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Zhang L, Shen M, Shu X, Zhou J, Ding J, Lin H, Pan B, Zhang C, Wang B, Guo W. The recommendation of re-classification of variants of uncertain significance (VUS) in adult genetic disorders patients. J Hum Genet 2024:10.1038/s10038-024-01263-4. [PMID: 38839994 DOI: 10.1038/s10038-024-01263-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/07/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
Since variants of uncertain significance (VUS) reported in genetic testing cannot be acted upon clinically, this classification may delay or prohibit precise diagnosis and genetic counseling in adult genetic disorders patients. Large-scale analyses about qualitatively distinct lines of evidence used for VUS can make them re-classification more accurately. We analyzed 458 Chinese adult patients WES data, within 15 pathogenic evidence PS1, PS2, PM1, PM6 and PP4 were not used for VUS pathogenic classification, meanwhile the PP3, BP4, PP2 were used much more frequently. The PM2_Supporting was used most widely for all reported variants. There were also 31 null variants (nonsense, frameshift, canonical ±1 or 2 splice sites) which were probably the disease-causing variants of the patients were classified as VUS. By analyzed the evidence used for all VUS we recommend that appropriate genetic counseling, reliable releasing of in-house data, allele frequency comparison between case and control, expanded verification in patient family, co-segregation analysis and functional assays were urgent need to gather more evidence to reclassify VUS. We also found adult patients with nervous system disease were reported the most phenotype-associated VUS and the lower the phenotypic specificity, the more reported VUS. This result emphasized the importance of pretest genetic counseling which would make less reporting of VUS. Our result revealed the characteristics of the pathogenic classification evidence used for VUS in adult genetic disorders patients for the first time, recommend a rules-based process to evaluate the pathogenicity of VUS which could provide a strong basis for accurately evaluating the pathogenicity and clinical grade information of VUS. Meanwhile, we further expanded the genetic spectrum and improve the diagnostic rate of adult genetic disorders.
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Affiliation(s)
- Li Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minna Shen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xianhong Shu
- Department of Echocardiography, Zhongshan Hospital, Shanghai Institute of Cardiovascular Diseases, Shanghai Institute of Medical Imaging, Fudan University, Shanghai, China
| | - Jingmin Zhou
- Department of Cardiology Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Ding
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Huandong Lin
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunyan Zhang
- Department of Laboratory Medicine, Shanghai Geriatric Medical Center, Shanghai, China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
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Audo I, Nassisi M, Zeitz C, Sahel JA. The Extraordinary Phenotypic and Genetic Variability of Retinal and Macular Degenerations: The Relevance to Therapeutic Developments. Cold Spring Harb Perspect Med 2024; 14:a041652. [PMID: 37604589 PMCID: PMC11146306 DOI: 10.1101/cshperspect.a041652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous group of rare conditions leading to various degrees of visual handicap and to progressive blindness in more severe cases. Besides visual rehabilitation, educational, and socio-professional support, there are currently limited therapeutic options, but the approval of the first gene therapy product for RPE65-related IRDs raised hope for therapeutic innovations. Such developments are facing obstacles intrinsic to the disease and the affected tissue including the extreme phenotypic and genetic variability of IRDs and the fine tuning of visual processing through the complex architecture of the postmitotic neural retina. A precise phenotypic characterization is required prior to genetic testing, which now relies on high-throughput sequencing. Their challenges will be discussed within this article as well as their implications in clinical trial design.
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Affiliation(s)
- Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris 75012, France
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, Paris F-75012, France
| | - Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris 75012, France
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
- Ophthalmology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan 20122, Italy
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris 75012, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris 75012, France
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, Paris F-75012, France
- Department of Ophthalmology, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania 15213, USA
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Cevik S, Zhao P, Zorluer A, Pir MS, Bian W, Kaplan OI. Matching variants for functional characterization of genetic variants. G3 (BETHESDA, MD.) 2023; 13:jkad227. [PMID: 37933433 PMCID: PMC10700107 DOI: 10.1093/g3journal/jkad227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/06/2023] [Indexed: 11/08/2023]
Abstract
Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we used Caenorhabditis elegans mutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carrying C. elegans mutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors into cilia. Functional analysis of all 10 variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of nonciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic in C. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9.
