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AlAbdi L, Rahbeeni Z, Maddirevula S, Helaby R, Abdulwahab F, Khan AO, Riley LG, Alhashem A, Chassaing N, Jamieson RV, Alkuraya FS. A founder variant expands the phenotype of WNT7B-related PDAC syndrome. Clin Genet 2024; 106:66-71. [PMID: 38417950 DOI: 10.1111/cge.14512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/22/2024] [Accepted: 02/15/2024] [Indexed: 03/01/2024]
Abstract
Pulmonary hypoplasia, Diaphragmatic anomalies, Anophthalmia/microphthalmia, and Cardiac defects (PDAC) syndrome is a genetically heterogeneous multiple congenital malformation syndrome. Although pathogenic variants in RARB and STRA6 are established causes of PDAC, many PDAC cases remain unsolved at the molecular level. Recently, we proposed biallelic WNT7B variants as a novel etiology based on several families with typical features of PDAC syndrome albeit with variable expressivity. Here, we report three patients from two families that share a novel founder variant in WNT7B (c.739C > T; Arg247Trp). The phenotypic expression of this variant ranges from typical PDAC features to isolated genitourinary anomalies. Similar to previously reported PDAC-associated WNT7B variants, this variant was found to significantly impair WNT7B signaling activity further corroborating its proposed pathogenicity. This report adds further evidence to WNT7B-related PDAC and expands its variable expressivity.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, New South Wales, Australia
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Amal Alhashem
- Division of Clinical Genetic and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Genetic and Metabolic, Sehha Virtual Hospital, Ministry of Health, Riyadh, Saudi Arabia
| | - Nicolas Chassaing
- Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, Purpan University Hospital, Toulouse, Midi-Pyrénées, France
- Department of Medical Genetics, Purpan University Hospital, Toulouse, Midi-Pyrénées, France
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, University of Sydney; The Children's Hospital at Westmead, Sydney Children's Hospitals Network; and Save Sight Institute, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health and Child and Adolescent Health, University of Sydney, Sydney, New South Wales, Australia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Division of Clinical Genetic and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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2
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He MF, Liu LH, Luo S, Wang J, Guo JJ, Wang PY, Zhai QX, He SL, Zou DF, Liu XR, Li BM, Ma HY, Qiao JD, Zhou P, He N, Yi YH, Liao WP. ZFHX3 variants cause childhood partial epilepsy and infantile spasms with favourable outcomes. J Med Genet 2024; 61:652-660. [PMID: 38508705 DOI: 10.1136/jmg-2023-109725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/18/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND The ZFHX3 gene plays vital roles in embryonic development, cell proliferation, neuronal differentiation and neuronal death. This study aims to explore the relationship between ZFHX3 variants and epilepsy. METHODS Whole-exome sequencing was performed in a cohort of 378 patients with partial (focal) epilepsy. A Drosophila Zfh2 knockdown model was used to validate the association between ZFHX3 and epilepsy. RESULTS Compound heterozygous ZFHX3 variants were identified in eight unrelated cases. The burden of ZFHX3 variants was significantly higher in the case cohort, shown by multiple/specific statistical analyses. In Zfh2 knockdown flies, the incidence and duration of seizure-like behaviour were significantly greater than those in the controls. The Zfh2 knockdown flies exhibited more firing in excitatory neurons. All patients presented partial seizures. The five patients with variants in the C-terminus/N-terminus presented mild partial epilepsy. The other three patients included one who experienced frequent non-convulsive status epilepticus and two who had early spasms. These three patients had also neurodevelopmental abnormalities and were diagnosed as developmental epileptic encephalopathy (DEE), but achieved seizure-free after antiepileptic-drug treatment without adrenocorticotropic-hormone/steroids. The analyses of temporal expression (genetic dependent stages) indicated that ZFHX3 orthologous were highly expressed in the embryonic stage and decreased dramatically after birth. CONCLUSION ZFHX3 is a novel causative gene of childhood partial epilepsy and DEE. The patients of infantile spasms achieved seizure-free after treatment without adrenocorticotropic-hormone/steroids implies a significance of genetic diagnosis in precise treatment. The genetic dependent stage provided an insight into the underlying mechanism of the evolutional course of illness.
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Affiliation(s)
- Ming-Feng He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Li-Hong Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
- Department of Neurology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Sheng Luo
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Juan Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Jia-Jun Guo
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Peng-Yu Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Qiong-Xiang Zhai
- Department of Pediatrics, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510120, China
| | - Su-Li He
- Department of Pediatrics, Shantou Chaonan Minsheng Hospital, Shantou 515000, China
| | - Dong-Fang Zou
- Epilepsy Center and Department of Neurology, Shenzhen Children's Hospital, Shenzhen 518029, China
| | - Xiao-Rong Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Bing-Mei Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Hai-Yan Ma
- Department of Functional Neurosurgery, Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jing-Da Qiao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Peng Zhou
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Yong-Hong Yi
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
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3
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AlAbdi L, Neuhann T, Prott EC, Schön U, Abdulwahab F, Faqeih E, Alkuraya FS. Human ABL1 deficiency syndrome (HADS) is a recognizable syndrome distinct from ABL1-related congenital heart defects and skeletal malformations syndrome. Hum Genet 2024; 143:739-745. [PMID: 38743093 DOI: 10.1007/s00439-024-02677-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/04/2024] [Indexed: 05/16/2024]
Abstract
Germline gain of function variants in the oncogene ABL1 cause congenital heart defects and skeletal malformations (CHDSKM) syndrome. Whether a corresponding ABL1 deficiency disorder exists in humans remains unknown although developmental defects in mice deficient for Abl1 support this notion. Here, we describe two multiplex consanguineous families, each segregating a different homozygous likely loss of function variant in ABL1. The associated phenotype is multiple congenital malformations and distinctive facial dysmorphism that are opposite in many ways to CHDSKM. We suggest that a tight balance of ABL1 activity is required during embryonic development and that both germline gain of function and loss of function variants result in distinctively different allelic congenital malformation disorders.
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Affiliation(s)
- Lama AlAbdi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | | | - Ulrike Schön
- MGZ Medizinisch Genetisches Zentrum, Munich, Germany
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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4
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Brown CM, Amendola LM, Chandrasekhar A, Hagelstrom RT, Halter G, Kesari A, Thorpe E, Perry DL, Taft RJ, Coffey AJ. A framework for the evaluation and reporting of incidental findings in clinical genomic testing. Eur J Hum Genet 2024; 32:665-672. [PMID: 38565640 PMCID: PMC11153510 DOI: 10.1038/s41431-024-01575-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/29/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Currently, there are no widely accepted recommendations in the genomics field guiding the return of incidental findings (IFs), defined here as unexpected results that are unrelated to the indication for testing. Consequently, reporting policies for IFs among laboratories offering genomic testing are variable and may lack transparency. Herein we describe a framework developed to guide the evaluation and return of IFs encountered in probands undergoing clinical genome sequencing (cGS). The framework prioritizes clinical significance and actionability of IFs and follows a stepwise approach with stopping points at which IFs may be recommended for return or not. Over 18 months, implementation of the framework in a clinical laboratory facilitated the return of actionable IFs in 37 of 720 (5.1%) individuals referred for cGS, which is reduced to 3.1% if glucose-6-phosphate dehydrogenase (G6PD) deficiency is excluded. This framework can serve as a model to standardize reporting of IFs identified during genomic testing.
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Affiliation(s)
- Carolyn M Brown
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
| | - Laura M Amendola
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | | | | | - Gillian Halter
- Scripps MD Anderson Cancer Center, San Diego, CA, 92121, USA
| | - Akanchha Kesari
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
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5
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Ozisik O, Gorokhova S, Cerino M, Bartoli M, Baudot A. System-level analysis of genes mutated in muscular dystrophies reveals a functional pattern associated with muscle weakness distribution. Sci Rep 2024; 14:11225. [PMID: 38755190 PMCID: PMC11099060 DOI: 10.1038/s41598-024-60761-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Muscular dystrophies (MDs) are inherited genetic diseases causing weakness and degeneration of muscles. The distribution of muscle weakness differs between MDs, involving distal muscles or proximal muscles. While the mutations in most of the MD-associated genes lead to either distal or proximal onset, there are also genes whose mutations can cause both types of onsets. We hypothesized that the genes associated with different MD onsets code proteins with distinct cellular functions. To investigate this, we collected the MD-associated genes and assigned them to three onset groups: genes mutated only in distal onset dystrophies, genes mutated only in proximal onset dystrophies, and genes mutated in both types of onsets. We then systematically evaluated the cellular functions of these gene sets with computational strategies based on functional enrichment analysis and biological network analysis. Our analyses demonstrate that genes mutated in either distal or proximal onset MDs code proteins linked with two distinct sets of cellular processes. Interestingly, these two sets of cellular processes are relevant for the genes that are associated with both onsets. Moreover, the genes associated with both onsets display high centrality and connectivity in the network of muscular dystrophy genes. Our findings support the hypothesis that the proteins associated with distal or proximal onsets have distinct functional characteristics, whereas the proteins associated with both onsets are multifunctional.
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Affiliation(s)
- Ozan Ozisik
- Aix Marseille University, INSERM, MMG, Marseille, France.
- Université Paris Cité, INSERM U976, Paris, France.
| | - Svetlana Gorokhova
- Aix Marseille University, INSERM, MMG, Marseille, France
- Department of Medical Genetics, La Timone Hospital, AP-HM, Marseille, France
| | - Mathieu Cerino
- Aix Marseille University, INSERM, MMG, Marseille, France
- Department of Medical Genetics, La Timone Hospital, AP-HM, Marseille, France
- Laboratory of Biochemistry, La Conception Hospital, AP-HM, Marseille, France
| | - Marc Bartoli
- Aix Marseille University, INSERM, MMG, Marseille, France
- CNRS, Marseille, France
| | - Anaïs Baudot
- Aix Marseille University, INSERM, MMG, Marseille, France.
- CNRS, Marseille, France.
- Barcelona Supercomputing Center, Barcelona, Spain.
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6
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Amendola LM, Coffey AJ, Lowry J, Avecilla J, Malhotra A, Chawla A, Thacker S, Taylor JP, Rajkumar R, Brown CM, Golden-Grant K, Hejja R, Lee JA, Medrano P, Milewski B, Mullen F, Walker A, Huertez-Vasquez A, Longoni M, Perry DL, Hostin D, Ajay SS, Kesari A, Strom SP, Margulies E, Belmont J, Lanfear DE, Taft RJ. Development of a comprehensive cardiovascular disease genetic risk assessment test. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.06.24306379. [PMID: 38766118 PMCID: PMC11100944 DOI: 10.1101/2024.05.06.24306379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background Despite monogenic and polygenic contributions to cardiovascular disease (CVD), genetic testing is not widely adopted, and current tests are limited by the breadth of surveyed conditions and interpretation burden. Methods We developed a comprehensive clinical genome CVD test with semi-automated interpretation. Monogenic conditions and risk alleles were selected based on the strength of disease association and evidence for increased disease risk, respectively. Non-CVD secondary findings genes, pharmacogenomic (PGx) variants and CVD polygenic risk scores (PRS) were assessed for inclusion. Test performance was modeled using 2,594 genomes from the 1000 Genomes Project, and further investigated in 20 previously tested individuals. Results The CVD genome test is composed of a panel of 215 CVD gene-disease pairs, 35 non-CVD secondary findings genes, 4 risk alleles or genotypes, 10 PGx genes and a PRS for coronary artery disease. Modeling of test performance using samples from the 1000 Genomes Project revealed ~6% of individuals with a monogenic finding in a CVD-associated gene, 6% with a risk allele finding, ~1% with a non-CVD secondary finding, and 93% with CVD-associated PGx variants. Assessment of blinded clinical samples showed complete concordance with prior testing. An average of 4 variants were reviewed per case, with interpretation and reporting time ranging from 9-96 min. Conclusions A genome sequencing based CVD genetic risk assessment can provide comprehensive genetic disease and genetic risk information to patients with CVD. The semi-automated and limited interpretation burden suggest that this testing approach could be scaled to support population-level initiatives.
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Affiliation(s)
| | | | | | | | | | | | - Stetson Thacker
- Illumina Inc., San Diego, CA 92122
- GenomOncology, Cleveland, OH 44113
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7
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Mohan S, McNulty S, Thaxton C, Elnagheeb M, Owens E, Flowers M, Nunnery T, Self A, Palus B, Gorokhova S, Kennedy A, Niu Z, Johari M, Maiga AB, Macalalad K, Clause AR, Beckmann JS, Bronicki L, Cooper ST, Ganesh VS, Kang PB, Kesari A, Lek M, Levy J, Rufibach L, Savarese M, Spencer MJ, Straub V, Tasca G, Weihl CC. Expert Panel Curation of 31 Genes in Relation to Limb Girdle Muscular Dystrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592369. [PMID: 38765987 PMCID: PMC11100593 DOI: 10.1101/2024.05.03.592369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Introduction Limb girdle muscular dystrophies (LGMDs) are a group of genetically heterogeneous autosomal conditions with some degree of phenotypic homogeneity. LGMD is defined as having onset >2 years of age with progressive proximal weakness, elevated serum creatine kinase levels and dystrophic features on muscle biopsy. Advances in massively parallel sequencing have led to a surge in genes linked to LGMD. Methods The ClinGen Muscular Dystrophies and Myopathies gene curation expert panel (MDM GCEP, formerly Limb Girdle Muscular Dystrophy GCEP) convened to evaluate the strength of evidence supporting gene-disease relationships (GDR) using the ClinGen gene-disease clinical validity framework to evaluate 31 genes implicated in LGMD. Results The GDR was exclusively LGMD for 17 genes, whereas an additional 14 genes were related to a broader phenotype encompassing congenital weakness. Four genes (CAPN3, COL6A1, COL6A2, COL6A3) were split into two separate disease entities, based on each displaying both dominant and recessive inheritance patterns, resulting in curation of 35 GDRs. Of these, 30 (86%) were classified as Definitive, 4 (11%) as Moderate and 1 (3%) as Limited. Two genes, POMGNT1 and DAG1, though definitively related to myopathy, currently have insufficient evidence to support a relationship specifically with LGMD. Conclusions The expert-reviewed assertions on the clinical validity of genes implicated in LGMDs form an invaluable resource for clinicians and molecular geneticists. We encourage the global neuromuscular community to publish case-level data that help clarify disputed or novel LGMD associations.
