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Al Eissa MM, Alotibi RS, Alhaddad B, Aloraini T, Samman MS, AlAsiri A, Abouelhoda M, AlQahtani AS. Reclassifying variations of unknown significance in diseases affecting Saudi Arabia's population reveal new associations. Front Genet 2023; 14:1250317. [PMID: 38028588 PMCID: PMC10646566 DOI: 10.3389/fgene.2023.1250317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Physicians face diagnostic dilemmas upon reports indicating disease variants of unknown significance (VUS). The most puzzling cases are patients with rare diseases, where finding another matched genotype and phenotype to associate their results is challenging. This study aims to prove the value of updating patient files with new classifications, potentially leading to better assessment and prevention. Methodology: We recruited retrospective phenotypic and genotypic data from King Saud Medical City, Riyadh, Kingdom of Saudi Arabia. Between September 2020 and December 2021, 1,080 patients' genetic profiles were tested in a College of American Pathologists accredited laboratory. We excluded all confirmed pathogenic variants, likely pathogenic variants and copy number variations. Finally, we further reclassified 194 VUS using different local and global databases, employing in silico prediction to justify the phenotype-genotype association. Results: Of the 194 VUS, 90 remained VUS, and the other 104 were reclassified as follows: 16 pathogenic, 49 likely pathogenic, nine benign, and 30 likely benign. Moreover, most of these variants had never been observed in other local or international databases. Conclusion: Reclassifying the VUS adds value to understanding the causality of the phenotype if it has been reported in another family or population. The healthcare system should establish guidelines for re-evaluating VUS, and upgrading VUS should reflect on individual/family risks and management strategies.
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Affiliation(s)
- Mariam M. Al Eissa
- Public Health Authority, Public Health Lab, Molecular Genetics Laboratory, Riyadh, Saudi Arabia
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
| | - Raniah S. Alotibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Bader Alhaddad
- Laboratory Medicine Department, King Fahd University Hospital, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Molecular Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Manar S. Samman
- Department of Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City (KFMC), Riyadh, Saudi Arabia
| | - Abdulrahman AlAsiri
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Mohamed Abouelhoda
- Chairman Computational Science Department at King Faisal Specialised Hospital and Research Center, KFSHRC, Riyadh, Saudi Arabia
| | - Amerh S. AlQahtani
- Medical Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
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Alqahtani AS, Alotibi RS, Aloraini T, Almsned F, Alassali Y, Alfares A, Alhaddad B, Al Eissa MM. Prospect of genetic disorders in Saudi Arabia. Front Genet 2023; 14:1243518. [PMID: 37799141 PMCID: PMC10548463 DOI: 10.3389/fgene.2023.1243518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction: Rare diseases (RDs) create a massive burden for governments and families because sufferers of these diseases are required to undergo long-term treatment or rehabilitation to maintain a normal life. In Saudi Arabia (SA), the prevalence of RDs is high as a result of cultural and socio-economic factors. This study, however, aims to shed light on the genetic component of the prevalence of RDs in SA. Methodology: A retrospective study was conducted between September 2020 and December 2021 at King Saud Medical City, a tertiary hospital of the Ministry of Health (MOH), SA. A total of 1080 individuals with 544 potentially relevant variants were included. The index was 738, and the samples were tested in a commercialized laboratory using different molecular techniques, including next-generation sequencing. Result: A total of 867 molecular genetics tests were conducted on 738 probands. These tests included 610 exome sequencing (ES) tests, four genome sequencing (GS) tests, 82 molecular panels, 106 single nucleotide polymorphism (SNP) array, four methylation studies, 58 single-gene studies and three mitochondrial genome sequencing tests. The diagnostic yield among molecular genetics studies was 41.8% in ES, 24% in panels, 12% in SNP array and 24% in single gene studies. The majority of the identified potential variants (68%) were single nucleotide variants (SNV). Other ascertained variants included frameshift (11%), deletion (10%), duplication (5%), splicing (9%), in-frame deletion (3%) and indels (1%). The rate of positive consanguinity was 56%, and the autosomal recessive accounted for 54%. We found a significant correlation between the ES detection rate and positive consanguinity. We illustrated the presence of rare treatable conditions in DNAJC12, SLC19A3, and ALDH7A1, and the presence of the founder effect variant in SKIC2. Neurodevelopmental disorders were the main phenotype for which genetics studies were required (35.7%). Conclusion: This is the sixth-largest local study reporting next-generation sequencing. The results indicate the influence of consanguineous marriages on genetic disease and the burden it causes for the Kingdom of SA. This study highlights the need to enrich our society's knowledge of genetic disorders. We recommend utilising ES as a first-tier test to establish genetic diagnosis in a highly consanguineous population.