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Affiliation(s)
- Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | - Pei Zhao
- School of Applied Science and Engineering, Fuzhou Institute of Technology, Fuzhou 350014, China
- SunyBiotech Co., Ltd., Fuzhou 35000, China
| | - Atiyye Zorluer
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | - Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
| | | | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey
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Muñoz-Pujol G, Ugarteburu O, Segur-Bailach E, Moliner S, Jurado S, Garrabou G, Guitart-Mampel M, García-Villoria J, Artuch R, Fons C, Ribes A, Tort F. CRISPR/Cas9-based functional genomics strategy to decipher the pathogenicity of genetic variants in inherited metabolic disorders. J Inherit Metab Dis 2023; 46:1029-1042. [PMID: 37718653 DOI: 10.1002/jimd.12681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/19/2023]
Abstract
The determination of the functional impact of variants of uncertain significance (VUS) is one of the major bottlenecks in the diagnostic workflow of inherited genetic diseases. To face this problem, we set up a CRISPR/Cas9-based strategy for knock-in cellular model generation, focusing on inherited metabolic disorders (IMDs). We selected variants in seven IMD-associated genes, including seven reported disease-causing variants and four benign/likely benign variants. Overall, 11 knock-in cell models were generated via homology-directed repair in HAP1 haploid cells using CRISPR/Cas9. The functional impact of the variants was determined by analyzing the characteristic biochemical alterations of each disorder. Functional studies performed in knock-in cell models showed that our approach accurately distinguished the functional effect of pathogenic from non-pathogenic variants in a reliable manner in a wide range of IMDs. Our study provides a generic approach to assess the functional impact of genetic variants to improve IMD diagnosis and this tool could emerge as a promising alternative to invasive tests, such as muscular or skin biopsies. Although the study has been performed only in IMDs, this strategy is generic and could be applied to other genetic disorders.
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Affiliation(s)
- Gerard Muñoz-Pujol
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Olatz Ugarteburu
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Eulàlia Segur-Bailach
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Sonia Moliner
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Susana Jurado
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Glòria Garrabou
- Inherited Metabolic diseases and Muscle Disorder's lab, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Service-Hospital Clinic of Barcelona and CIBERER, Barcelona, Spain
| | - Mariona Guitart-Mampel
- Inherited Metabolic diseases and Muscle Disorder's lab, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Service-Hospital Clinic of Barcelona and CIBERER, Barcelona, Spain
| | - Judit García-Villoria
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry and Molecular Medicine and Genetics Departments, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, and CIBERER, Esplúgues de Llobregat, Barcelona, Spain
| | - Carme Fons
- Neurology Department, Fetal, Neonatal Neurology and Early Epilepsy Unit, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Frederic Tort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
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Hopkins CE, Brock T, Caulfield TR, Bainbridge M. Phenotypic screening models for rapid diagnosis of genetic variants and discovery of personalized therapeutics. Mol Aspects Med 2022; 91:101153. [PMID: 36411139 PMCID: PMC10073243 DOI: 10.1016/j.mam.2022.101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 11/19/2022]
Abstract
Precision medicine strives for highly individualized treatments for disease under the notion that each individual's unique genetic makeup and environmental exposures imprints upon them not only a disposition to illness, but also an optimal therapeutic approach. In the realm of rare disorders, genetic predisposition is often the predominant mechanism driving disease presentation. For such, mostly, monogenic disorders, a causal gene to phenotype association is likely. As a result, it becomes important to query the patient's genome for the presence of pathogenic variations that are likely to cause the disease. Determining whether a variant is pathogenic or not is critical to these analyses and can be challenging, as many disease-causing variants are novel and, ergo, have no available functional data to help categorize them. This problem is exacerbated by the need for rapid evaluation of pathogenicity, since many genetic diseases present in young children who will experience increased morbidity and mortality without rapid diagnosis and therapeutics. Here, we discuss the utility of animal models, with a focus mainly on C. elegans, as a contrast to tissue culture and in silico approaches, with emphasis on how these systems are used in determining pathogenicity of variants with uncertain significance and then used to screen for novel therapeutics.