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Affiliation(s)
- Shruthi Mohan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Shannon McNulty
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Marwa Elnagheeb
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Emma Owens
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - May Flowers
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Teagan Nunnery
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Autumn Self
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Brooke Palus
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Svetlana Gorokhova
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
- Department of Medical Genetics, Timone Children's Hospital, APHM, Marseille, France
| | | | - Zhiyv Niu
- Department of Laboratory Medicine and Pathology, Mayo Clinic
| | - Mridul Johari
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
- Folkhälsan Research Center, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Finland
| | | | | | | | | | - Lucas Bronicki
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Sandra T Cooper
- Kids Neuroscience Centre, Children's Hospital at Westmead; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney; Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Vijay S Ganesh
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Peter B Kang
- Greg Marzolf Jr. Muscular Dystrophy Center and Department of Neurology, University of Minnesota, Minneapolis, MN, USA
| | | | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | | | | | - Marco Savarese
- Folkhälsan Research Center, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Finland
| | | | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trusts, Newcastle Upon Tyne, UK
| | - Giorgio Tasca
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trusts, Newcastle Upon Tyne, UK
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Lemire G, Sanchis-Juan A, Russell K, Baxter S, Chao KR, Singer-Berk M, Groopman E, Wong I, England E, Goodrich J, Pais L, Austin-Tse C, DiTroia S, O'Heir E, Ganesh VS, Wojcik MH, Evangelista E, Snow H, Osei-Owusu I, Fu J, Singh M, Mostovoy Y, Huang S, Garimella K, Kirkham SL, Neil JE, Shao DD, Walsh CA, Argilli E, Le C, Sherr EH, Gleeson JG, Shril S, Schneider R, Hildebrandt F, Sankaran VG, Madden JA, Genetti CA, Beggs AH, Agrawal PB, Bujakowska KM, Place E, Pierce EA, Donkervoort S, Bönnemann CG, Gallacher L, Stark Z, Tan TY, White SM, Töpf A, Straub V, Fleming MD, Pollak MR, Õunap K, Pajusalu S, Donald KA, Bruwer Z, Ravenscroft G, Laing NG, MacArthur DG, Rehm HL, Talkowski ME, Brand H, O'Donnell-Luria A. Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease. Am J Hum Genet 2024; 111:863-876. [PMID: 38565148 PMCID: PMC11080278 DOI: 10.1016/j.ajhg.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and, with new innovative methods, can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.
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Affiliation(s)
- Gabrielle Lemire
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Alba Sanchis-Juan
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn Russell
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha Baxter
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine R Chao
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moriel Singer-Berk
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Groopman
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Isaac Wong
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eleina England
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Julia Goodrich
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lynn Pais
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christina Austin-Tse
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephanie DiTroia
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily O'Heir
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vijay S Ganesh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Monica H Wojcik
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Emily Evangelista
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hana Snow
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mugdha Singh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yulia Mostovoy
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve Huang
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran Garimella
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha L Kirkham
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Diane D Shao
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Le
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shirlee Shril
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Ronen Schneider
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Alan H Beggs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Pankaj B Agrawal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Kinga M Bujakowska
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Emily Place
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Eric A Pierce
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Tiong Yang Tan
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mark D Fleming
- Harvard Medical School, Boston, MA, USA; Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Martin R Pollak
- Harvard Medical School, Boston, MA, USA; Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Zandre Bruwer
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Gianina Ravenscroft
- University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Daniel G MacArthur
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Heidi L Rehm
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison Brand
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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9
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Lim E, Borden C, Mehta S, Roberts MB, Mazzola S, Zhao F, Wang X. Reclassification of Variants Following Renal Genetics Testing: Uncommon Yet Impactful for Diagnosis and Management. Kidney Int Rep 2024; 9:1441-1450. [PMID: 38707809 PMCID: PMC11068948 DOI: 10.1016/j.ekir.2024.01.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Genetic testing is increasingly utilized in nephrology practice, but limited real-world data exist on variant reclassification following renal genetics testing. Methods A cohort of patients at the Cleveland Clinic Renal Genetics Clinic who underwent genetic testing through clinical laboratories was assessed with their clinical and laboratory data analyzed. Results Between January 2019 and June 2023, 425 new patients with variable kidney disorders from 413 pedigrees completed genetic testing through 10 clinical laboratories, including 255 (60%) females with median (25th, 75th percentiles) age of 36 (22-54) years. Multigene panel was the most frequently used modality followed by single-gene testing, exome sequencing (ES), chromosomal microarray (CMA), and genome sequencing (GS). At initial report, 52% of patients had ≥1 variants of uncertain significance (VUS) with or without concurrent pathogenic variant(s). Twenty amendments were issued across 19 pedigrees involving 19 variants in 17 genes. The overall variant reclassification rate was 5%, with 63% being upgrades and 32% downgrades. Of the reclassified variants, 79% were initially reported as VUS. The median time-to-amendments from initial reports was 8.4 (4-27) months. Following the variant reclassifications, 60% of the patients received a new diagnosis or a change in diagnosis. Among these, 67% of patients received significant changes in clinical management. Conclusion Variant reclassification following genetic testing is infrequent but important for diagnosis and management of patients with suspected genetic kidney disease. The majority of variant reclassifications involve VUS and are upgrades in clinically issued amended reports. Further studies are needed to investigate the predictors of such events.
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Affiliation(s)
- Euyn Lim
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Chloe Borden
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Seysha Mehta
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary-Beth Roberts
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sarah Mazzola
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Fang Zhao
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Xiangling Wang
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
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10
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You M, Shamseldin HE, Fogle HM, Rushing BR, AlMalki RH, Jaafar A, Hashem M, Abdulwahab F, Rahman AMA, Krupenko NI, Alkuraya FS, Krupenko SA. Further delineation of the phenotypic and metabolomic profile of ALDH1L2-related neurodevelopmental disorder. Clin Genet 2024; 105:488-498. [PMID: 38193334 PMCID: PMC10990829 DOI: 10.1111/cge.14479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024]
Abstract
ALDH1L2, a mitochondrial enzyme in folate metabolism, converts 10-formyl-THF (10-formyltetrahydrofolate) to THF (tetrahydrofolate) and CO2. At the cellular level, deficiency of this NADP+-dependent reaction results in marked reduction in NADPH/NADP+ ratio and reduced mitochondrial ATP. Thus far, a single patient with biallelic ALDH1L2 variants and the phenotype of a neurodevelopmental disorder has been reported. Here, we describe another patient with a neurodevelopmental disorder associated with a novel homozygous missense variant in ALDH1L2, Pro133His. The variant caused marked reduction in the ALDH1L2 enzyme activity in skin fibroblasts derived from the patient as probed by 10-FDDF, a stable synthetic analog of 10-formyl-THF. Additional associated abnormalities in these fibroblasts include reduced NADPH/NADP+ ratio and pool of mitochondrial ATP, upregulated autophagy and dramatically altered metabolomic profile. Overall, our study further supports a link between ALDH1L2 deficiency and abnormal neurodevelopment in humans.
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Affiliation(s)
- Mikyoung You
- UNC Nutrition Research Institute, Kannapolis, NC, USA
| | - Hanan E. Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Halle M. Fogle
- UNC Nutrition Research Institute, Kannapolis, NC, USA
- Department of Nutrition, University of North Carolina-Chapel Hill, NC, USA
| | - Blake R. Rushing
- UNC Nutrition Research Institute, Kannapolis, NC, USA
- Department of Nutrition, University of North Carolina-Chapel Hill, NC, USA
| | - Reem H. AlMalki
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Anas M. Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Al Faisal University, Riyadh, Saudi Arabia
| | - Natalia I. Krupenko
- UNC Nutrition Research Institute, Kannapolis, NC, USA
- Department of Nutrition, University of North Carolina-Chapel Hill, NC, USA
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Sergey A. Krupenko
- UNC Nutrition Research Institute, Kannapolis, NC, USA
- Department of Nutrition, University of North Carolina-Chapel Hill, NC, USA
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11
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Torres-Esquius S, Beas F, Chen-Liang TH, Pomares H, Santiago M, Varela ND, Liquori A, Hernandez F, Xicoy B, Hermosín L, Arnan M, Tazón-Vega B, Blanco A, Cervera J, Diez-Campelo M, Lozano ML, Valcárcel D, Bosch F, Montoro MJ, Jerez A. Germline assessment for alloHSCT candidates over 50 years: A 'Fast-Track' screening in myeloid neoplasms. Br J Haematol 2024. [PMID: 38639421 DOI: 10.1111/bjh.19460] [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: 11/10/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
Patients aged 50 or above diagnosed with myeloid neoplasms (MNs) are typically not candidates for germline testing. However, approximately 8% carry pathogenic germline variants. Allogeneic haematopoietic stem cell transplantation (alloHSCT) remains an option for those aged over 50; neglecting germline testing could mask the risk for relative donor cell-derived MN. We propose a germline-augmented somatic panel (GASP), combining MN predisposition genes with a myeloid somatic panel for timely germline variant identification when initial testing is not indicated. Out of our 133 whole-exome-sequenced MN cases aged over 50 years, 9% had pathogenic/likely variants. GASP detected 92%, compared to 50% with somatic-only panel. Our study highlights the relevance of germline screening in MN, particularly for alloHSCT candidates without established germline-testing recommendations.
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Affiliation(s)
- Sara Torres-Esquius
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francisco Beas
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Tzu Hua Chen-Liang
- Department of Hematology, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Helena Pomares
- Department of Hematology, Institut Català d'Oncologia. Hospital Duran i Reynals, IDIBELL. Hospitalet, Badalona, Barcelona, Spain
| | - Marta Santiago
- Department of Hematology, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Nicolás Díaz Varela
- Department of Hematology, Hospital Universitario Central de Asturias, Instituto. Universitario (IUOPA), Instituto de Investigación del Principado de Asturias (ISPA), Oviedo, Spain
| | - Alessandro Liquori
- Department of Hematology, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | | | - Blanca Xicoy
- Department of Hematology, Hospital Germans Trias i Pujol, Badalona, Spain
| | | | - Montserrat Arnan
- Department of Hematology, Institut Català d'Oncologia. Hospital Duran i Reynals, IDIBELL. Hospitalet, Badalona, Barcelona, Spain
| | - Bárbara Tazón-Vega
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Adoración Blanco
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - José Cervera
- Department of Hematology, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - María Diez-Campelo
- Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca, Spain
| | - María Luisa Lozano
- Department of Hematology, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - David Valcárcel
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesc Bosch
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Maria Julia Montoro
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Andrés Jerez
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
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12
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Sahu S, Rao AR, Sahu TK, Pandey J, Varshney S, Kumar A, Gaikwad K. Predictive Role of Cluster Bean ( Cyamopsis tetragonoloba) Derived miRNAs in Human and Cattle Health. Genes (Basel) 2024; 15:448. [PMID: 38674383 PMCID: PMC11049822 DOI: 10.3390/genes15040448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 04/28/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding conserved molecules with lengths varying between 18-25nt. Plants miRNAs are very stable, and probably they might have been transferred across kingdoms via food intake. Such miRNAs are also called exogenous miRNAs, which regulate the gene expression in host organisms. The miRNAs present in the cluster bean, a drought tolerant legume crop having high commercial value, might have also played a regulatory role for the genes involved in nutrients synthesis or disease pathways in animals including humans due to dietary intake of plant parts of cluster beans. However, the predictive role of miRNAs of cluster beans for gene-disease association across kingdoms such as cattle and humans are not yet fully explored. Thus, the aim of the present study is to (i) find out the cluster bean miRNAs (cb-miRs) functionally similar to miRNAs of cattle and humans and predict their target genes' involvement in the occurrence of complex diseases, and (ii) identify the role of cb-miRs that are functionally non-similar to the miRNAs of cattle and humans and predict their targeted genes' association with complex diseases in host systems. Here, we predicted a total of 33 and 15 functionally similar cb-miRs (fs-cb-miRs) to human and cattle miRNAs, respectively. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the participation of targeted genes of fs-cb-miRs in 24 and 12 different pathways in humans and cattle, respectively. Few targeted genes in humans like LCP2, GABRA6, and MYH14 were predicted to be associated with disease pathways of Yesinia infection (hsa05135), neuroactive ligand-receptor interaction (hsa04080), and pathogenic Escherichia coli infection (hsa05130), respectively. However, targeted genes of fs-cb-miRs in humans like KLHL20, TNS1, and PAPD4 are associated with Alzheimer's, malignant tumor of the breast, and hepatitis C virus infection disease, respectively. Similarly, in cattle, targeted genes like ATG2B and DHRS11 of fs-cb-miRs participate in the pathways of Huntington disease and steroid biosynthesis, respectively. Additionally, the targeted genes like SURF4 and EDME2 of fs-cb-miRs are associated with mastitis and bovine osteoporosis, respectively. We also found a few cb-miRs that do not have functional similarity with human and cattle miRNAs but are found to target the genes in the host organisms and as well being associated with human and cattle diseases. Interestingly, a few genes such as NRM, PTPRE and SUZ12 were observed to be associated with Rheumatoid Arthritis, Asthma and Endometrial Stromal Sarcoma diseases, respectively, in humans and genes like SCNN1B associated with renal disease in cattle.