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Affiliation(s)
- Amerh S. Alqahtani
- Medical Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Raniah S. Alotibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre (KAIMRC), Riyadh, Saudi Arabia
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Department of Genetics, King Abdullah Specialized Children Hospital, MNGHA, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- Department of Genetics, King Abdullah Specialized Children Hospital, MNGHA, Riyadh, Saudi Arabia
| | - Fahad Almsned
- Research Centre, King Fahad Specialist Hospital in Dammam (KFSH-D), Dammam, Saudi Arabia
- Population Health Management, Eastern Health Cluster, Dammam, Saudi Arabia
- Research and Development Department, NovoGenomics, Riyadh, Saudi Arabia
| | - Yara Alassali
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
| | - Ahmed Alfares
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Bader Alhaddad
- Molecular Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
- Laboratory Medicine Department, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Al Khobar, Saudi Arabia
| | - Mariam M. Al Eissa
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
- Public Health Authority, Public Health Lab, Molecular Genetics Laboratory, Riyadh, Saudi Arabia
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3
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Aloraini T, Aljouie A, Alniwaider R, Alharbi W, Alsubaie L, AlTuraif W, Qureshi W, Alswaid A, Eyiad W, Al Mutairi F, Ababneh F, Alfadhel M, Alfares A. The variant artificial intelligence easy scoring (VARIES) system. Comput Biol Med 2022; 145:105492. [PMID: 35585733 DOI: 10.1016/j.compbiomed.2022.105492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 11/03/2022]
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Aleissa M, Aloraini T, Alsubaie LF, Hassoun M, Abdulrahman G, Swaid A, Eyaid WA, Mutairi FA, Ababneh F, Alfadhel M, Alfares A. Common disease-associated gene variants in a Saudi Arabian population. Ann Saudi Med 2022; 42:29-35. [PMID: 35112591 PMCID: PMC8812157 DOI: 10.5144/0256-4947.2022.29] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Screening programs for the most prevalent conditions occurring in a country is an evidence-based prevention strategy. The burden of autosomal recessive disease variations in Saudi Arabia is high because of the highly consanguineous population. The optimal solution for estimating the carrier frequency of the most prevalent diseases is carrier screening. OBJECTIVES Identify the most influential recessive alleles associated with disease in the Saudi population. DESIGN We used clinical whole-exome sequencing data from an in-house familial database to evaluate the most prevalent genetic variations associated with disease in a Saudi population. SETTINGS King Abdullah International Medical Research Center (KAIMRC) and King Abdulaziz Medical City. METHODS Whole exome sequencing data obtained from clinical studies of family members, a cohort of 1314 affected and unaffected individuals, were filtered using the in-house pipeline to extract the most prevalent variant in the dataset. MAIN OUTCOME MEASURES Most prevalent genetic variations associated with disease in the Saudi population. SAMPLE SIZE 1314 affected and unaffected individuals. RESULTS We identified 37 autosomal recessive variants and two heterozygous X-linked variants in 35 genes associated with the most prevalent disorders, which included hematologic (32%), endocrine (21%), metabolic (11%) and immunological (10%) diseases. CONCLUSION This study provides an update of the most frequently occurring alleles, which support future carrier screening programs. LIMITATIONS Single center that might represent the different regions but may be biased. In addition, most of the families included in the database are part of the proband's genetic identification for specific phenotypes. CONFLICT OF INTEREST None.
