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

AbstractVariants 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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APP, PSEN1, and PSEN2 Variants in Alzheimer’s Disease: Systematic Re-evaluation According to ACMG Guidelines

Frontiers in Aging Neuroscience ◽

10.3389/fnagi.2021.695808 ◽

2021 ◽

Vol 13 ◽

Author(s):

Xuewen Xiao ◽

Hui Liu ◽

Xixi Liu ◽

Weiwei Zhang ◽

Sizhe Zhang ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Molecular Pathology ◽

Medical Genetics ◽

Variants Of Uncertain Significance ◽

Pathogenic Variants ◽

Pubmed Database ◽

Uncertain Significance ◽

Genetics And Genomics

The strategies of classifying APP, PSEN1, and PSEN2 variants varied substantially in the previous studies. We aimed to re-evaluate these variants systematically according to the American college of medical genetics and genomics and the association for molecular pathology (ACMG-AMP) guidelines. In our study, APP, PSEN1, and PSEN2 variants were collected by searching Alzforum and PubMed database with keywords “PSEN1,” “PSEN2,” and “APP.” These variants were re-evaluated based on the ACMG-AMP guidelines. We compared the number of pathogenic/likely pathogenic variants of APP, PSEN1, and PSEN2. In total, 66 APP variants, 323 PSEN1 variants, and 63 PSEN2 variants were re-evaluated in our study. 94.91% of previously reported pathogenic variants were re-classified as pathogenic/likely pathogenic variants, while 5.09% of them were variants of uncertain significance (VUS). PSEN1 carried the most prevalent pathogenic/likely pathogenic variants, followed by APP and PSEN2. Significant statistically difference was identified among these three genes when comparing the number of pathogenic/likely pathogenic variants (P < 2.2 × 10–16). Most of the previously reported pathogenic variants were re-classified as pathogenic/likely pathogenic variants while the others were re-evaluated as VUS, highlighting the importance of interpreting APP, PSEN1, and PSEN2 variants with caution according to ACMG-AMP guidelines.

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Strong functional data for pathogenicity or neutrality classify BRCA2 DNA-binding-domain variants of uncertain significance

The American Journal of Human Genetics ◽

10.1016/j.ajhg.2021.02.005 ◽

2021 ◽

Author(s):

Marcy E. Richardson ◽

Chunling Hu ◽

Kun Y. Lee ◽

Holly LaDuca ◽

Kelly Fulk ◽

...

Keyword(s):

Dna Binding ◽

Functional Data ◽

Binding Domain ◽

Dna Binding Domain ◽

Variants Of Uncertain Significance ◽

Uncertain Significance

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Variant Selection and Interpretation: An Example of Modified VarSome Classifier of ACMG Guidelines in the Diagnostic Setting

Genes ◽

10.3390/genes12121885 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1885

Author(s):

Francesca Cristofoli ◽

Elisa Sorrentino ◽

Giulia Guerri ◽

Roberta Miotto ◽

Roberta Romanelli ◽

...

Keyword(s):

Medical Genetics ◽

Patient Specific ◽

Specific Information ◽

Variant Selection ◽

Variant Classification ◽

Variant Interpretation ◽

Bioinformatics Pipeline ◽

Different Levels ◽

Diagnostic Setting

Variant interpretation is challenging as it involves combining different levels of evidence in order to evaluate the role of a specific variant in the context of a patient’s disease. Many in-depth refinements followed the original 2015 American College of Medical Genetics (ACMG) guidelines to overcome subjective interpretation of criteria and classification inconsistencies. Here, we developed an ACMG-based classifier that retrieves information for variant interpretation from the VarSome Stable-API environment and allows molecular geneticists involved in clinical reporting to introduce the necessary changes to criterion strength and to add or exclude criteria assigned automatically, ultimately leading to the final variant classification. We also developed a modified ACMG checklist to assist molecular geneticists in adjusting criterion strength and in adding literature-retrieved or patient-specific information, when available. The proposed classifier is an example of integration of automation and human expertise in variant curation, while maintaining the laboratory analytical workflow and the established bioinformatics pipeline.