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Affiliation(s)
- Sarika Sahu
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Atmakuri Ramakrishna Rao
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Indian Council of Agricultural Research, New Delhi 110001, India
| | - Tanmaya Kumar Sahu
- Indian Grassland and Fodder Research Institute, ICAR, Jhansi 284003, India;
| | - Jaya Pandey
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Shivangi Varshney
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Archna Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Kishor Gaikwad
- National Institute for Plant Biotechnology, ICAR, New Delhi 110012, India;
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13
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Rips J, Halstuk O, Fuchs A, Lang Z, Sido T, Gershon-Naamat S, Abu-Libdeh B, Edvardson S, Salah S, Breuer O, Hadhud M, Eden S, Simon I, Slae M, Damseh NS, Abu-Libdeh A, Eskin-Schwartz M, Birk OS, Varga J, Schueler-Furman O, Rosenbluh C, Elpeleg O, Yanovsky-Dagan S, Mor-Shaked H, Harel T. Unbiased phenotype and genotype matching maximizes gene discovery and diagnostic yield. Genet Med 2024; 26:101068. [PMID: 38193396 DOI: 10.1016/j.gim.2024.101068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/10/2024] Open
Abstract
PURPOSE Widespread application of next-generation sequencing, combined with data exchange platforms, has provided molecular diagnoses for countless families. To maximize diagnostic yield, we implemented an unbiased semi-automated genematching algorithm based on genotype and phenotype matching. METHODS Rare homozygous variants identified in 2 or more affected individuals, but not in healthy individuals, were extracted from our local database of ∼12,000 exomes. Phenotype similarity scores (PSS), based on human phenotype ontology terms, were assigned to each pair of individuals matched at the genotype level using HPOsim. RESULTS 33,792 genotype-matched pairs were discovered, representing variants in 7567 unique genes. There was an enrichment of PSS ≥0.1 among pathogenic/likely pathogenic variant-level pairs (94.3% in pathogenic/likely pathogenic variant-level matches vs 34.75% in all matches). We highlighted founder or region-specific variants as an internal positive control and proceeded to identify candidate disease genes. Variant-level matches were particularly helpful in cases involving inframe indels and splice region variants beyond the canonical splice sites, which may otherwise have been disregarded, allowing for detection of candidate disease genes, such as KAT2A, RPAIN, and LAMP3. CONCLUSION Semi-automated genotype matching combined with PSS is a powerful tool to resolve variants of uncertain significance and to identify candidate disease genes.
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Affiliation(s)
- Jonathan Rips
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Orli Halstuk
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Adina Fuchs
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ziv Lang
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Tal Sido
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | | | - Bassam Abu-Libdeh
- Department of Pediatrics & Genetics, Makassed Hospital & Al-Quds Medical School, E. Jerusalem, Palestine
| | - Simon Edvardson
- Faculty of Medicine, Hebrew University of Jerusalem, Israel; Pediatric Neurology Unit, Hadassah Medical Center, Jerusalem, Israel
| | - Somaya Salah
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Oded Breuer
- Faculty of Medicine, Hebrew University of Jerusalem, Israel; Pediatric Pulmonology and CF Unit, Department of Pediatrics, Hadassah Medical Center, Jerusalem, Israel
| | - Mohamad Hadhud
- Faculty of Medicine, Hebrew University of Jerusalem, Israel; Pediatric Pulmonology and CF Unit, Department of Pediatrics, Hadassah Medical Center, Jerusalem, Israel
| | - Sharon Eden
- Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Itamar Simon
- Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Mordechai Slae
- Pediatric Gastroenterology Unit, Department of Pediatrics, Hadassah Medical Center, Jerusalem, Israel
| | - Nadirah S Damseh
- Department of Pediatrics & Genetics, Makassed Hospital & Al-Quds Medical School, E. Jerusalem, Palestine
| | - Abdulsalam Abu-Libdeh
- Department of Pediatrics & Genetics, Makassed Hospital & Al-Quds Medical School, E. Jerusalem, Palestine; Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Marina Eskin-Schwartz
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel; Genetics Institute, Soroka University Medical Center, Beer-Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel; Genetics Institute, Soroka University Medical Center, Beer-Sheva, Israel
| | - Julia Varga
- Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ora Schueler-Furman
- Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | | | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel.
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Cordova I, Blesson A, Savatt JM, Sveden A, Mahida S, Hazlett H, Rooney Riggs E, Chopra M. Expansion of the Genotypic and Phenotypic Spectrum of ASH1L-Related Syndromic Neurodevelopmental Disorder. Genes (Basel) 2024; 15:423. [PMID: 38674358 PMCID: PMC11049257 DOI: 10.3390/genes15040423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Pathogenic ASH1L variants have been reported in probands with broad phenotypic presentations, including intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, seizures, congenital anomalies, and other skeletal, muscular, and sleep differences. Here, we review previously published individuals with pathogenic ASH1L variants and report three further probands with novel ASH1L variants and previously unreported phenotypic features, including mixed receptive language disorder and gait disturbances. These novel data from the Brain Gene Registry, an accessible repository of clinically derived genotypic and phenotypic data, have allowed for the expansion of the phenotypic and genotypic spectrum of this condition.
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Affiliation(s)
- Ineke Cordova
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Alyssa Blesson
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Juliann M. Savatt
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Abigail Sveden
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Sonal Mahida
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Heather Hazlett
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC 27510, USA
| | - Erin Rooney Riggs
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
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15
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Faundes V, Repetto GM, Valdivia LE. Discovery of novel genetic syndromes in Latin America: Opportunities and challenges. Genet Mol Biol 2024; 47Suppl 1:e20230318. [PMID: 38466870 DOI: 10.1590/1678-4685-gmb-2023-0318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Latin America (LatAm) has a rich and historically significant role in delineating both novel and well-documented genetic disorders. However, the ongoing advancements in the field of human genetics pose challenges to the relatively slow adaption of LatAm in the field. Here, we describe past and present contributions of LatAm to the discovery of novel genetic disorders, often referred as novel gene-disease associations (NGDA). We also describe the current methodologies for discovery of NGDA, taking into account the latest developments in genomics. We provide an overview of opportunities and challenges for NGDA research in LatAm considering the steps currently performed to identify and validate such associations. Given the multiple and diverse needs of populations and countries in LatAm, it is imperative to foster collaborations amongst patients, indigenous people, clinicians and scientists. Such collaborative effort is essential for sustaining and enhancing the LatAm´s contributions to the field of NGDA.
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Affiliation(s)
- Víctor Faundes
- Universidad de Chile, Instituto de Nutrición y Tecnología de los Alimentos, Laboratorio de Genética y Enfermedades Metabólicas, Santiago, Chile
| | - Gabriela M Repetto
- Universidad del Desarrollo, Facultad de Medicina, Instituto de Ciencias e Innovación en Medicina, Centro de Genética y Genómica, Programa de Enfermedades Raras, Santiago, Chile
| | - Leonardo E Valdivia
- Universidad Mayor, Facultad de Ciencias, Centro de Biología Integrativa, Santiago, Chile
- Universidad Mayor, Facultad de Ciencias, Escuela de Biotecnología, Santiago, Chile
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16
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Demetriou D, Lockhat Z, Brzozowski L, Saini KS, Dlamini Z, Hull R. The Convergence of Radiology and Genomics: Advancing Breast Cancer Diagnosis with Radiogenomics. Cancers (Basel) 2024; 16:1076. [PMID: 38473432 DOI: 10.3390/cancers16051076] [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: 01/12/2024] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Despite significant progress in the prevention, screening, diagnosis, prognosis, and therapy of breast cancer (BC), it remains a highly prevalent and life-threatening disease affecting millions worldwide. Molecular subtyping of BC is crucial for predictive and prognostic purposes due to the diverse clinical behaviors observed across various types. The molecular heterogeneity of BC poses uncertainties in its impact on diagnosis, prognosis, and treatment. Numerous studies have highlighted genetic and environmental differences between patients from different geographic regions, emphasizing the need for localized research. International studies have revealed that patients with African heritage are often diagnosed at a more advanced stage and exhibit poorer responses to treatment and lower survival rates. Despite these global findings, there is a dearth of in-depth studies focusing on communities in the African region. Early diagnosis and timely treatment are paramount to improving survival rates. In this context, radiogenomics emerges as a promising field within precision medicine. By associating genetic patterns with image attributes or features, radiogenomics has the potential to significantly improve early detection, prognosis, and diagnosis. It can provide valuable insights into potential treatment options and predict the likelihood of survival, progression, and relapse. Radiogenomics allows for visual features and genetic marker linkage that promises to eliminate the need for biopsy and sequencing. The application of radiogenomics not only contributes to advancing precision oncology and individualized patient treatment but also streamlines clinical workflows. This review aims to delve into the theoretical underpinnings of radiogenomics and explore its practical applications in the diagnosis, management, and treatment of BC and to put radiogenomics on a path towards fully integrated diagnostics.
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Affiliation(s)
- Demetra Demetriou
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Zarina Lockhat
- Department of Radiology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Luke Brzozowski
- Translational Research and Core Facilities, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kamal S Saini
- Fortrea Inc., 8 Moore Drive, Durham, NC 27709, USA
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Rodney Hull
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield, Pretoria 0028, South Africa
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17
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Li Q, Hu Z, He J, Liu X, Liu Y, Wei J, Wu B, Lu X, He H, Zhang Y, He J, Li M, Wu C, Lv L, Wang Y, Zhou L, Zhang Q, Zhang J, Cheng X, Shao H, Lu X. Deciphering the comprehensive knowledgebase landscape featuring infertility with IDDB Xtra. Comput Biol Med 2024; 170:108105. [PMID: 38330823 DOI: 10.1016/j.compbiomed.2024.108105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/15/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Infertility affects ∼15% of couples globally and half of cases are related to genetic disorders. Despite growing data and unprecedented improvements in high-throughput sequencing technologies, accumulated fertility-related issues concerning genetic diagnosis and potential treatment are urgent to be solved. However, there is a lack of comprehensive platforms that characterise various infertility-related records to provide research applications for exploring infertility in-depth and genetic counselling of infertility couple. To solve this problem, we provide IDDB Xtra by further integrating phenotypic manifestations, genomic datasets, epigenetics, modulators in collaboration with numerous interactive tools into our previous infertility database, IDDB. IDDB Xtra houses manually-curated 2369 genes of human and nine model organisms, 273 chromosomal abnormalities, 884 phenotypes, 60 genomic datasets, 464 epigenetic records, 1144 modulators relevant to infertility diagnosis and treatment. Additionally, IDDB Xtra incorporated customized graphical applications for researchers and clinicians to decipher in-depth disease mechanisms from the perspectives of developmental atlas, mutation effects, and clinical manifestations. Users can browse genes across developmental stages of human and mouse, filter candidate genes, mine potential variants and retrieve infertility biomedical network in an intuitive web interface. In summary, IDDB Xtra not only captures valuable research and data, but also provides useful applications to facilitate the genetic counselling and drug discovery of infertility. IDDB Xtra is freely available at https://mdl.shsmu.edu.cn/IDDB/and http://www.allostery.net/IDDB.
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Affiliation(s)
- Qian Li
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200011, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Zhijie Hu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200011, China
| | - Jiayin He
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200011, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Xinyi Liu
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Yini Liu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200011, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Jiale Wei
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Binjian Wu
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Xun Lu
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Hongxi He
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200011, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510000, China
| | - Yuqi Zhang
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200011, China
| | - Jixiao He
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Mingyu Li
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Chengwei Wu
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Lijun Lv
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Yang Wang
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Linxuan Zhou
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Quan Zhang
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Jian Zhang
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510000, China.
| | - Xiaoyue Cheng
- Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China.
| | - Hongfang Shao
- Center of Reproductive Medicine, Department of Gynecology and Obstetrics, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai, 200233, China.
| | - Xuefeng Lu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200011, China.
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18
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Yang JH, Liu ZG, Liu CL, Zhang MR, Jia YL, Zhai QX, He MF, He N, Qiao JD. MED12 variants associated with X-linked recessive partial epilepsy without intellectual disability. Seizure 2024; 116:30-36. [PMID: 36894399 DOI: 10.1016/j.seizure.2023.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVES The MED12 gene encodes mediator complex subunit 12, which is a component of the mediator complex involved in the transcriptional regulation of nearly all RNA polymerase II-dependent genes. MED12 variants have previously been associated with developmental disorders with or without nonspecific intellectual disability. This study aims to explore the association between MED12 variants and epilepsy. MATERIALS AND METHODS Trios-based whole-exome sequencing was performed in a cohort of 349 unrelated cases with partial (focal) epilepsy without acquired causes. The genotype-phenotype correlations of MED12 variants were analyzed. RESULTS Five hemizygous missense MED12 variants, including c.958A>G/p.Ile320Val, c.1757G>A/p.Ser586Asn, c.2138C>T/p.Pro713Leu, c.3379T>C/p.Ser1127Pro, and c.4219A>C/p.Met1407Leu were identified in five unrelated males with partial epilepsy. All patients showed infrequent focal seizures and achieved seizure free without developmental abnormalities or intellectual disability. All the hemizygous variants were inherited from asymptomatic mothers (consistent with the X-linked recessive inheritance pattern) and were absent in the general population. The two variants with damaging hydrogen bonds were associated with early-onset seizures. Further genotype-phenotype analysis revealed that congenital anomaly disorder (Hardikar syndrome) was associated with (de novo) destructive variants in an X-linked dominant inheritance pattern, whereas epilepsy was associated with missense variants in an X-linked recessive inheritance pattern. Phenotypic features of intellectual disability appeared as the intermediate phenotype in terms of both genotype and inheritance. Epilepsy-related variants were located at the MED12-LCEWAV domain and the regions between MED12-LCEWAV and MED12-POL. CONCLUSION MED12 is a potentially causative gene for X-linked recessive partial epilepsy without developmental or intellectual abnormalities. The genotype-phenotype correlation of MED12 variants explains the phenotypic variations and can help the genetic diagnosis.
