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Abuzenadah A, Alganmi N, AlQurashi R, Hawsa E, AlOtibi A, Hummadi A, Nahari AA, AlZelaye S, Aljuhani NR, Al-Attas M, Abusamra H, Turkistany S, Karim S, Mirza Z, Al-Qahtani M, Chaudhary A, Al Eissa MM. Familial Screening for the Prevention of Rare Diseases: A Focus on Lipodystrophy in Southern Saudi Arabia. J Epidemiol Glob Health 2024; 14:162-168. [PMID: 38231342 PMCID: PMC11043304 DOI: 10.1007/s44197-023-00182-5] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Lipodystrophy is a relatively rare, complex disease characterised by a deficiency of adipose tissue and can present as either generalised lipodystrophy (GLD) or partial lipodystrophy (PLD). The prevalence of this disease varies by region. This study aimed to identify the genetic variations associated with lipodystrophy in the southern part of Saudi Arabia. METHODOLOGY We conducted a retrospective study by recruiting nine patients from six families, recruiting the proband whole exome sequencing results or any other genetic test results, screening other family members using Sanger sequencing and analysing the carrier status of the latter. These patients were recruited from the Endocrinology and Diabetes Clinic at Jazan General Hospital and East Jeddah Hospital, both in the Kingdom of Saudi Arabia. RESULT Eight patients were diagnosed with GLD, and one was diagnosed with PLD. Of the six families, four were consanguineously married from the same tribe, while the remaining belonged to the same clan. The majority of GLD patients had an AGPAT2 c.158del mutation, but some had a BSCL2 c.942dup mutation. The single PLD case had a PPARG c.1024C > T mutation but no family history of the disease. In all families evaluated in this study, some family members were confirmed to be carriers of the mutation observed in the corresponding patient. CONCLUSION Familial screening of relatives of patients with rare, autosomal recessive diseases, such as lipodystrophy, especially when there is a family history, allows the implementation of measures to prevent the onset or reduced severity of disease and reduces the chances of the pathogenic allele being passed onto future generations. Creating a national registry of patients with genetic diseases and carriers of familial pathogenic alleles will allow the assessment of preventive measures and accelerate disease intervention via gene therapy.
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Affiliation(s)
- Adel Abuzenadah
- Faculty of Applied Medical Sciences, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Nofe Alganmi
- Faculty of Applied Medical Sciences, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Computer Science Department, Faculty of Computing and Information Technology, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Raghad AlQurashi
- Molecular Genetics Laboratory, Public Health Laboratory, Public Health Authority, Riyadh, Saudi Arabia
| | - Esraa Hawsa
- Molecular Genetics Laboratory, Public Health Laboratory, Public Health Authority, Riyadh, Saudi Arabia
| | - Abdullah AlOtibi
- Molecular Genetics Laboratory, Public Health Laboratory, Public Health Authority, Riyadh, Saudi Arabia
| | - Abdulrahman Hummadi
- Jazan Endocrinology and Diabetes Center, Ministry of Health, Jazan, Saudi Arabia
| | - Ahmed Ali Nahari
- Jazan Endocrinology and Diabetes Center, Ministry of Health, Jazan, Saudi Arabia
- Pediatric Department, King Fahd Hospital, Jazan, Saudi Arabia
| | - Somaya AlZelaye
- Centre of Endocrinology and Diabetes Mellitus, Al-Qunfudah General Hospital, Al-Qunfudah, Makkah Province, Saudi Arabia
| | - Nasser R Aljuhani
- Department of Medicine Endocrinology and Diabetes, East Jeddah Hospital, Jeddah, Saudi Arabia
| | - Manal Al-Attas
- Faculty of Applied Medical Sciences, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Heba Abusamra
- Faculty of Applied Medical Sciences, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Shereen Turkistany
- Center of Innovation in Personalized Medicine, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Faculty of Applied Medical Sciences, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Mohammed Al-Qahtani
- Faculty of Applied Medical Sciences, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Adeel Chaudhary
- Faculty of Applied Medical Sciences, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Mariam M Al Eissa
- Molecular Genetics Laboratory, Public Health Laboratory, Public Health Authority, Riyadh, Saudi Arabia.
- Medical School, AlFaisal University, Riyadh, Saudi Arabia.