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Affiliation(s)
- Mariam Aleissa
- From the Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City.,From the Department of Molecular Genetics, Public Health Laboratory, Public Health Authority, Riyadh.,From the College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- From the Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Lamia Fahad Alsubaie
- From the Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Madawi Hassoun
- From the Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Ghada Abdulrahman
- From the Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Abdulrahman Swaid
- From the Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Wafa Al Eyaid
- From the Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Fuad Al Mutairi
- From the Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Faroug Ababneh
- From the Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Majid Alfadhel
- From the Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences
| | - Ahmed Alfares
- From the Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City.,From the King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences.,From the Department of Pediatrics, College of Medicine, Qassim University, Qassim
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5
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Althagafi A, Alsubaie L, Kathiresan N, Mineta K, Aloraini T, Al Mutairi F, Alfadhel M, Gojobori T, Alfares A, Hoehndorf R. DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning. Bioinformatics 2021; 38:1677-1684. [PMID: 34951628 PMCID: PMC8896633 DOI: 10.1093/bioinformatics/btab859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Structural genomic variants account for much of human variability and are involved in several diseases. Structural variants are complex and may affect coding regions of multiple genes, or affect the functions of genomic regions in different ways from single nucleotide variants. Interpreting the phenotypic consequences of structural variants relies on information about gene functions, haploinsufficiency or triplosensitivity and other genomic features. Phenotype-based methods to identifying variants that are involved in genetic diseases combine molecular features with prior knowledge about the phenotypic consequences of altering gene functions. While phenotype-based methods have been applied successfully to single nucleotide variants as well as short insertions and deletions, the complexity of structural variants makes it more challenging to link them to phenotypes. Furthermore, structural variants can affect a large number of coding regions, and phenotype information may not be available for all of them. RESULTS We developed DeepSVP, a computational method to prioritize structural variants involved in genetic diseases by combining genomic and gene functions information. We incorporate phenotypes linked to genes, functions of gene products, gene expression in individual cell types and anatomical sites of expression, and systematically relate them to their phenotypic consequences through ontologies and machine learning. DeepSVP significantly improves the success rate of finding causative variants in several benchmarks and can identify novel pathogenic structural variants in consanguineous families. AVAILABILITY AND IMPLEMENTATION https://github.com/bio-ontology-research-group/DeepSVP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Azza Althagafi
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia,Computer Science Department, College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Lamia Alsubaie
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia,Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | | | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia,King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Fuad Al Mutairi
- Genetics & Precision Medicine Department, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh, Saudi Arabia,King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Genetics & Precision Medicine Department, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh, Saudi Arabia,King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Takashi Gojobori
- KCBRC, Biological and Environmental Science and Engineering Division (BESE), KAUST, Thuwal, Saudi Arabia
| | - Ahmad Alfares
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia,King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh, Saudi Arabia,Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
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Aloraini T, Alsubaie L, Alasker S, Al Muitiri A, Alswaid A, Eyiad W, Al Mutairi F, Ababneh F, Alfadhel M, Alfares A. The rate of secondary genomic findings in the Saudi population. Am J Med Genet A 2021; 188:83-88. [PMID: 34515413 DOI: 10.1002/ajmg.a.62491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 06/28/2021] [Accepted: 08/18/2021] [Indexed: 11/09/2022]
Abstract
Secondary findings (SF) are defined as genetic conditions discovered unintentionally during an evaluation of raw data for another disease. We aimed to identify the rate of secondary genetic findings in the Saudi population in the 59 genes of the American College of Medical Genetics and Genomics (ACMG) list. In our study, the raw data of 1254 individuals, generated from exome sequencing for clinical purposes, were studied. Variants detected in the 59 genes on the ACMG list of secondary findings were investigated. Pathogenicity classifications were assigned to those variants based on the ACMG scoring system. We identified 2409 variants in the 59 gene list, 45 variants were classified as pathogenic/likely pathogenic variants according to the ACMG classification. The LDLR gene had the greatest number of pathogenic/likely pathogenic variants 12%. Cardiovascular genetic diseases had the highest frequency of disorders detected as secondary findings. In this study, the overall rate of positive cases identified with secondary findings in the Saudi population was 8%. The different in our current study and the previous studies in Saudi Arabia can be explained by the differences between the sequencing method, the criteria used for variant classification, the availability of newer evidence at the time of the publication, and the fact that we identified Saudi novel variants never reported in other populations.