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Affiliation(s)
- Jie-Hua Yang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China; Department of Neurology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhi-Gang Liu
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Chun-Ling Liu
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Rui Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yan-Lu Jia
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qiong-Xiang Zhai
- Department of pediatrics, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ming-Feng He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Jing-Da Qiao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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Sieper MH, Gaikwad AS, Fros M, Weber P, Di Persio S, Oud MS, Kliesch S, Neuhaus N, Stallmeyer B, Tüttelmann F, Wyrwoll MJ. Scrutinizing the human TEX genes in the context of human male infertility. Andrology 2024; 12:570-584. [PMID: 37594251 DOI: 10.1111/andr.13511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/12/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Infertility affects around 15% of all couples worldwide and is increasingly linked to variants in genes specifically expressed in the testis. Well-established causes of male infertility include pathogenic variants in the genes TEX11, TEX14, and TEX15, while few studies have recently reported variants in TEX13B, TEX13C, FAM9A (TEX39A), and FAM9B (TEX39B). OBJECTIVES We aimed at screening for novel potential candidate genes among the human TEX ("testis expressed") genes as well as verifying previously described disease associations in this set of genes. MATERIALS AND METHODS To this end, we screened the exome sequencing data of 1305 men, including 1056 crypto- and azoospermic individuals, and determined cell-specific expression by analyzing testis-specific single-cell RNA sequencing data for genes with identified variants. To investigate the overarching role in male fertility, we generated testis-specific knockdown (KD) models of all 10 orthologous TEX genes in Drosophila melanogaster. RESULTS We detected rare potential disease-causing variants in TEX10, TEX13A, TEX13B, TEX13C, TEX13D, ZFAND3 (TEX27), TEX33, FAM9A (TEX39A), and FAM9B (TEX39B), in 28 infertile men, of which 15 men carried variants in TEX10, TEX27, and TEX33. The KD of TEX2, TEX9, TEX10, TEX13, ZFAND3 (TEX27), TEX28, TEX30, NFX1 (TEX42), TEX261, and UTP4 (TEX292) in Drosophila resulted in normal fertility. DISCUSSION Based on our findings, the autosomal dominant predicted genes TEX10 and ZFAND3 (TEX27) and the autosomal recessive predicted gene TEX33, which all three are conceivably required for germ cell maturation, were identified as novel potential candidate genes for human non-obstructive azoospermia. We additionally identified hemizygous loss-of-function (LoF) variants in TEX13B, TEX13C, and FAM9A (TEX39A) as unlikely monogenic culprits of male infertility as LoF variants were also found in control men. CONCLUSION Our findings concerning the X-linked genes TEX13B, TEX13C, and FAM9A (TEX39A) contradict previous reports and will decrease false-positive reports in genetic diagnostics of azoospermic men.
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Affiliation(s)
- Marie H Sieper
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Avinash S Gaikwad
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Marion Fros
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Philipp Weber
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Sara Di Persio
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Manon S Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Birgit Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
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20
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Chopra M, Savatt JM, Bingaman TI, Good ME, Morgan A, Cooney C, Rossel AM, VanHoute B, Cordova I, Mahida S, Lanzotti V, Baldridge D, Gurnett CA, Piven J, Hazlett H, Pomeroy SL, Sahin M, Payne PRO, Riggs ER, Constantino JN. Clinical variants paired with phenotype: A rich resource for brain gene curation. Genet Med 2024; 26:101035. [PMID: 38059438 PMCID: PMC10939875 DOI: 10.1016/j.gim.2023.101035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
PURPOSE Clinically ascertained variants are under-utilized in neurodevelopmental disorder research. We established the Brain Gene Registry (BGR) to coregister clinically identified variants in putative brain genes with participant phenotypes. Here, we report 179 genetic variants in the first 179 BGR registrants and analyze the proportion that were novel to ClinVar at the time of entry and those that were absent in other disease databases. METHODS From 10 academically affiliated institutions, 179 individuals with 179 variants were enrolled into the BGR. Variants were cross-referenced for previous presence in ClinVar and for presence in 6 other genetic databases. RESULTS Of 179 variants in 76 genes, 76 (42.5%) were novel to ClinVar, and 62 (34.6%) were absent from all databases analyzed. Of the 103 variants present in ClinVar, 37 (35.9%) were uncertain (ClinVar aggregate classification of variant of uncertain significance or conflicting classifications). For 5 variants, the aggregate ClinVar classification was inconsistent with the interpretation from the BGR site-provided classification. CONCLUSION A significant proportion of clinical variants that are novel or uncertain are not shared, limiting the evidence base for new gene-disease relationships. Registration of paired clinical genetic test results with phenotype has the potential to advance knowledge of the relationships between genes and neurodevelopmental disorders.
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Affiliation(s)
- Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital; Boston, MA; Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA.
| | - Juliann M Savatt
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Taylor I Bingaman
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Molly E Good
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Alexis Morgan
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Caitlin Cooney
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Allison M Rossel
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Bryanna VanHoute
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Ineke Cordova
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Virginia Lanzotti
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Dustin Baldridge
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Christina A Gurnett
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Joseph Piven
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC
| | - Heather Hazlett
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Mustafa Sahin
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital; Boston, MA; Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Philip R O Payne
- Institute for Informatics Washington University in St. Louis, St. Louis, MO
| | - Erin Rooney Riggs
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - John N Constantino
- Division of Behavioural and Mental Health, Children's Healthcare of Atlanta, Departments of Psychiatry and Paediatrics, Emory University, Atlanta, GA
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21
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SoRelle JA, Funke BH, Eno CC, Ji J, Santani A, Bayrak-Toydemir P, Wachsmann M, Wain KE, Mao R. Slice Testing-Considerations from Ordering to Reporting: A Joint Report of the Association for Molecular Pathology, College of American Pathologists, and National Society of Genetic Counselors. J Mol Diagn 2024; 26:159-167. [PMID: 38103592 DOI: 10.1016/j.jmoldx.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 10/09/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
As the number of genes associated with various germline disorders continues to grow, it is becoming more difficult for clinical laboratories to maintain separate assays for interrogating disease-focused gene panels. One solution to this challenge is termed slice testing, where capture backbone is used to analyze data specific to a set of genes, and for this article, we will focus on exome. A key advantage to this strategy is greater flexibility by adding genes as they become associated with disease or the ability to accommodate specific provider requests. Here, we provide expert consensus recommendations and results from an Association for Molecular Pathology-sponsored survey of clinical laboratories performing exome sequencing to compare a slice testing approach with traditional static gene panels and comprehensive exome analysis. We explore specific considerations for slices, including gene selection, analytic performance, coverage, quality, and interpretation. Our goal is to provide comprehensive guidance for clinical laboratories interested in designing and using slice tests as a diagnostic.
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Affiliation(s)
- Jeffrey A SoRelle
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Birgit H Funke
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Sema4, Stamford, Connecticut; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Celeste C Eno
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Academic Pathology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jianling Ji
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, University of Southern California, Los Angeles, California
| | - Avni Santani
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pinar Bayrak-Toydemir
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah
| | - Megan Wachsmann
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas; VA North Texas Health Care System, Dallas, Texas
| | - Karen E Wain
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; GeneDx, LLC, Gaithersburg, Maryland
| | - Rong Mao
- Whole Exome Sequencing Standards Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah.
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22
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Zhang MW, Liang XY, Wang J, Gao LD, Liao HJ, He YH, Yi YH, He N, Liao WP. Epilepsy-associated genes: an update. Seizure 2024; 116:4-13. [PMID: 37777370 DOI: 10.1016/j.seizure.2023.09.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/31/2023] [Accepted: 09/23/2023] [Indexed: 10/02/2023] Open
Abstract
PURPOSE To provide an updated list of epilepsy-associated genes based on clinical-genetic evidence. METHODS Epilepsy-associated genes were systematically searched and cross-checked from the OMIM, HGMD, and PubMed databases up to July 2023. To facilitate the reference for the epilepsy-associated genes that are potentially common in clinical practice, the epilepsy-associated genes were ranked by the mutation number in the HGMD database and by case number in the China Epilepsy Gene 1.0 project, which targeted common epilepsy. RESULTS Based on the OMIM database, 1506 genes were identified to be associated with epilepsy and were classified into three categories according to their potential association with epilepsy or other abnormal phenotypes, including 168 epilepsy genes that were associated with epilepsies as pure or core symptoms, 364 genes that were associated with neurodevelopmental disorders as the main symptom and epilepsy, and 974 epilepsy-related genes that were associated with gross physical/systemic abnormalities accompanied by epilepsy/seizures. Among the epilepsy genes, 115 genes (68.5%) were associated with epileptic encephalopathy. After cross-checking with the HGMD and PubMed databases, an additional 1440 genes were listed as potential epilepsy-associated genes, of which 278 genes have been repeatedly identified variants in patients with epilepsy. The top 100 frequently reported/identified epilepsy-associated genes from the HGMD database and the China Epilepsy Gene 1.0 project were listed, among which 40 genes were identical in both sources. SIGNIFICANCE Recognition of epilepsy-associated genes will facilitate genetic screening strategies and be helpful for precise molecular diagnosis and treatment of epilepsy in clinical practice.
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Affiliation(s)
- Meng-Wen Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiao-Yu Liang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Liang-Di Gao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Han-Jun Liao
- University of South China, Hengyang, 421001, China
| | - Yun-Hua He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Yong-Hong Yi
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
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23
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Herbst C, Bothe V, Wegler M, Axer-Schaefer S, Audebert-Bellanger S, Gecz J, Cogne B, Feldman HB, Horn AHC, Hurst ACE, Kelly MA, Kruer MC, Kurolap A, Laquerriere A, Li M, Mark PR, Morawski M, Nizon M, Pastinen T, Polster T, Saugier-Veber P, SeSong J, Sticht H, Stieler JT, Thifffault I, van Eyk CL, Marcorelles P, Vezain-Mouchard M, Abou Jamra R, Oppermann H. Heterozygous loss-of-function variants in DOCK4 cause neurodevelopmental delay and microcephaly. Hum Genet 2024; 143:455-469. [PMID: 38526744 PMCID: PMC11043173 DOI: 10.1007/s00439-024-02655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024]
Abstract
Neurons form the basic anatomical and functional structure of the nervous system, and defects in neuronal differentiation or formation of neurites are associated with various psychiatric and neurodevelopmental disorders. Dynamic changes in the cytoskeleton are essential for this process, which is, inter alia, controlled by the dedicator of cytokinesis 4 (DOCK4) through the activation of RAC1. Here, we clinically describe 7 individuals (6 males and one female) with variants in DOCK4 and overlapping phenotype of mild to severe global developmental delay. Additional symptoms include coordination or gait abnormalities, microcephaly, nonspecific brain malformations, hypotonia and seizures. Four individuals carry missense variants (three of them detected de novo) and three individuals carry null variants (two of them maternally inherited). Molecular modeling of the heterozygous missense variants suggests that the majority of them affect the globular structure of DOCK4. In vitro functional expression studies in transfected Neuro-2A cells showed that all missense variants impaired neurite outgrowth. Furthermore, Dock4 knockout Neuro-2A cells also exhibited defects in promoting neurite outgrowth. Our results, including clinical, molecular and functional data, suggest that loss-of-function variants in DOCK4 probable cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.
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Affiliation(s)
- Charlotte Herbst
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Viktoria Bothe
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Meret Wegler
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Susanne Axer-Schaefer
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anselm H C Horn
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Erlangen National High Performance Computing Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melissa A Kelly
- HudsonAlpha Clinical Services Lab, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital University of Arizona College of Medicine, Phoenix, USA
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Annie Laquerriere
- Department of Anatomy, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Megan Li
- Invitae Corp, San Francisco, CA, USA
| | - Paul R Mark
- Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Markus Morawski
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Tilman Polster
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Jang SeSong
- Genomic Medicine Institute, Seoul National University, Seoul, Republic of Korea
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jens T Stieler
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Isabelle Thifffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Clare L van Eyk
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Myriam Vezain-Mouchard
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.
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24
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Zou DF, Li XY, Lu XG, Wang HL, Song W, Zhang MW, Liu XR, Li BM, Liao JX, Zhong JM, Meng H, Li B. Association of FAT1 with focal epilepsy and correlation between seizure relapse and gene expression stage. Seizure 2024; 116:37-44. [PMID: 36941137 DOI: 10.1016/j.seizure.2023.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/13/2023] Open
Abstract
PURPOSE The FAT1 gene encodes FAT atypical cadherin 1, which is essential for foetal development, including brain development. This study aimed to investigate the relationship between FAT1 variants and epilepsy. METHODS Trio-based whole-exome sequencing was performed on a cohort of 313 patients with epilepsy. Additional cases with FAT1 variants were collected from the China Epilepsy Gene V.1.0 Matching Platform. RESULTS Four pairs of compound heterozygous missense FAT1 variants were identified in four unrelated patients with partial (focal) epilepsy and/or febrile seizures, but without intellectual disability/developmental abnormalities. These variants presented no/very low frequencies in the gnomAD database, and the aggregate frequencies in this cohort were significantly higher than those in controls. Two additional compound heterozygous missense variants were identified in two unrelated cases using the gene-matching platform. All patients experienced infrequent (yearly/monthly) complex partial seizures or secondary generalised tonic-clonic seizures. They responded well toantiseizure medication, but seizures relapsed in three cases when antiseizure medication were decreased or withdrawn after being seizure-free for three to six years, which correlated with the expression stage of FAT1. Genotype-phenotype analysis showed that epilepsy-associated FAT1 variants were missense, whereas non-epilepsy-associated variants were mainly truncated. The relationship between FAT1 and epilepsy was evaluated to be "Strong" by the Clinical Validity Framework of ClinGen. CONCLUSIONS FAT1 is a potential causative gene of partial epilepsy and febrile seizures. Gene expression stage was suggested to be one of the considerations in determining the duration ofantiseizure medication. Genotype-phenotype correlation helps to explain the mechanisms underlying phenotypic variation.
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Affiliation(s)
- Dong-Fang Zou
- Institute of Neuroscience of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Epilepsy Center and Department of Neurology, Shenzhen Children's Hospital, Shantou University Medical College, Shenzhen, China
| | - Xiao-Yan Li
- Institute of Neuroscience of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Department of Neurology, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Xin-Guo Lu
- Epilepsy Center and Department of Neurology, Shenzhen Children's Hospital, Shantou University Medical College, Shenzhen, China
| | - Huai-Li Wang
- Department of Pediatric Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wang Song
- Institute of Neuroscience of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China
| | - Meng-Wen Zhang
- Institute of Neuroscience of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China
| | - Xiao-Rong Liu
- Institute of Neuroscience of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China
| | - Bing-Mei Li
- Institute of Neuroscience of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China
| | - Jian-Xiang Liao
- Epilepsy Center and Department of Neurology, Shenzhen Children's Hospital, Shantou University Medical College, Shenzhen, China
| | - Jian-Min Zhong
- Department of Neurology, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Heng Meng
- Department of Neurology, The First Affiliated Hospital, & Clinical Neuroscience Institute of Jinan University, 613 West Huangpu Ave, Guangzhou, China..
| | - Bin Li
- Institute of Neuroscience of Guangzhou Medical University and Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China.