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The critical role of segregation analysis in determining the pathogenicity of variants of uncertain significance in patients with suspected familial hypercholesterolaemia

Atherosclerosis ◽

10.1016/j.atherosclerosis.2017.06.736 ◽

2017 ◽

Vol 263 ◽

pp. e226

Author(s):

Lisa Gritzmacher ◽

Graham Bayly ◽

Julie Honeychurch ◽

Maggie Williams ◽

Paul Downie

Keyword(s):

Segregation Analysis ◽

Familial Hypercholesterolaemia ◽

Critical Role ◽

Variants Of Uncertain Significance ◽

Uncertain Significance

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Clinical Utility of a Phenotype-Enhanced MYH7 -Specific Variant Classification Framework in Hypertrophic Cardiomyopathy Genetic Testing

Circulation Genomic and Precision Medicine ◽

10.1161/circgen.120.003039 ◽

2020 ◽

Vol 13 (5) ◽

pp. 453-459

Author(s):

Connor L. Mattivi ◽

J. Martijn Bos ◽

Richard D. Bagnall ◽

Natalie Nowak ◽

John R. Giudicessi ◽

...

Keyword(s):

Genetic Testing ◽

Hypertrophic Cardiomyopathy ◽

Mayo Clinic ◽

Clinical Utility ◽

Similar Distribution ◽

Variant Classification ◽

Classification Framework ◽

Uncertain Significance ◽

Genetics And Genomics ◽

Independent Cohort

Background: Missense variants in the MYH7 -encoded MYH7 (beta myosin heavy chain 7) represent a leading cause of hypertrophic cardiomyopathy (HCM). MYH7 -specific American College of Medical Genetics and Genomics (ACMG) variant classification guidelines were released recently but have yet to be assessed independently. We set out to assess the performance of the MYH7 -specific ACMG guidelines and determine if the addition of phenotype-enhanced criteria (PE-ACMG) using the HCM Genotype Predictor Score can further reduce the burden of variants of uncertain significance (VUS). Methods: Re-assessment was performed on 70 MYH7 -variants in 121 unique patients from Mayo Clinic, and an independent cohort of 54 variants in 70 patients from Royal Prince Alfred Hospital (Australia). Qualifying variants were re-adjudicated using both standard ACMG and MYH7 -ACMG guidelines, and HCM Genotype Predictor Score was used to provide a validated measure of strength of clinical phenotype to be incorporated into the MYH7 -ACMG framework. Results: Among Mayo Clinic identified variants, 11/70 (16%) were classified as pathogenic (P), 10/70 (14%) as likely pathogenic, and 49/70 (70%) as a VUS. A similar distribution was seen in the Australian patients (12/54 [22%] P, 12/54 [22%] likely pathogenic, and 30/54 [56%] VUS; P =not significant). Application of the MYH7 -ACMG resulted in a nonsignificant reduction of the VUS burden in both cohorts from 49/70 to 39/70 (56%; P =0.1; Mayo Clinic) and from 30/54 to 20/54 (37%; P =0.1; Australia). Using the combined PE-MYH7-ACMG framework, the VUS decreased significantly from 49 to 27 ( P <0.001, Mayo Clinic) and from 30 to 16 ( P <0.001; Australia). Conclusions: Use of the MYH7 -specific guidelines alone failed to significantly decrease VUS burden in 2 independent cohorts. However, a significant reduction in VUS burden was observed after the addition of phenotypic criteria. Using a patient’s strength of sarcomeric HCM phenotype for variant adjudication can increase significantly the clinical utility of genetic testing for patients with HCM.

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Clostridioides difficile therapeutics: guidelines and beyond

Therapeutic Advances in Infectious Disease ◽

10.1177/2049936119868548 ◽

2019 ◽

Vol 6 ◽

pp. 204993611986854 ◽

Cited By ~ 1

Author(s):

Robert Orenstein ◽

Roberto L. Patron

Keyword(s):