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Affiliation(s)
| | | | - Thomas R Caulfield
- Mayo Clinic, Department of Neuroscience, Department of Computational Biology, Department of Clinical Genomics, Jacksonville, FL, 32224, Rochester, MN, 55905, USA
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Mew M, Caldwell KA, Caldwell GA. From bugs to bedside: functional annotation of human genetic variation for neurological disorders using invertebrate models. Hum Mol Genet 2022; 31:R37-R46. [PMID: 35994032 PMCID: PMC9585664 DOI: 10.1093/hmg/ddac203] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 02/02/2023] Open
Abstract
The exponential accumulation of DNA sequencing data has opened new avenues for discovering the causative roles of single-nucleotide polymorphisms (SNPs) in neurological diseases. The opportunities emerging from this are staggering, yet only as good as our abilities to glean insights from this surplus of information. Whereas computational biology continues to improve with respect to predictions and molecular modeling, the differences between in silico and in vivo analysis remain substantial. Invertebrate in vivo model systems represent technically advanced, experimentally mature, high-throughput, efficient and cost-effective resources for investigating a disease. With a decades-long track record of enabling investigators to discern function from DNA, fly (Drosophila) and worm (Caenorhabditis elegans) models have never been better poised to serve as living engines of discovery. Both of these animals have already proven useful in the classification of genetic variants as either pathogenic or benign across a range of neurodevelopmental and neurodegenerative disorders-including autism spectrum disorders, ciliopathies, amyotrophic lateral sclerosis, Alzheimer's and Parkinson's disease. Pathogenic SNPs typically display distinctive phenotypes in functional assays when compared with null alleles and frequently lead to protein products with gain-of-function or partial loss-of-function properties that contribute to neurological disease pathogenesis. The utility of invertebrates is logically limited by overt differences in anatomical and physiological characteristics, and also the evolutionary distance in genome structure. Nevertheless, functional annotation of disease-SNPs using invertebrate models can expedite the process of assigning cellular and organismal consequences to mutations, ascertain insights into mechanisms of action, and accelerate therapeutic target discovery and drug development for neurological conditions.
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Affiliation(s)
- Melanie Mew
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Departments of Neurobiology and Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Research in the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Departments of Neurobiology and Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Research in the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Kabzińska D, Chabros K, Kamińska J, Kochański A. The GDAP1 p.Glu222Lys Variant-Weak Pathogenic Effect, Cumulative Effect of Weak Sequence Variants, or Synergy of Both Factors? Genes (Basel) 2022; 13:genes13091546. [PMID: 36140714 PMCID: PMC9498914 DOI: 10.3390/genes13091546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022] Open
Abstract
Charcot−Marie−Tooth disorders (CMT) represent a highly heterogeneous group of diseases of the peripheral nervous system in which more than 100 genes are involved. In some CMT patients, a few weak sequence variants toward other CMT genes are detected instead of one leading CMT mutation. Thus, the presence of a few variants in different CMT-associated genes raises the question concerning the pathogenic status of one of them. In this study, we aimed to analyze the pathogenic effect of c.664G>A, p.Glu222Lys variant in the GDAP1 gene, whose mutations are known to be causative for CMT type 4A (CMT4A). Due to low penetrance and a rare occurrence limited to five patients from two Polish families affected by the CMT phenotype, there is doubt as to whether we are dealing with real pathogenic mutation. Thus, we aimed to study the pathogenic effect of the c.664G>A, p.Glu222Lys variant in its natural environment, i.e., the neuronal SH-SY5Y cell line. Additionally, we have checked the pathogenic status of p.Glu222Lys in the broader context of the whole exome. We also have analyzed the impact of GDAP1 gene mutations on the morphology of the transfected cells. Despite the use of several tests to determine the pathogenicity of the p.Glu222Lys variant, we cannot point to one that would definitively solve the problem of pathogenicity.
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Affiliation(s)
- Dagmara Kabzińska
- Neuromuscular Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Katarzyna Chabros
- Neuromuscular Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Joanna Kamińska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Andrzej Kochański
- Neuromuscular Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, 02-106 Warsaw, Poland
- Correspondence:
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