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25
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Ross JE, Mohan S, Zhang J, Sullivan MJ, Bury L, Lee K, Futchi I, Frantz A, McDougal D, Perez Botero J, Cattaneo M, Cooper N, Downes K, Gresele P, Keenan C, Lee AI, Megy K, Morange PE, Morgan NV, Schulze H, Zimowski K, Freson K, Lambert MP. Evaluating the clinical validity of genes related to hemostasis and thrombosis using the Clinical Genome Resource gene curation framework. J Thromb Haemost 2024; 22:645-665. [PMID: 38016518 PMCID: PMC10922649 DOI: 10.1016/j.jtha.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Inherited bleeding, thrombotic, and platelet disorders (BTPDs) are a heterogeneous set of diseases, many of which are very rare globally. Over the past 5 decades, the genetic basis of some of these disorders has been identified, and recently, high-throughput sequencing has become the primary means of identifying disease-causing genetic variants. OBJECTIVES Knowledge of the clinical validity of a gene-disease relationship is essential to provide an accurate diagnosis based on results of diagnostic gene panel tests and inform the construction of such panels. The Scientific and Standardization Committee for Genetics in Thrombosis and Hemostasis undertook a curation process for selecting 96 TIER1 genes for BTPDs. The purpose of the process was to evaluate the evidence supporting each gene-disease relationship and provide an expert-reviewed classification for the clinical validity of genes associated with BTPDs. METHODS The Clinical Genome Resource (ClinGen) Hemostasis/Thrombosis Gene Curation Expert Panel assessed the strength of evidence for TIER1 genes using the semiquantitative ClinGen gene-disease clinical validity framework. ClinGen Lumping and Splitting guidelines were used to determine the appropriate disease entity or entities for each gene, and 101 gene-disease relationships were identified for curation. RESULTS The final outcome included 68 Definitive (67%), 26 Moderate (26%), and 7 Limited (7%) classifications. The summary of each curation is available on the ClinGen website. CONCLUSION Expert-reviewed assignment of gene-disease relationships by the ClinGen Hemostasis/Thrombosis Gene Curation Expert Panel facilitates accurate molecular diagnoses of BTPDs by clinicians and diagnostic laboratories. These curation efforts can allow genetic testing to focus on genes with a validated role in disease.
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Affiliation(s)
- Justyne E Ross
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shruthi Mohan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Zhang
- KingMed Diagnostics, Guangzhou, Guangdong, China
| | - Mia J Sullivan
- Versiti Blood Center of Wisconsin, Milwaukee, Wisconsin, USA
| | - Loredana Bury
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isabella Futchi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Annabelle Frantz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dara McDougal
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Juliana Perez Botero
- Versiti Blood Center of Wisconsin, Milwaukee, Wisconsin, USA; Division of Hematology/Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marco Cattaneo
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan, Italy
| | - Nichola Cooper
- Centre for Haematology, Imperial College London, London, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gresele
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Catriona Keenan
- Haemostasis Molecular Diagnostic Laboratory, National Coagulation Centre, St James's Hospital, Dublin, Ireland
| | - Alfred I Lee
- Section of Hematology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Pierre-Emmanuel Morange
- INSERM, INRAE, C2VN, Aix Marseille University, Marseille, France; Hematology Laboratory, La Timone Hospital, APHM, Marseille, France
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Harald Schulze
- Institute of Experimental Biomedicine, Julius-Maximilians-University Wuerzburg, Wuerzburg, Germany
| | - Karen Zimowski
- Aflac Cancer and Blood Disorders Center, Emory University/Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
| | - Michele P Lambert
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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26
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Tang X, Lan X, Song X, Xu W, Zhang Y, Wang S, Xiao M, Yang Y, Zhang H, Wu S. Clinical characteristics and identification of novel CNOT1 variants in three unrelated Chinese families with Vissers-Bodmer Syndrome. Heliyon 2024; 10:e26743. [PMID: 38434094 PMCID: PMC10906421 DOI: 10.1016/j.heliyon.2024.e26743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 02/04/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Vissers-Bodmer Syndrome, an autosomal dominant disease, is a neurodevelopmental disorder characterized by global developmental delay, intellectual disability, hypotonia and autistic features with a highly variable phenotype. It is caused by variants in the CCR4-NOT transcription complex, subunit 1 gene (CNOT1). However, the pathophysiologic mechanism of the Vissers-Bodmer Syndrome remains unclear. Notably, this syndrome has not been previously reported in the Chinese. In this study, we utilized whole exome sequencing to identify three novel variants in the CNOT1 gene, encompassing one frameshift variant and two missense variants, in three Chinese patients mainly presenting with developmental delay, intellectual disability and/or autism. Interestingly, three patients exhibited novel manifestations including spina bifida occulta, horse-shoe kidney and café-au-lait spot. The frameshift variant, p.Gly172Alafs*5, occurring de novo, leading to a premature stop codon in the protein, was classified into pathogenic. Two missense variants c.3451A > G (p.Asn1151Asp) and c.557C > T (p.Ser186Phe) were predicted to be deleterious by multiple prediction algorithms with high conservation among a variety of species. Additionally, three-dimensional structure modeling and predicting indicated the substitution of the mutated amino acids would decrease the stability of CNOT1 protein. Given that CNOT1 is a relatively novel disease gene, we evaluated the gene-disease validity following ClinGen Standard Operating Procedure. The existing evidence substantiates a "Definitive" level of gene-disease relationship. The genetic findings provide a reliable basis for the genetic counseling of the family reproduction. Moreover, our results expand the genetic and phenotypic spectrum of CNOT1-related Vissers-Bodmer Syndrome.
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Affiliation(s)
- Xiaojun Tang
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoping Lan
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaozhen Song
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wuhen Xu
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanfeng Zhang
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Simei Wang
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Man Xiao
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongchen Yang
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Zhang
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengnan Wu
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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27
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Nadimpalli Kobren S, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Willett J, Berselli M, Ronchetti W, Sherwood R, Krier J, Kohane IS, Sunyaev SR. Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580158. [PMID: 38405764 PMCID: PMC10888768 DOI: 10.1101/2024.02.13.580158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients. The increasing sizes of ultra-rare, "N-of-1" disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development.1,2 The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale N-of-1 analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We apply existing and introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We make our gene-level findings and variant-level information across the cohort available in a public-facing browser (https://dbmi-bgm.github.io/udn-browser/). These results show that N-of-1 efforts should be supplemented by a joint genomic analysis across cohorts.
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Affiliation(s)
| | | | | | - Daniel Traviglia
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Xinyun Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | | | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Julian Willett
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Michele Berselli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - William Ronchetti
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Richard Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joel Krier
- Department of Genetics, Atrius Health, Boston, MA
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | | | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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Mudau MM, Seymour H, Nevondwe P, Kerr R, Spencer C, Feben C, Lombard Z, Honey E, Krause A, Carstens N. A feasible molecular diagnostic strategy for rare genetic disorders within resource-constrained environments. J Community Genet 2024; 15:39-48. [PMID: 37815686 PMCID: PMC10858011 DOI: 10.1007/s12687-023-00674-8] [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: 02/03/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Timely and accurate diagnosis of rare genetic disorders is critical, as it enables improved patient management and prognosis. In a resource-constrained environment such as the South African State healthcare system, the challenge is to design appropriate and cost-effective assays that will enable accurate genetic diagnostic services in patients of African ancestry across a broad disease spectrum. Next-generation sequencing (NGS) has transformed testing approaches for many Mendelian disorders, but this technology is still relatively new in our setting and requires cost-effective ways to implement. As a proof of concept, we describe a feasible diagnostic strategy for genetic disorders frequently seen in our genetics clinics (RASopathies, Cornelia de Lange syndrome, Treacher Collins syndrome, and CHARGE syndrome). The custom-designed targeted NGS gene panel enabled concurrent variant screening for these disorders. Samples were batched during sequencing and analyzed selectively based on the clinical phenotype. The strategy employed in the current study was cost-effective, with sequencing and analysis done at USD849.68 per sample and achieving an overall detection rate of 54.5%. The strategy employed is cost-effective as it allows batching of samples from patients with different diseases in a single run, an approach that can be utilized with rare and less frequently ordered molecular diagnostic tests. The subsequent selective analysis pipeline allowed for timeous reporting back of patients results. This is feasible with a reasonable yield and can be employed for the molecular diagnosis of a wide range of rare monogenic disorders in a resource-constrained environment.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Careni Spencer
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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29
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Zhang J, Wu Y, Chen S, Luo Q, Xi H, Li J, Qin X, Peng Y, Ma N, Yang B, Qiu X, Lu W, Chen Y, Jiang Y, Chen P, Liu Y, Zhang C, Zhang Z, Xiong Y, Shen J, Liang H, Ren Y, Ying C, Dong M, Li X, Xu C, Wang H, Zhang D, Xu C, Huang H. Prospective prenatal cell-free DNA screening for genetic conditions of heterogenous etiologies. Nat Med 2024; 30:470-479. [PMID: 38253798 DOI: 10.1038/s41591-023-02774-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Prenatal cell-free DNA (cfDNA) screening uses extracellular fetal DNA circulating in the peripheral blood of pregnant women to detect prevalent fetal chromosomal anomalies. However, numerous severe conditions with underlying single-gene defects are not included in current prenatal cfDNA screening. In this prospective, multicenter and observational study, pregnant women at elevated risk for fetal genetic conditions were enrolled for a cfDNA screening test based on coordinative allele-aware target enrichment sequencing. This test encompasses the following three of the most frequent pathogenic genetic variations: aneuploidies, microdeletions and monogenic variants. The cfDNA screening results were compared to invasive prenatal or postnatal diagnostic test results for 1,090 qualified participants. The comprehensive cfDNA screening detected a genetic alteration in 135 pregnancies with 98.5% sensitivity and 99.3% specificity relative to standard diagnostics. Of 876 fetuses with suspected structural anomalies on ultrasound examination, comprehensive cfDNA screening identified 55 (56.1%) aneuploidies, 6 (6.1%) microdeletions and 37 (37.8%) single-gene pathogenic variants. The inclusion of targeted monogenic conditions alongside chromosomal aberrations led to a 60.7% increase (from 61 to 98) in the detection rate. Overall, these data provide preliminary evidence that a comprehensive cfDNA screening test can accurately identify fetal pathogenic variants at both the chromosome and single-gene levels in high-risk pregnancies through a noninvasive approach, which has the potential to improve prenatal evaluation of fetal risks for severe genetic conditions arising from heterogenous molecular etiologies. ClinicalTrials.gov registration: ChiCTR2100045739 .
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Affiliation(s)
- Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Beijing BioBiggen Technology Co., Ltd, Beijing, China.
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Qiong Luo
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Xi
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ying Peng
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Na Ma
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yuan Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Jiang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Panpan Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifeng Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Yu Xiong
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jie Shen
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Huan Liang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yunyun Ren
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Minyue Dong
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Hua Wang
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.
- NHC Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China.
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
- Shanghai Frontiers Science Research Center of Reproduction and Development, Shanghai, China.
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30
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, Sant DW, Stark Z, Whiffin N, Rehm HL, Ware JS. Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms. Genet Med 2024; 26:101029. [PMID: 37982373 PMCID: PMC11039201 DOI: 10.1016/j.gim.2023.101029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023] Open
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here, we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both Sequence Ontology (SO) and Human Phenotype Ontology (HPO) ontologies. Gene Curation Coalition member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom.
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Katherine S Josephs
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, United Kingdom
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; Open Targets, Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David W Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia; University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, United Kingdom
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
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31
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Ciesielski TH, Sirugo G, Iyengar SK, Williams SM. Characterizing the pathogenicity of genetic variants: the consequences of context. NPJ Genom Med 2024; 9:3. [PMID: 38195641 PMCID: PMC10776585 DOI: 10.1038/s41525-023-00386-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Affiliation(s)
- Timothy H Ciesielski
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Mary Ann Swetland Center for Environmental Health at Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Ronin Institute, Montclair, NJ, USA.
| | - Giorgio Sirugo
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Institute of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sudha K Iyengar
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- The Department of Genetics and Genome Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Scott M Williams
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- The Department of Genetics and Genome Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
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32
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Vokač D, Stangler Herodež Š, Krgović D, Kokalj Vokač N. The Role of Next-Generation Sequencing in the Management of Patients with Suspected Non-Ischemic Cardiomyopathy after Syncope or Termination of Sudden Arrhythmic Death. Genes (Basel) 2024; 15:72. [PMID: 38254962 PMCID: PMC10815304 DOI: 10.3390/genes15010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Cardiac arrhythmias and sudden death are frequent in patients with non-ischemic cardiomyopathy and can precede heart failure or additional symptoms where malignant cardiac arrhythmias are mostly the consequence of advanced cardiomyopathy and heart failure. Finding these subgroups and making an early diagnosis could be lifesaving. In our retrospective study, we are presenting arrhythmic types of frequent cardiomyopathies where an arrhythmogenic substrate is less well defined, as in ischemic or structural heart disease. In the period of 2 years, next-generation sequencing (NGS) tests along with standard clinical tests were performed in 208 patients (67 women and 141 men; mean age, 51.2 ± 19.4 years) without ischemic or an overt structural heart disease after syncope or aborted sudden cardiac death. Genetic variants were detected in 34.4% of the study population, with a significant proportion of pathogenic variants (P) (14.4%) and variants of unknown significance (VUS) (20%). Regardless of genotype, all patients were stratified according to clinical guidelines for aggressive treatment of sudden cardiac death with an implantable cardioverter defibrillator (ICD). The P variant identified by NGS serves for an accurate diagnosis and, thus, better prevention and specific treatment of patients and their relatives. Results in our study suggest that targeted sequencing of genes associated with cardiovascular disease is an important addendum for final diagnosis, allowing the identification of a molecular genetic cause in a vast proportion of patients for a definitive diagnosis and a more specific way of treatment. VUS in this target population poses a high risk and should be considered possibly pathogenic in reanalysis.