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Affiliation(s)
- Taghrid Aloraini
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Lamia Alsubaie
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Sarah Alasker
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman Al Muitiri
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Alswaid
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Wafaa Eyiad
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Fuad Al Mutairi
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Farouq Ababneh
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Ahmed Alfares
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
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7
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Macken WL, Godwin A, Wheway G, Stals K, Nazlamova L, Ellard S, Alfares A, Aloraini T, AlSubaie L, Alfadhel M, Alajaji S, Wai HA, Self J, Douglas AGL, Kao AP, Guille M, Baralle D. Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly. Genome Med 2021; 13:34. [PMID: 33632302 PMCID: PMC7908744 DOI: 10.1186/s13073-021-00850-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as "coatopathies". METHODS Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1's splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2's missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2's mutation. RESULTS We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β'-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. CONCLUSIONS This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.
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Affiliation(s)
- William L Macken
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK
| | - Annie Godwin
- European Xenopus Resource Centre, University of Portsmouth School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Level 3 RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Liliya Nazlamova
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Level 3 RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- University of Exeter Medical School, RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Ahmed Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Lamia AlSubaie
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Sulaiman Alajaji
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Division of Allergy and Clinical Immunology, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Htoo A Wai
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Jay Self
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Alexander P Kao
- Zeiss Global Centre, School of Mechanical and Design Engineering, University of Portsmouth, Portsmouth, PO1 3DJ, UK
| | - Matthew Guille
- European Xenopus Resource Centre, University of Portsmouth School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK.
| | - Diana Baralle
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK.
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK.
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8
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Umair M, Ballow M, Asiri A, Alyafee Y, Al Tuwaijri A, Alhamoudi KM, Aloraini T, Abdelhakim M, Althagafi AT, Kafkas S, Alsubaie L, Alrifai MT, Hoehndorf R, Alfares A, Alfadhel M. EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay. Clin Genet 2020; 98:555-561. [PMID: 32869858 PMCID: PMC7756316 DOI: 10.1111/cge.13842] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022]
Abstract
In recent years, several genes have been implicated in the variable disease presentation of global developmental delay (GDD) and intellectual disability (ID). The endoplasmic reticulum membrane protein complex (EMC) family is known to be involved in GDD and ID. Homozygous variants of EMC1 are associated with GDD, scoliosis, and cerebellar atrophy, indicating the relevance of this pathway for neurogenetic disorders. EMC10 is a bone marrow‐derived angiogenic growth factor that plays an important role in infarct vascularization and promoting tissue repair. However, this gene has not been previously associated with human disease. Herein, we describe a Saudi family with two individuals segregating a recessive neurodevelopmental disorder. Both of the affected individuals showed mild ID, speech delay, and GDD. Whole‐exome sequencing (WES) and Sanger sequencing were performed to identify candidate genes. Further, to elucidate the functional effects of the variant, quantitative real‐time PCR (RT‐qPCR)‐based expression analysis was performed. WES revealed a homozygous splice acceptor site variant (c.679‐1G>A) in EMC10 (chromosome 19q13.33) that segregated perfectly within the family. RT‐qPCR showed a substantial decrease in the relative EMC10 gene expression in the patients, indicating the pathogenicity of the identified variant. For the first time in the literature, the EMC10 gene variant was associated with mild ID, speech delay, and GDD. Thus, this gene plays a key role in developmental milestones, with the potential to cause neurodevelopmental disorders in humans.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Mariam Ballow
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Abdulaziz Asiri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Kheloud M Alhamoudi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Marwa Abdelhakim
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Azza Thamer Althagafi
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Senay Kafkas
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lamia Alsubaie
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Muhammad Talal Alrifai
- Department of Pediatrics, Division of Neurology, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ahmed Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia
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9