Recurrent Disease ◽

Hospital Setting ◽

Humoral Response ◽

Clostridioides Difficile ◽

Clostridioides Difficile Infection ◽

New Guidelines ◽

Evidence Based Guidelines ◽

Common Infection

Clostridioides difficile infection (CDI) has become an increasingly common infection both within and outside of the hospital setting. The management of this infection has been evolving as we learn more about the role of the human microbiota in protecting us from this gastrointestinal opportunist. For many years the focus of treatment had been on eradication of the vegetative, toxin-producing form of the organism, with little regard for its collateral impact on the host’s microbiota or risk of recurrence. With the marked increase in C. difficile disease, and, particularly, recurrent disease in the last decade, new guidelines are more focused on targeting and reducing collateral damage to the colonic microbiota. Immune-based strategies that manipulate the microbiota and provide a humoral response to toxins have now become mainstream. Newer strategies are needed to look beyond simply resolving the primary episode but are focused on delayed outcomes such as cure at 90 days, reduced morbidity and mortality, and patient quality of life. The purpose of this review is to familiarize readers with the most recent evidence-based guidelines for C. difficile management, and to describe the role of newer antimicrobials, immunological-, and microbiota-based therapeutics to prevent recurrence and improve the outcomes of people with CDI.

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Closing the gap: Systematic integration of multiplexed functional data resolves variants of uncertain significance in BRCA1, TP53, and PTEN

The American Journal of Human Genetics ◽

10.1016/j.ajhg.2021.11.001 ◽

2021 ◽

Author(s):

Shawn Fayer ◽

Carrie Horton ◽

Jennifer N. Dines ◽

Alan F. Rubin ◽

Marcy E. Richardson ◽

...

Keyword(s):

Functional Data ◽

Variants Of Uncertain Significance ◽

Uncertain Significance ◽

Closing The Gap

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Exome Sequencing Highlights a Potential Role for Concealed Cardiomyopathies in Youthful Sudden Cardiac Death

Circulation Genomic and Precision Medicine ◽

10.1161/circgen.121.003497 ◽

2021 ◽

Author(s):

Raquel Neves ◽

David J. Tester ◽

Michael A. Simpson ◽

Elijah R. Behr ◽

Michael J. Ackerman ◽

...

Keyword(s):

Exome Sequencing ◽

Strong Evidence ◽

Susceptibility Gene ◽

Susceptibility Genes ◽

Medical Genetics ◽

Variant Of Uncertain Significance ◽

Pathogenic Variants ◽

Genetic Test Results ◽

Uncertain Significance ◽

Genetics And Genomics

Background: Sudden cardiac arrest (SCA) and sudden unexplained death (SUD) are feared sequelae of many genetic heart diseases. In rare circumstances, pathogenic variants in cardiomyopathy-susceptibility genes may result in electrical instability leading to SCA/SUD before any structural manifestations of underlying cardiomyopathy are evident. Methods: Collectively, 38 unexplained SCA survivors (21 males; mean age at SCA 26.4±13.1 years), 68 autopsy-inconclusive SUD cases (49 males; mean age at death 20.4±9.0 years) without disease-causative variants in the channelopathy genes, and 973 ostensibly healthy controls were included. Following exome sequencing, ultrarare (minor allele frequency ≤0.00005 in any ethnic group within Genome Aggregation Database [gnomAD, n=141 456 individuals]) nonsynonymous variants identified in 24 ClinGen adjudicated definitive/strong evidence cardiomyopathy-susceptibility genes were analyzed. Eligible variants were adjudicated as pathogenic, likely pathogenic, or variant of uncertain significance in accordance with current American College of Medical Genetics and Genomics guidelines. Results: Overall, 7 out of 38 (18.4%) SCA survivors and 14 out of 68 (20.5%) autopsy-inconclusive, channelopathic-negative SUD cases had at least one pathogenic/likely pathogenic or a variant of uncertain significance nonsynonymous variant within a strong evidence, cardiomyopathy-susceptibility gene. Following American College of Medical Genetics and Genomics criterion variant adjudication, a pathogenic or likely pathogenic variant was identified in 3 out of 38 (7.9%; P =0.05) SCA survivors and 8 out of 68 (11.8%; P =0.0002) autopsy-inconclusive SUD cases compared to 20 out of 973 (2.1%) European controls. Interestingly, the yield of pathogenic/likely pathogenic variants was significantly greater in autopsy-inconclusive SUD cases with documented interstitial fibrosis (4/11, 36%) compared with only 4 out of 57 (7%, P <0.02) SUD cases without ventricular fibrosis. Conclusion: Our data further supports the inclusion of strongevidence cardiomyopathy-susceptibility genes on the genetic testing panels used to evaluate unexplained SCA survivors and autopsy-inconclusive/negative SUD decedents. However, to avoid diagnostic miscues, the careful interpretation of genetic test results in patients without overt phenotypes is vital.

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