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Affiliation(s)
- Damijan Vokač
- Department of Cardiology and Angiology, Division of Internal Medicine, University Medical Centre Maribor, 2000 Maribor, Slovenia;
| | - Špela Stangler Herodež
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| | - Danijela Krgović
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| | - Nadja Kokalj Vokač
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
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33
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Biesecker LG, Byrne AB, Harrison SM, Pesaran T, Schäffer AA, Shirts BH, Tavtigian SV, Rehm HL. ClinGen guidance for use of the PP1/BS4 co-segregation and PP4 phenotype specificity criteria for sequence variant pathogenicity classification. Am J Hum Genet 2024; 111:24-38. [PMID: 38103548 PMCID: PMC10806742 DOI: 10.1016/j.ajhg.2023.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023] Open
Abstract
The 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology variant classification publication established a standard employed internationally to guide laboratories in variant assessment. Those recommendations included both pathogenic (PP1) and benign (BS4) criteria for evaluating the inheritance patterns of variants, but details of how to apply those criteria at appropriate evidence levels were sparse. Several publications have since attempted to provide additional guidance, but anecdotally, this issue is still challenging. Additionally, it is not clear that those prior efforts fully distinguished disease-gene identification considerations from variant pathogenicity considerations nor did they address autosomal-recessive and X-linked inheritance. Here, we have taken a mixed inductive and deductive approach to this problem using real diseases as examples. We have developed a practical heuristic for genetic co-segregation evidence and have also determined that the specific phenotype criterion (PP4) is inseparably coupled to the co-segregation criterion. We have also determined that negative evidence at one locus constitutes positive evidence for other loci for disorders with locus heterogeneity. Finally, we provide a points-based system for evaluating phenotype and co-segregation as evidence types to support or refute a locus and show how that can be integrated into the Bayesian framework now used for variant classification and consistent with the 2015 guidelines.
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Affiliation(s)
- Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian H Shirts
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine and Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
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Houweling AC, Lekanne Deprez RH, Wilde AAM. Human Genetics of Cardiomyopathies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:977-990. [PMID: 38884765 DOI: 10.1007/978-3-031-44087-8_63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
The identification of a disease-causing variant in a patient diagnosed with cardiomyopathy allows for presymptomatic testing in at risk relatives. Carriers of a pathogenic variant can subsequently be screened at intervals by a cardiologist to assess the risk for potentially life-threatening arrhythmias which can be life-saving. In addition, gene-specific recommendations for risk stratification and disease specific pharmacological options for therapy are beginning to emerge. The large variability in disease penetrance, symptoms, and prognosis, and in some families even in cardiomyopathy subtype, makes genetic counseling both of great importance and complicated.
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Affiliation(s)
- Arjan C Houweling
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
| | - Ronald H Lekanne Deprez
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Arthur A M Wilde
- Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands
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Xu H, Pu J, Yang N, Wu Z, Han C, Yao J, Li X. First preimplantation genetic testing case of Meckel syndrome with a novel homozygous TXNDC15 variant in a non-consanguineous Chinese family. Mol Genet Genomic Med 2024; 12:e2340. [PMID: 38073519 PMCID: PMC10767674 DOI: 10.1002/mgg3.2340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/19/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Meckel-Gruber syndrome (MKS) is a perinatally lethal, genetically heterogeneous, autosomal recessive condition caused by defective primary cilium formation. So far, the association of TXNDC15-related MKS has been reported in only five independent families from diverse ethnic origins, including Saudi, Pakistani, Estonian, and Indian. Here, we report a fetus diagnosed with MKS at 12 weeks, exhibiting typical ultrasound findings. METHODS Low-coverage whole-genome sequencing was used to identify chromosomal abnormalities. Trio-base whole exome sequencing (trio-WES) was performed to investigate the potential pathogenic variants associated with MKS. Preimplantation genetic testing for monogenic disorders (PGT-M) was applied to prevent the transmission of the pathogenic variant. RESULTS A novel homozygous pathogenic variant in the TXNDC15 gene was identified through trio-WES. The application of PGT-M successfully prevented the transmission of the pathogenic variant and resulted in an ongoing pregnancy. CONCLUSION This is the first report of a TXNDC15 variant in the Chinese population and the first PGT case of TXNDC15-related MKS worldwide. The successful application of PGT-M in this family provides a potential approach for other monogenic diseases. Our case expands the variant spectrum of TXNDC15 and contributes to the molecular diagnosis and genetic counseling for MKS. This case underscores the importance of appropriate genetic testing methods and accurate genetic counseling in the diagnosis of rare monogenic diseases.
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Affiliation(s)
- Huiling Xu
- Department of Reproductive MedicineShenzhen Maternity & Child Healthcare HospitalShenzhenGuangdongChina
| | - Jiajie Pu
- Department of Bioinformatics01life InstituteShenzhenGuangdongChina
| | - Ningjie Yang
- Department of Reproductive MedicineShenzhen Maternity & Child Healthcare HospitalShenzhenGuangdongChina
| | - Zhengzhong Wu
- Department of Reproductive MedicineShenzhen Maternity & Child Healthcare HospitalShenzhenGuangdongChina
| | - Chanlin Han
- Department of Reproductive MedicineShenzhen Maternity & Child Healthcare HospitalShenzhenGuangdongChina
| | - Jilong Yao
- Department of Reproductive MedicineShenzhen Maternity & Child Healthcare HospitalShenzhenGuangdongChina
| | - Xuemei Li
- Department of Reproductive MedicineShenzhen Maternity & Child Healthcare HospitalShenzhenGuangdongChina
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Mintoff D, Borg I, Pace NP. NOD2 at the interface of hidradenitis suppurativa and inflammatory bowel disease-An in silico analysis. Exp Dermatol 2024; 33:e14928. [PMID: 37694954 DOI: 10.1111/exd.14928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Affiliation(s)
- Dillon Mintoff
- Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- Department of Dermatology, Mater Dei Hospital, Msida, Malta
| | - Isabella Borg
- Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- Department of Pathology, Section of Clinical Genetics, Mater Dei Hospital, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Nikolai P Pace
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
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Potter SN, Reynolds E, Okoniewski KC, Edwards A, Gable J, Hill C, Bakalov V, Zentz S, Whiting C, Cheves E, Garbarini K, Jalazo E, Howell C, Moore A, Wheeler A. Linking Angelman and dup15q data for expanded research (LADDER) database: a model for advancing research, clinical guidance, and therapeutic development for rare conditions. THERAPEUTIC ADVANCES IN RARE DISEASE 2024; 5:26330040241254122. [PMID: 38808315 PMCID: PMC11131393 DOI: 10.1177/26330040241254122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/18/2024] [Indexed: 05/30/2024]
Abstract
Angelman syndrome (AS) and duplication 15q (dup15q) syndrome are rare neurogenetic conditions arising from a common locus on the long arm of chromosome 15. Individuals with both conditions share some clinical features (e.g. intellectual disability, epilepsy) and often require lifelong care. Disease-modifying therapies for both conditions are emerging, resulting in a significant need for a better understanding of the natural history of both AS and dup15q. Patient advocacy groups for both conditions recognized a need for a data repository that would link data on individuals from multiple sources to expand research, increase understanding of natural history, and accelerate the development of treatments, resulting in the Linking Angelman and Dup15q Data for Expanded Research (LADDER) Database. This paper describes the development and functionality of the LADDER Database - including challenges, lessons learned, and preliminary feasibility - and how it can be used as a model for other rare conditions.
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Affiliation(s)
- Sarah Nelson Potter
- RTI International, 3040 E. Cornwallis Road, Research Triangle Park, NC 27709-2194, USA
| | | | | | - Anne Edwards
- RTI International, Research Triangle Park, NC, USA
| | - Julia Gable
- RTI International, Research Triangle Park, NC, USA
| | | | | | | | | | - Emily Cheves
- RTI International, Research Triangle Park, NC, USA
| | - Katie Garbarini
- Angelman Syndrome Foundation, Aurora, IL, USA
- Dup15q Alliance, Matthews, NC, USA
| | - Elizabeth Jalazo
- Department of Pediatrics, The University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | | | - Anne Wheeler
- RTI International, Research Triangle Park, NC, USA
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AlAbdi L, Shamseldin HE, Khouj E, Helaby R, Aljamal B, Alqahtani M, Almulhim A, Hamid H, Hashem MO, Abdulwahab F, Abouyousef O, Jaafar A, Alshidi T, Al-Owain M, Alhashem A, Al Tala S, Khan AO, Mardawi E, Alkuraya H, Faqeih E, Afqi M, Alkhalifi S, Rahbeeni Z, Hagos ST, Al-Ahmadi W, Nadeef S, Maddirevula S, Khabar KSA, Putra A, Angelov A, Park C, Reyes-Ramos AM, Umer H, Ullah I, Driguez P, Fukasawa Y, Cheung MS, Gallouzi IE, Alkuraya FS. Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases. Genome Med 2023; 15:114. [PMID: 38098057 PMCID: PMC10720148 DOI: 10.1186/s13073-023-01270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bayan Aljamal
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Pediatric Department, Division of Genetic and Metabolic Medicine, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Pediatric Department, Neonatal Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Elham Mardawi
- Maternal Fetal Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery and Ocular Genetics, Global Eye Care/Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Manal Afqi
- Metabolic and Genetic Center, King Salman Bin Abdulaziz Medical City, Almadinah Almunwarah, Saudi Arabia
| | - Salwa Alkhalifi
- Newborn Screening, Ministry of Health, Eastern Province, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wijdan Al-Ahmadi
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alexander Putra
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Angel Angelov
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Changsook Park
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ana M Reyes-Ramos
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Husen Umer
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ikram Ullah
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Patrick Driguez
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ming Sin Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Imed Eddine Gallouzi
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Odogwu NM, Hagen C, Nelson TJ. Transcriptome studies of congenital heart diseases: identifying current gaps and therapeutic frontiers. Front Genet 2023; 14:1278747. [PMID: 38152655 PMCID: PMC10751320 DOI: 10.3389/fgene.2023.1278747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
Congenital heart disease (CHD) are genetically complex and comprise a wide range of structural defects that often predispose to - early heart failure, a common cause of neonatal morbidity and mortality. Transcriptome studies of CHD in human pediatric patients indicated a broad spectrum of diverse molecular signatures across various types of CHD. In order to advance research on congenital heart diseases (CHDs), we conducted a detailed review of transcriptome studies on this topic. Our analysis identified gaps in the literature, with a particular focus on the cardiac transcriptome signatures found in various biological specimens across different types of CHDs. In addition to translational studies involving human subjects, we also examined transcriptomic analyses of CHDs in a range of model systems, including iPSCs and animal models. We concluded that RNA-seq technology has revolutionized medical research and many of the discoveries from CHD transcriptome studies draw attention to biological pathways that concurrently open the door to a better understanding of cardiac development and related therapeutic avenue. While some crucial impediments to perfectly studying CHDs in this context remain obtaining pediatric cardiac tissue samples, phenotypic variation, and the lack of anatomical/spatial context with model systems. Combining model systems, RNA-seq technology, and integrating algorithms for analyzing transcriptomic data at both single-cell and high throughput spatial resolution is expected to continue uncovering unique biological pathways that are perturbed in CHDs, thus facilitating the development of novel therapy for congenital heart disease.
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Affiliation(s)
- Nkechi Martina Odogwu
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
| | - Clinton Hagen
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
| | - Timothy J. Nelson
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States
- Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
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Riviello FN, Daponte A, Ponzi E, Ficarella R, Orsini P, Bucci R, Ventura M, Antonacci F, Catacchio CR, Gentile M. A Rare Case of Concurrent 2q34q36 Duplication and 2q37 Deletion in a Neonate with Syndromic Features. Genes (Basel) 2023; 14:2194. [PMID: 38137016 PMCID: PMC10742419 DOI: 10.3390/genes14122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Large-scale genomic structural variations can have significant clinical implications, depending on the specific altered genomic region. Briefly, 2q37 microdeletion syndrome is a prevalent subtelomeric deletion disorder characterized by variable-sized deletions. Affected patients exhibit a wide range of clinical manifestations, including short stature, facial dysmorphism, and features of autism spectrum disorder, among others. Conversely, isolated duplications of proximal chromosome 2q are rare and lack a distinct phenotype. In this report, we provide an extensive molecular analysis of a 15-day-old newborn referred for syndromic features. Our analysis reveals an 8.5 Mb microdeletion at 2q37.1, which extends to the telomere, in conjunction with an 8.6 Mb interstitial microduplication at 2q34q36.1. Our findings underscore the prominence of 2q37 terminal deletions as commonly reported genomic anomalies. We compare our patient's phenotype with previously reported cases in the literature to contribute to a more refined classification of 2q37 microdeletion syndrome and assess the potential impact of 2q34q36.1 microduplication. We also investigate multiple hypotheses to clarify the genetic mechanisms responsible for the observed genomic rearrangement.
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Affiliation(s)
- Francesco Nicola Riviello
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Alessia Daponte
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Emanuela Ponzi
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Romina Ficarella
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Paola Orsini
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Roberta Bucci
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Mario Ventura
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Francesca Antonacci
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Claudia Rita Catacchio
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Mattia Gentile
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
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Ren Z, Tang H, Zhang W, Guo M, Cui J, Wang H, Xie B, Yu J, Chen Y, Zhang M, Han C, Chu T, Liang Q, Zhao S, Huang Y, He X, Liu K, Liu C, Chen C. The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling During Neurodevelopment. Neurosci Bull 2023:10.1007/s12264-023-01161-3. [PMID: 38060137 DOI: 10.1007/s12264-023-01161-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/13/2023] [Indexed: 12/08/2023] Open
Abstract
Intellectual disability (ID) is a condition characterized by cognitive impairment and difficulties in adaptive functioning. In our research, we identified two de novo mutations (c.955C>T and c.732C>A) at the KDM2A locus in individuals with varying degrees of ID. In addition, by using the Gene4Denovo database, we discovered five additional cases of de novo mutations in KDM2A. The mutations we identified significantly decreased the expression of the KDM2A protein. To investigate the role of KDM2A in neural development, we used both 2D neural stem cell models and 3D cerebral organoids. Our findings demonstrated that the reduced expression of KDM2A impairs the proliferation of neural progenitor cells (NPCs), increases apoptosis, induces premature neuronal differentiation, and affects synapse maturation. Through ChIP-Seq analysis, we found that KDM2A exhibited binding to the transcription start site regions of genes involved in neurogenesis. In addition, the knockdown of KDM2A hindered H3K36me2 binding to the downstream regulatory elements of genes. By integrating ChIP-Seq and RNA-Seq data, we made a significant discovery of the core genes' remarkable enrichment in the MAPK signaling pathway. Importantly, this enrichment was specifically linked to the p38 MAPK pathway. Furthermore, disease enrichment analysis linked the differentially-expressed genes identified from RNA-Seq of NPCs and cerebral organoids to neurodevelopmental disorders such as ID, autism spectrum disorder, and schizophrenia. Overall, our findings suggest that KDM2A plays a crucial role in regulating the H3K36me2 modification of downstream genes, thereby modulating the MAPK signaling pathway and potentially impacting early brain development.