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Alfares A, Alsubaie L, Aloraini T, Alaskar A, Althagafi A, Alahmad A, Rashid M, Alswaid A, Alothaim A, Eyaid W, Ababneh F, Albalwi M, Alotaibi R, Almutairi M, Altharawi N, Alsamer A, Abdelhakim M, Kafkas S, Mineta K, Cheung N, Abdallah AM, Büchmann-Møller S, Fukasawa Y, Zhao X, Rajan I, Hoehndorf R, Al Mutairi F, Gojobori T, Alfadhel M. What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations. BMC Med Genomics 2020; 13:103. [PMID: 32680510 PMCID: PMC7368798 DOI: 10.1186/s12920-020-00743-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/19/2020] [Indexed: 02/04/2023] Open
Abstract
Background Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases. Methods Three cohorts were used for this analysis: one cohort to assess the hit rate between solo, trio and trio plus testing, another cohort to examine the impact of the testing strategy of sibship genome vs trio-based analysis, and a third cohort to test the impact of an extended family analysis of up to eight family members to lower the number of candidate variants. Results The hit rates in solo, trio and trio plus testing were 39, 40, and 41%, respectively. The total number of candidate variants in the sibship testing strategy was 117 variants compared to 59 variants in the trio-based analysis. We noticed that the average number of coding candidate variants in trio-based analysis was 1192 variants and 26,454 noncoding variants, and this number was lowered by 50–75% after adding additional family members, with up to two coding and 66 noncoding homozygous variants only, in families with eight family members. Conclusion There was no difference in the hit rate between solo and extended family members. Trio-based analysis was a better approach than sibship testing, even in a consanguineous population. Finally, each additional family member helped to narrow down the number of variants by 50–75%. Our findings could help clinicians, researchers and testing laboratories select the most cost-effective and appropriate sequencing approach for their patients. Furthermore, using extended family analysis is a very useful tool for complex cases with novel genes.
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Affiliation(s)
- Ahmed Alfares
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia. .,Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia. .,Qassim University, Department of Pediatrics, Almulyda, Saudi Arabia.
| | - Lamia Alsubaie
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Aljoharah Alaskar
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Azza Althagafi
- Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ahmed Alahmad
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Mamoon Rashid
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Abdulrahman Alswaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ali Alothaim
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Wafaa Eyaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Faroug Ababneh
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Mohammed Albalwi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Raniah Alotaibi
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mashael Almutairi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Nouf Altharawi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alhanouf Alsamer
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Marwa Abdelhakim
- Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Senay Kafkas
- Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Katsuhiko Mineta
- Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Nicole Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Abdallah M Abdallah
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Stine Büchmann-Møller
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Xiang Zhao
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Issaac Rajan
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Robert Hoehndorf
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Fuad Al Mutairi
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Takashi Gojobori
- Biological and Environmental Science and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
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10
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Alsubaie L, Aloraini T, Amoudi M, Swaid A, Eyiad W, Al Mutairi F, Ababneh F, Alrifai MT, Baarmah D, Altwaijri W, Alotaibi N, Harthi A, Rumayyan A, Alanazi A, Qrimli M, Alfadhel M, Alfares A. Genomic testing and counseling: The contribution of next-generation sequencing to epilepsy genetics. Ann Hum Genet 2020; 84:431-436. [PMID: 32533790 DOI: 10.1111/ahg.12397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Currently, next-generation sequencing (NGS) technology is more accessible and available to detect the genetic causation of diseases. Though NGS technology benefited some clinical phenotypes, for some clinical diagnoses such as seizures and epileptic disorders, adaptation occurred slowly. The genetic diagnosis was mainly based on epilepsy gene panels and not on whole exome and/or genome sequencing. METHOD We retrospectively analyzed 420 index cases, referred for NGS over a period of 18 months, to investigate the challenges in diagnosing epilepsy. RESULT Of the 420 cases, 65 (15%) were referred due to epilepsy with one third having a positive family history. The result of the NGS was 14 positive cases (21.5%), 16 inconclusive cases (24%), and 35 (53%) negative cases. No gene has been detected twice in the inconclusive and positive groups. Comparative genomic hybridization has been performed for all 30 NGS negative cases and four cases with pathogenic variants (deletion in 15q11.213.1, deletion of 2p16.3, deletion in Xq22.1, and deletion in 17p13.3) were identified. CONCLUSION These findings have implications for our understanding of the approach to genetic testing and counseling of patients affected with seizures and epilepsy disorders. The overall diagnostic yield of exome/genome sequencing in our cohort was 23%. The main characteristic is genetic heterogeneity, supporting NGS technology as a suitable testing approach for seizures and epilepsy disorders. Genetic counseling for newly identified disease-causing variants depends on the pedigree interpretation, within the context of disease penetrance and variable expressivity.
