic testing, pathogenicity assessment
MeSH terms
Genetic Testing, Humans, Quality Control, Societies, Medical, Genetic Variation, Gene Library, Guidelines as Topic, Sequence Analysis, DNA, Precision Medicine

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