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Affiliation(s)
- Zongyao Ren
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Haiyan Tang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Wendiao Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Minghui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jingjie Cui
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Children's Hospital, Changsha, 410007, China
| | - Bin Xie
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jing Yu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yonghao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Ming Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Cong Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Tianyao Chu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Qiuman Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Shunan Zhao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yingjie Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Xuelian He
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430014, China.
| | - Kefu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410011, China.
- Furong Laboratory, Changsha, 410000, China.
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Seed E, Noon F, Milnes D, Roscioli T, Kristensen K, Ellwood D, DaSilva Costa F. Biallellic variants in CACNA1S cause fetal akinesia sequence, progressive hydrops and stillbirth. Prenat Diagn 2023; 43:1678-1681. [PMID: 38111203 DOI: 10.1002/pd.6471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
Fetal arthrogryposis is a well-recognised ultrasonographic phenotype, caused by both genetic, maternal and extrinsic factors. When present with fetal growth restriction, pulmonary hypoplasia and multiple joint contractures, it is often referred to as fetal akinesia deformation sequence (FADS). Historically, elucidating genetic causes of arthryogryposis/FADS has been challenging; there are now more than 150 genes known to cause arthrogryposis through myopathic, neuromuscular and metabolic pathways affecting fetal movement. FADS is associated with over 400 medical conditions making prenatal diagnosis challenging. Here we present a case of FADS diagnosed at 19 weeks gestation with progression to severe fetal hydrops and stillbirth at 26-weeks gestation. Initial investigations including combined first trimester screening, TORCH (infection) screen and chromosomal microarray were normal. Trio whole exome sequencing (WES) detected compound heterozygous likely pathogenic CACNA1S gene variants associated with autosomal dominant (AD) and autosomal recessive (AR) congenital myopathy and FADS. To our knowledge, this is the first prenatal diagnosis of this condition.
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Affiliation(s)
- Emma Seed
- Maternal Fetal Medicine, The Gold Coast University Hospital, Southport, Queensland, Australia
- The Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Fallon Noon
- Clinical Genetics Advanced Trainee, Genetic Health Queensland, Herston, Queensland, Australia
| | - Di Milnes
- Clinical Geneticist, Genetic Health Queensland, Herston, Queensland, Australia
| | - Tony Roscioli
- Prince of Wales Hospital and Community Health Services, NSW Health Pathology Randwick Genomics, Randwick, New South Wales, Australia
| | - Karl Kristensen
- Maternal Fetal Medicine, The Gold Coast University Hospital, Southport, Queensland, Australia
| | - David Ellwood
- Maternal Fetal Medicine, The Gold Coast University Hospital, Southport, Queensland, Australia
- Griffith University School of Medicine, Gold Coast, Queensland, Australia
| | - Fabricio DaSilva Costa
- Maternal Fetal Medicine, The Gold Coast University Hospital, Southport, Queensland, Australia
- Griffith University School of Medicine, Gold Coast, Queensland, Australia
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43
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Quaio CRDC, Ceroni JRM, Pereira MA, Teixeira ACB, Yamada RY, Cintra VP, Perrone E, De França M, Chen K, Minillo RM, Biondo CA, de Mello MRB, Moura LR, do Nascimento ATB, de Oliveira Pelegrino K, de Lima LB, do Amaral Virmond L, Moreno CA, Prota JRM, de Araujo Espolaor JG, Silva TYT, Moraes GHI, de Oliveira GS, Moura LMS, Caraciolo MP, Guedes RLM, Gretschischkin MC, Chazanas PLN, Nakamura CNI, de Souza Reis R, Toledo CM, Lage FSD, de Almeida GB, do Nascimento Júnior JB, Cardoso MA, de Paula Azevedo V, de Almeida TF, Cervato MC, de Oliveira Filho JB. The hospital Israelita Albert Einstein standards for constitutional sequence variants classification: version 2023. Hum Genomics 2023; 17:102. [PMID: 37968704 PMCID: PMC10652504 DOI: 10.1186/s40246-023-00549-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Next-generation sequencing has had a significant impact on genetic disease diagnosis, but the interpretation of the vast amount of genomic data it generates can be challenging. To address this, the American College of Medical Genetics and Genomics and the Association for Molecular Pathology have established guidelines for standardized variant interpretation. In this manuscript, we present the updated Hospital Israelita Albert Einstein Standards for Constitutional Sequence Variants Classification, incorporating modifications from leading genetics societies and the ClinGen initiative. RESULTS First, we standardized the scientific publications, documents, and other reliable sources for this document to ensure an evidence-based approach. Next, we defined the databases that would provide variant information for the classification process, established the terminology for molecular findings, set standards for disease-gene associations, and determined the nomenclature for classification criteria. Subsequently, we defined the general rules for variant classification and the Bayesian statistical reasoning principles to enhance this process. We also defined bioinformatics standards for automated classification. Our workgroup adhered to gene-specific rules and workflows curated by the ClinGen Variant Curation Expert Panels whenever available. Additionally, a distinct set of specifications for criteria modulation was created for cancer genes, recognizing their unique characteristics. CONCLUSIONS The development of an internal consensus and standards for constitutional sequence variant classification, specifically adapted to the Brazilian population, further contributes to the continuous refinement of variant classification practices. The aim of these efforts from the workgroup is to enhance the reliability and uniformity of variant classification.
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Affiliation(s)
| | - José Ricardo Magliocco Ceroni
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Michele Araújo Pereira
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - Renata Yoshiko Yamada
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Vivian Pedigone Cintra
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Eduardo Perrone
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Marina De França
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Kelin Chen
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Renata Moldenhauer Minillo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Cheysa Arielly Biondo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | | | - Lais Rodrigues Moura
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | | | - Karla de Oliveira Pelegrino
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Larissa Barbosa de Lima
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Luiza do Amaral Virmond
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Carolina Araujo Moreno
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Joana Rosa Marques Prota
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | | | | | - Gabriel Hideki Izuka Moraes
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Gustavo Santos de Oliveira
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Livia Maria Silva Moura
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Marcel Pinheiro Caraciolo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Rafael Lucas Muniz Guedes
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Michel Chieregato Gretschischkin
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Pedro Lui Nigro Chazanas
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Carolina Naomi Izo Nakamura
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Rodrigo de Souza Reis
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Carmen Melo Toledo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Fernanda Stussi Duarte Lage
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Giovanna Bloise de Almeida
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - José Bandeira do Nascimento Júnior
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Milena Andreuzo Cardoso
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Victor de Paula Azevedo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Tatiana Ferreira de Almeida
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Murilo Castro Cervato
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Joao Bosco de Oliveira Filho
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil.
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Zhang L, Li X, Xu F, Gao L, Wang Z, Wang X, Li X, Liu M, Zhu J, Yao T, Ye J, Qi X, Wang Y, Zhao G, Wang C. Multidisciplinary molecular consultation increases the diagnosis of pediatric epileptic encephalopathy and neurodevelopmental disorders. Mol Genet Genomic Med 2023; 11:e2243. [PMID: 37489029 PMCID: PMC10655525 DOI: 10.1002/mgg3.2243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Epilepsy (EP) is a common neurological disease in which 70-80% are thought to have a genetic cause. In patients with epilepsy, neurodevelopmental delay (NDD) was prevalent. Next generation of sequencing has been widely used in diagnosing EP/NDD. However, the diagnostic yield remains to be 40%-50%. Many reanalysis pipelines and software have been developed for automated reanalysis and decision making for the diseases. Nevertheless, it is a highly challenging task for smaller genetic centers or a routine pediatric practice. To address the clinical and genetic "diagnostic odyssey," we organized a Multidisciplinary Molecular Consultation (MMC) team for molecular consultation for 202 children with EP/NDD patients referred by lower level hospitals. METHODS All the patients had undergone an aligned and sequential consultations and discussions by a "triple reanalysis" procedure by clinical, genetic specialists, and researchers. RESULTS Among the 202 cases for MMC, we totally identified 47 cases (23%) harboring causative variants in 24 genes and 15 chromosomal regions after the MMC. In the 15 cases with positive CNVs, 3 cases harbor the deletions or duplications in 16p11.2, and 2 cases for 1p36. The bioinformatical reanalysis revealed 47 positive cases, in which 12 (26%) were reported to be negative, VUS or incorrectly positive in pre-MMC reports. Additionally, among 87 cases with negative cases, 4 (5%) were reported to be positive in pre-MMC reports. CONCLUSION We established a workflow allowing for a "one-stop" collaborative assessments by experts of multiple fields and helps for correct the diagnosis of cases with falsenegative and -positive and VUS genetic reports and may have significant influences for intervention, prevention and genetic counseling of pediatric epilepsy and neurodevelopmental disorders.
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Affiliation(s)
- Liping Zhang
- Department of PediatricsXuanwu Hospital of Capital Medical UniversityBeijingChina
| | - Xu‐Ying Li
- Department of Neurology and NeurobiologyXuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Fanxi Xu
- Department of Neurology and NeurobiologyXuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Lehong Gao
- Department of NeurologyXuanwu Hospital of Capital Medical UniversityBeijingChina
| | - Zhanjun Wang
- Department of NeurologyXuanwu Hospital of Capital Medical UniversityBeijingChina
| | - Xianling Wang
- Department of NeurologyXuanwu Hospital of Capital Medical UniversityBeijingChina
| | - Xian Li
- Department of Neurology and NeurobiologyXuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Mengyu Liu
- Department of Neurology and NeurobiologyXuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Junge Zhu
- Department of Neurology and NeurobiologyXuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Tingyan Yao
- Department of Neurology and NeurobiologyXuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Jing Ye
- Department of NeurologyXuanwu Hospital of Capital Medical UniversityBeijingChina
| | - Xiao‐Hong Qi
- Department of PediatricsXuanwu Hospital of Capital Medical UniversityBeijingChina
| | - Yaqing Wang
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Guoguang Zhao
- Department of NeurosurgeryXuanwu Hospital of Capital Medical University, Clinical Research Center for Epilepsy Capital Medical UniversityBeijingChina
| | - Chaodong Wang
- Department of Neurology and NeurobiologyXuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric DiseasesBeijingChina
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45
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Welch CL, Aldred MA, Balachandar S, Dooijes D, Eichstaedt CA, Gräf S, Houweling AC, Machado RD, Pandya D, Prapa M, Shaukat M, Southgate L, Tenorio-Castano J, Chung WK. Defining the clinical validity of genes reported to cause pulmonary arterial hypertension. Genet Med 2023; 25:100925. [PMID: 37422716 PMCID: PMC10766870 DOI: 10.1016/j.gim.2023.100925] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE Pulmonary arterial hypertension (PAH) is a rare, progressive vasculopathy with significant cardiopulmonary morbidity and mortality. Genetic testing is currently recommended for adults diagnosed with heritable, idiopathic, anorexigen-, hereditary hemorrhagic telangiectasia-, and congenital heart disease-associated PAH, PAH with overt features of venous/capillary involvement, and all children diagnosed with PAH. Variants in at least 27 genes have putative evidence for PAH causality. Rigorous assessment of the evidence is needed to inform genetic testing. METHODS An international panel of experts in PAH applied a semi-quantitative scoring system developed by the NIH Clinical Genome Resource to classify the relative strength of evidence supporting PAH gene-disease relationships based on genetic and experimental evidence. RESULTS Twelve genes (BMPR2, ACVRL1, ATP13A3, CAV1, EIF2AK4, ENG, GDF2, KCNK3, KDR, SMAD9, SOX17, and TBX4) were classified as having definitive evidence and 3 genes (ABCC8, GGCX, and TET2) with moderate evidence. Six genes (AQP1, BMP10, FBLN2, KLF2, KLK1, and PDGFD) were classified as having limited evidence for causal effects of variants. TOPBP1 was classified as having no known PAH relationship. Five genes (BMPR1A, BMPR1B, NOTCH3, SMAD1, and SMAD4) were disputed because of a paucity of genetic evidence over time. CONCLUSION We recommend that genetic testing includes all genes with definitive evidence and that caution be taken in the interpretation of variants identified in genes with moderate or limited evidence. Genes with no known evidence for PAH or disputed genes should not be included in genetic testing.
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Affiliation(s)
- Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Micheala A Aldred
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, IN
| | - Srimmitha Balachandar
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, IN
| | - Dennis Dooijes
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Christina A Eichstaedt
- Center for Pulmonary Hypertension, Thoraxklinik-Heidelberg gGmbH, at Heidelberg University Hospital and Translational Lung Research Center, German Center for Lung Research, Heidelberg, Germany; Laboratory for Molecular Genetic Diagnostics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Stefan Gräf
- NIHR BioResource for Translational Research - Rare Diseases, Department of Haemotology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom; Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Arjan C Houweling
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Rajiv D Machado
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, United Kingdom
| | - Divya Pandya
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Matina Prapa
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom; St. George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Memoona Shaukat
- Center for Pulmonary Hypertension, Thoraxklinik-Heidelberg gGmbH, at Heidelberg University Hospital and Translational Lung Research Center, German Center for Lung Research, Heidelberg, Germany; Laboratory for Molecular Genetic Diagnostics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Laura Southgate
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, United Kingdom
| | - Jair Tenorio-Castano
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IDiPAZ, Universidad Autonoma de Madrid, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; ITHACA, European Reference Network, Brussels, Belgium
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY; Department of Medicine, Columbia University Irving Medical Center, New York, NY.