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Affiliation(s)
- Lamia Alsubaie
- Department of Pediatrics, Division of Genetics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Lab Medicine, Division of Translational Pathology, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Manal Amoudi
- Department of Lab Medicine, Division of Translational Pathology, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman Swaid
- Department of Pediatrics, Division of Genetics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Wafaa Eyiad
- Department of Pediatrics, Division of Genetics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Fuad Al Mutairi
- Department of Pediatrics, Division of Genetics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Farouq Ababneh
- Department of Pediatrics, Division of Genetics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Muhammad Talal Alrifai
- Department of Pediatrics, Division of Neurology, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Duaa Baarmah
- Department of Pediatrics, Division of Neurology, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Waleed Altwaijri
- Department of Pediatrics, Division of Neurology, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Naser Alotaibi
- Department of Medicine, Division of Neurology, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ashraf Harthi
- Department of Medicine, Division of Neurology, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ahmad Rumayyan
- Department of Pediatrics, Division of Neurology, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ali Alanazi
- Department of Medicine, Division of Neurology, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mohammad Qrimli
- Department of Medicine, Division of Neurology, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Department of Pediatrics, Division of Genetics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ahmed Alfares
- Department of Lab Medicine, Division of Translational Pathology, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, Qassim University, Buraidah, Saudi Arabia
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11
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Alsubaie L, Alkhalaf R, Aloraini T, Amoudi M, Swaid A, Al Mutairi F, Alfadhel M, Eyaid W, Sewairi W, Alfares A. MEFV c.2230G>T p.(Ala744Ser) rs61732874 previously misclassified as pathogenic variant due to lack of a population specific database. Ann Hum Genet 2020; 84:370-379. [PMID: 32401353 DOI: 10.1111/ahg.12385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/17/2023]
Abstract
BACKGROUND Familial Mediterranean fever is a hereditary inflammatory disorder caused by variants in MEFV. c.2230G>T p.(Ala744Ser) rs61732874 is considered to be an established pathogenic variant in MEFV, but in this study we provide a complete evaluation that suggests this variant is likely benign. METHODS Using an in-house exome database from 924 individuals, we extracted all individuals harboring this variant for clinical, laboratory, and familial evaluation. RESULTS We identified the variant in 58 individuals from 39 families. The allele frequency of this variant in our database is 4.2%. None of the identified individuals match the diagnosis of Familial Mediterranean Fever. Using the American College of Medical Genetics and Genomics guidelines for variant classification, this variant is classified as likely benign and not pathogenic. CONCLUSION Conflicting evidence about variants creates challenges for testing laboratories and impacts patient care. Sharing information drawn mainly from underrepresented populations and clinical phenotyping are important tools for precise curation of genetic variants.
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Affiliation(s)
- Lamia Alsubaie
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Randa Alkhalaf
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Manal Amoudi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman Swaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Fuad Al Mutairi
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Wafaa Eyaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Wafaa Sewairi
- King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,Division of Rheumatology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmed Alfares
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
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12
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Alfares A, Aloraini T, subaie LA, Alissa A, Qudsi AA, Alahmad A, Mutairi FA, Alswaid A, Alothaim A, Eyaid W, Albalwi M, Alturki S, Alfadhel M. Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing. Genet Med 2018; 20:1328-1333. [DOI: 10.1038/gim.2018.41] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/05/2018] [Indexed: 12/31/2022] Open
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