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

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.

The genetic landscape for amyloid beta fibril nucleation accurately discriminates familial Alzheimer’s disease mutations

“…Indeed, we would argue that this simple system is now better-validated as a model of fAD than any other, including animal models where the effects of only one or a few mutations (including control mutations) have ever been tested. Similarly-strong agreement between mutational effects in a cellular assay and the set of mutations already known to cause a disease is observed for other diseases (Starita et al 2017;Gelman et al 2019), suggesting the generality of this approach.…”

“…As for nearly all disease genes, therefore, the molecular mechanism by which mutations cause the disease remains unclear and the vast majority of possible mutations in Aß are variants of uncertain significance (VUS). This makes the clinical interpretation of genetic variation in this locus a difficult challenge (Starita et al 2017;Gelman et al 2019). Moreover, given the human mutation rate and population size, it is likely that nearly all of these possible variants in Aß actually exist in at least one individual currently alive on the planet (Conrad et al 2011).…”

Is Gene-Size an Issue for the Diagnosis of Skeletal Muscle Disorders?

“…A crucial aspect for a proper evaluation of the sequence variants is represented by the choice of appropriate functional studies. Although recommendations have been recently issued to provide a detailed guidance on the evaluation of functional data [143,144], for the large genes discussed here, we do not have a general agreement on the assays providing sufficient evidence. Moreover, the large size of the coding region is a considerable issue for specific applications (e.g.…”

Yeast-based assays for the functional characterization of cancer-associated variants of human DNA repair genes

“…The approach named multiplexed assay of variant effect (MAVE) could really contribute to evaluate functional consequences of human genetic variation [81]. MAVE has allowed the assessment of thousand variants located in coding sequence, enhancers and promoters [82]. Importantly, MAVE analysis have been carried out in several genetic systems including yeast [83,84].…”