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46
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Wang Q, Lin X, Lai K, Liu Y, Qin T, Tan H, Li J, Lin Z, Zhang X, Li X, Lin H, Chen W. Novel compound heterozygous variants of the SEC23A gene in a Chinese family with cranio-lenticulo-sutural dysplasia based on data from a large cohort of congenital cataract patients. BMC Med Genomics 2023; 16:241. [PMID: 37828500 PMCID: PMC10568747 DOI: 10.1186/s12920-023-01667-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Cranio-lenticulo-sutural dysplasia (CLSD) is a rare dysmorphic syndrome characterized by skeletal dysmorphism, late-closing fontanels, and cataracts. CLSD is caused by mutations in the SEC23A gene (OMIM# 607812) and can be inherited in either an autosomal dominant or autosomal recessive pattern. To date, only four mutations have been reported to cause CLSD. This study aims to identify the disease-causing variants in a large cohort of congenital cataract patients, to expand the genotypic and phenotypic spectrum of CLSD, and to confirm the association between SEC23A and autosomal recessive CLSD (ARCLSD). METHODS We collected detailed medical records and performed comprehensive ocular examinations and whole-exome sequencing (WES) on 115 patients with congenital cataracts. After suspecting that a patient may have CLSD based on the sequencing results, we proceeded to conduct transmission electron microscopy (TEM) on the cultured skin fibroblasts. The clinical validity of the reported gene-disease relationships for the gene and the disease was evaluated using the ClinGen gene curation framework. RESULTS Two novel compound heterozygous variants (c.710A > C p.Asp237Ala, c.1946T > C p.Leu649Pro) of the SEC23A gene, classified as variant of uncertain significance, were identified in the proband with skeletal, cardiac, ocular, and hearing defects. The observation of typical distended endoplasmic reticulum cisternae further supported the diagnosis of CLSD. Application of the ClinGen gene curation framework confirmed the association between SEC23A and ARCLSD. CONCLUSION This study expands the genotypic and phenotypic spectrum of CLSD, proposes TEM as a supplemental diagnostic method, and indicates that congenital cataracts are a typical sign of ARCLSD.
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Affiliation(s)
- Qiwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Xiaoshan Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Kunbei Lai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Yinghui Liu
- Department of Dermatology, Dermatology Hospital, Southern Medical University, 510091, Guangzhou, Guangdong Province, China
| | - Tingfeng Qin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Haowen Tan
- Aegicare Biotech, 518000, Shenzhen, Guangdong Province, China
| | - Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Zhuoling Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Xulin Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Xiaoyan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China.
| | - Weirong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China.
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47
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Alsentzer E, Finlayson SG, Li MM, Kobren SN, Kohane IS. Simulation of undiagnosed patients with novel genetic conditions. Nat Commun 2023; 14:6403. [PMID: 37828001 PMCID: PMC10570269 DOI: 10.1038/s41467-023-41980-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Rare Mendelian disorders pose a major diagnostic challenge and collectively affect 300-400 million patients worldwide. Many automated tools aim to uncover causal genes in patients with suspected genetic disorders, but evaluation of these tools is limited due to the lack of comprehensive benchmark datasets that include previously unpublished conditions. Here, we present a computational pipeline that simulates realistic clinical datasets to address this deficit. Our framework jointly simulates complex phenotypes and challenging candidate genes and produces patients with novel genetic conditions. We demonstrate the similarity of our simulated patients to real patients from the Undiagnosed Diseases Network and evaluate common gene prioritization methods on the simulated cohort. These prioritization methods recover known gene-disease associations but perform poorly on diagnosing patients with novel genetic disorders. Our publicly-available dataset and codebase can be utilized by medical genetics researchers to evaluate, compare, and improve tools that aid in the diagnostic process.
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Grants
- U01 HG007690 NHGRI NIH HHS
- U54 NS108251 NINDS NIH HHS
- U01 HG010219 NHGRI NIH HHS
- U01 HG007672 NHGRI NIH HHS
- U01 HG010233 NHGRI NIH HHS
- U01 HG010230 NHGRI NIH HHS
- U01 HG007943 NHGRI NIH HHS
- U01 HG010217 NHGRI NIH HHS
- U01 HG007942 NHGRI NIH HHS
- U01 HG010215 NHGRI NIH HHS
- U01 HG007708 NHGRI NIH HHS
- T32 HG002295 NHGRI NIH HHS
- T32 GM007753 NIGMS NIH HHS
- U01 HG007674 NHGRI NIH HHS
- U01 TR001395 NCATS NIH HHS
- U01 HG007709 NHGRI NIH HHS
- U54 NS093793 NINDS NIH HHS
- U01 HG007530 NHGRI NIH HHS
- U01 TR002471 NCATS NIH HHS
- U01 HG007703 NHGRI NIH HHS
- UDN research reported in this manuscript was supported by the NIH Common Fund, through the Office of Strategic Coordination/Office of the NIH Director under Award Number(s) U01HG007709, U01HG010219, U01HG010230, U01HG010217, U01HG010233, U01HG010215, U01HG007672, U01HG007690, U01HG007708, U01HG007703, U01HG007674, U01HG007530, U01HG007942, U01HG007943, U01TR001395, U01TR002471, U54NS108251, and U54NS093793.
- E.A. is supported by a Microsoft Research PhD Fellowship.
- S.F. is supported by award Number T32GM007753 from the National Institute of General Medical Sciences.
- M.L. is supported by T32HG002295 from the National Human Genome Research Institute and a National Science Foundation Graduate Research Fellowship.
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Affiliation(s)
- Emily Alsentzer
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Program in Health Sciences and Technology, MIT, Cambridge, MA, 02139, USA
| | - Samuel G Finlayson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Program in Health Sciences and Technology, MIT, Cambridge, MA, 02139, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, 98105, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98105, USA
| | - Michelle M Li
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, 02115, USA
| | - Shilpa N Kobren
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
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48
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Lipov A, Jurgens SJ, Mazzarotto F, Allouba M, Pirruccello JP, Aguib Y, Gennarelli M, Yacoub MH, Ellinor PT, Bezzina CR, Walsh R. Exploring the complex spectrum of dominance and recessiveness in genetic cardiomyopathies. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1078-1094. [PMID: 38666070 PMCID: PMC11041721 DOI: 10.1038/s44161-023-00346-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/07/2023] [Indexed: 04/28/2024]
Abstract
Discrete categorization of Mendelian disease genes into dominant and recessive models often oversimplifies their underlying genetic architecture. Cardiomyopathies (CMs) are genetic diseases with complex etiologies for which an increasing number of recessive associations have recently been proposed. Here, we comprehensively analyze all published evidence pertaining to biallelic variation associated with CM phenotypes to identify high-confidence recessive genes and explore the spectrum of monoallelic and biallelic variant effects in established recessive and dominant disease genes. We classify 18 genes with robust recessive association with CMs, largely characterized by dilated phenotypes, early disease onset and severe outcomes. Several of these genes have monoallelic association with disease outcomes and cardiac traits in the UK Biobank, including LMOD2 and ALPK3 with dilated and hypertrophic CM, respectively. Our data provide insights into the complex spectrum of dominance and recessiveness in genetic heart disease and demonstrate how such approaches enable the discovery of unexplored genetic associations.
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Affiliation(s)
- Alex Lipov
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
| | - Sean J. Jurgens
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Francesco Mazzarotto
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - James P. Pirruccello
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Division of Cardiology, University of California, San Francisco, San Francisco, CA USA
| | - Yasmine Aguib
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Magdi H. Yacoub
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
- Harefield Heart Science Centre, Uxbridge, UK
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA USA
| | - Connie R. Bezzina
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, Amsterdam, the Netherlands
| | - Roddy Walsh
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
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49
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Murphy R, Colclough K, Pollin TI, Ikle JM, Svalastoga P, Maloney KA, Saint-Martin C, Molnes J, Misra S, Aukrust I, de Franco E, Flanagan SE, Njølstad PR, Billings LK, Owen KR, Gloyn AL. The use of precision diagnostics for monogenic diabetes: a systematic review and expert opinion. COMMUNICATIONS MEDICINE 2023; 3:136. [PMID: 37794142 PMCID: PMC10550998 DOI: 10.1038/s43856-023-00369-8] [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: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Monogenic diabetes presents opportunities for precision medicine but is underdiagnosed. This review systematically assessed the evidence for (1) clinical criteria and (2) methods for genetic testing for monogenic diabetes, summarized resources for (3) considering a gene or (4) variant as causal for monogenic diabetes, provided expert recommendations for (5) reporting of results; and reviewed (6) next steps after monogenic diabetes diagnosis and (7) challenges in precision medicine field. METHODS Pubmed and Embase databases were searched (1990-2022) using inclusion/exclusion criteria for studies that sequenced one or more monogenic diabetes genes in at least 100 probands (Question 1), evaluated a non-obsolete genetic testing method to diagnose monogenic diabetes (Question 2). The risk of bias was assessed using the revised QUADAS-2 tool. Existing guidelines were summarized for questions 3-5, and review of studies for questions 6-7, supplemented by expert recommendations. Results were summarized in tables and informed recommendations for clinical practice. RESULTS There are 100, 32, 36, and 14 studies included for questions 1, 2, 6, and 7 respectively. On this basis, four recommendations for who to test and five on how to test for monogenic diabetes are provided. Existing guidelines for variant curation and gene-disease validity curation are summarized. Reporting by gene names is recommended as an alternative to the term MODY. Key steps after making a genetic diagnosis and major gaps in our current knowledge are highlighted. CONCLUSIONS We provide a synthesis of current evidence and expert opinion on how to use precision diagnostics to identify individuals with monogenic diabetes.
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Affiliation(s)
- Rinki Murphy
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
- Auckland Diabetes Centre, Te Whatu Ora Health New Zealand, Te Tokai Tumai, Auckland, New Zealand.
| | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jennifer M Ikle
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA
| | - Pernille Svalastoga
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin A Maloney
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cécile Saint-Martin
- Department of Medical Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Shivani Misra
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Diabetes and Endocrinology, Imperial College Healthcare NHS Trust, London, UK
| | - Ingvild Aukrust
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Elisa de Franco
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Pål R Njølstad
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Liana K Billings
- Division of Endocrinology, NorthShore University HealthSystem, Skokie, IL, USA
- Department of Medicine, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Katharine R Owen
- Oxford Center for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anna L Gloyn
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
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50
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Chen E, Facio FM, Aradhya KW, Rojahn S, Hatchell KE, Aguilar S, Ouyang K, Saitta S, Hanson-Kwan AK, Capurro NN, Takamine E, Jamuar SS, McKnight D, Johnson B, Aradhya S. Rates and Classification of Variants of Uncertain Significance in Hereditary Disease Genetic Testing. JAMA Netw Open 2023; 6:e2339571. [PMID: 37878314 PMCID: PMC10600581 DOI: 10.1001/jamanetworkopen.2023.39571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/12/2023] [Indexed: 10/26/2023] Open
Abstract
Importance Variants of uncertain significance (VUSs) are rampant in clinical genetic testing, frustrating clinicians, patients, and laboratories because the uncertainty hinders diagnoses and clinical management. A comprehensive assessment of VUSs across many disease genes is needed to guide efforts to reduce uncertainty. Objective To describe the sources, gene distribution, and population-level attributes of VUSs and to evaluate the impact of the different types of evidence used to reclassify them. Design, Setting, and Participants This cohort study used germline DNA variant data from individuals referred by clinicians for diagnostic genetic testing for hereditary disorders. Participants included individuals for whom gene panel testing was conducted between September 9, 2014, and September 7, 2022. Data were analyzed from September 1, 2022, to April 1, 2023. Main Outcomes and Measures The outcomes of interest were VUS rates (stratified by age; clinician-reported race, ethnicity, and ancestry groups; types of gene panels; and variant attributes), percentage of VUSs reclassified as benign or likely benign vs pathogenic or likely pathogenic, and enrichment of evidence types used for reclassifying VUSs. Results The study cohort included 1 689 845 individuals ranging in age from 0 to 89 years at time of testing (median age, 50 years), with 1 203 210 (71.2%) female individuals. There were 39 150 Ashkenazi Jewish individuals (2.3%), 64 730 Asian individuals (3.8%), 126 739 Black individuals (7.5%), 5539 French Canadian individuals (0.3%), 169 714 Hispanic individuals (10.0%), 5058 Native American individuals (0.3%), 2696 Pacific Islander individuals (0.2%), 4842 Sephardic Jewish individuals (0.3%), and 974 383 White individuals (57.7%). Among all individuals tested, 692 227 (41.0%) had at least 1 VUS and 535 385 (31.7%) had only VUS results. The number of VUSs per individual increased as more genes were tested, and most VUSs were missense changes (86.6%). More VUSs were observed per sequenced gene in individuals who were not from a European White population, in middle-aged and older adults, and in individuals who underwent testing for disorders with incomplete penetrance. Of 37 699 unique VUSs that were reclassified, 30 239 (80.2%) were ultimately categorized as benign or likely benign. A mean (SD) of 30.7 (20.0) months elapsed for VUSs to be reclassified to benign or likely benign, and a mean (SD) of 22.4 (18.9) months elapsed for VUSs to be reclassified to pathogenic or likely pathogenic. Clinical evidence contributed most to reclassification. Conclusions and Relevance This cohort study of approximately 1.6 million individuals highlighted the need for better methods for interpreting missense variants, increased availability of clinical and experimental evidence for variant classification, and more diverse representation of race, ethnicity, and ancestry groups in genomic databases. Data from this study could provide a sound basis for understanding the sources and resolution of VUSs and navigating appropriate next steps in patient care.
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Affiliation(s)
- Elaine Chen
- Invitae Corporation, San Francisco, California
| | | | | | | | | | | | | | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Nicole Nakousi Capurro
- School of Medicine, University of Valparaíso, Valparaíso, Chile
- Facultad de Medicina, Universidad Andrés Bello, Viña del Mar, Chile
| | - Eriko Takamine
- Department of Medical Genetics, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Saumya Shekhar Jamuar
- Genetics Service, KK Women’s and Children’s Hospital, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | | | | | - Swaroop Aradhya
- Invitae Corporation, San Francisco, California
- Department of Pathology, Stanford University, Stanford, California
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