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Al Eissa MM, Almsned F, AlQurashi R, Alsanosi SM, Alshanberi AM, Saleh N, Alsaieedi AA, Alkharji RR, Halawani AJ. Perceptions of Saudis Toward Participating in the COVID-19 Convalescent Plasma Clinical Trial. Cureus 2023; 15:e48879. [PMID: 38106720 PMCID: PMC10724773 DOI: 10.7759/cureus.48879] [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] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction The COVID-19 pandemic has been a major public health and economic issue worldwide. Even though vaccines have been developed to reduce the spread of the infection, treating patients remains a significant challenge. This study aims to measure the perceptions of Saudis toward participating in the COVID-19 Convalescent Plasma Clinical Trial. Method A cross-sectional study measuring the perceptions of Saudis toward participating in the COVID-19 Convalescent Plasma Clinical Trial was conducted with participants who had recovered from COVID-19. The study used an online questionnaire covering variables related to demographics, awareness, attitudes, perceptions, and plans for improvement. Results A sample of 1,051 participants participated in the questionnaire. A total of 85% had recovered from COVID-19, only 2.76% had participated in clinical trials before, and 83.44% would participate if they were advised or knew about them. The participants showed a high level of education, with 88% having obtained a degree and most used social media. The results can be biased toward the participants who get their knowledge from social media and hope to learn about things on social media. The gap in knowledge about clinical trials among the participants indicated that certain age groups could be targeted through channels where they communicate the most. Conclusion Engaging the community in clinical trials and educating others about their value by sharing experiences would help promote clinical trials and activate donations.
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Affiliation(s)
- Mariam M Al Eissa
- Medical School, Alfaisal University, Riyadh, SAU
- Molecular Genetics, Public Health Authority, Public health Lab, Riyadh, SAU
| | - Fahad Almsned
- Epidemiology and Public Health, King Fahad Specialist Hospital, Research Centre, Dammam, SAU
- Research and Development, NovoGenomics, Riyadh, SAU
| | - Raghad AlQurashi
- Molecular Genetics, Public Health Lab, Public Health Authority, Riyadh, SAU
| | - Safaa M Alsanosi
- Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Makkah, SAU
- Cardiovascular and Metabolic Health, University of Glasgow, BHF Glasgow Cardiovascular Research Centre, Glasgow, GBR
| | - Asim M Alshanberi
- Community Medicine, Faculty of Medicine, Umm Alqura University, Makkah, SAU
- General Medicine Practice, Batterjee Medical College, Jeddah, SAU
| | - Nada Saleh
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, SAU
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Riyadh, SAU
| | - Ahdab A Alsaieedi
- Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, SAU
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, SAU
| | - Reem R Alkharji
- Research, Princess Nourah Bint Abdulrahman University Health Sciences, Research Centre, Riyadh, SAU
| | - Amr J Halawani
- Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, SAU
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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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Al Eissa MM, Sharp SI, O’ Brien NL, Fiorentino A, Bass NJ, Curtis D, McQuillin A. Genetic association and functional characterization of MCPH1 gene variation in bipolar disorder and schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2019; 180:258-265. [PMID: 30859703 PMCID: PMC8005923 DOI: 10.1002/ajmg.b.32722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/10/2018] [Accepted: 01/08/2019] [Indexed: 12/12/2022]
Abstract
A rare microcephalin 1 gene (MCPH1) variant rs61749465A>G (p.Asp61Gly) with prior evidence for association with schizophrenia (p = 3.78 × 10-7 ) was tested for association in 2,300 bipolar disorder (BPD) participants, 1,930 SCZ participants and 1,820 normal comparison subjects. We report evidence for association of rs61749465A>G with BPD (p = 0.0009). rs61749465 is located in the N-terminal of the BRCT1 domain of MCPH1. Bioinformatic analysis predicted the Asp61Gly substitution to be damaging to MCPH1 function. A second MCPH1 BRCT1 domain variant (rs199422124C>G; p.Thr27Arg), reported to cause autosomal recessive microcephaly, was not detected in the participants tested here. We sought to characterize the functional effects of these variants on MCPH1 function. Cell count assays indicated that rs199422124 allele G had a greater impact on cell survival compared to the G allele of rs61749465. Gene expression analysis combined with gene network and pathway analysis indicated that rs61749465 allele G may impact protein translation and cell cycle control. The evidence for association between rs61749465A>G and psychosis in both BPD and SCZ warrants further replication. Likewise, the data from the functional analyses point to molecular mechanisms that may underlie the proposed MCPH1 mediated risk of psychosis and pathogenesis in autosomal recessive microcephaly require additional experimental validation.
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Affiliation(s)
- Mariam M Al Eissa
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, Rockefeller Building, 21 University Street, London WC1E 6BT, UK
| | - Sally I Sharp
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, Rockefeller Building, 21 University Street, London WC1E 6BT, UK
| | - Niamh L O’ Brien
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, Rockefeller Building, 21 University Street, London WC1E 6BT, UK
| | - Alessia Fiorentino
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, Rockefeller Building, 21 University Street, London WC1E 6BT, UK
| | - Nicholas J Bass
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, Rockefeller Building, 21 University Street, London WC1E 6BT, UK
| | - David Curtis
- UCL Genetics Institute, UCL, Darwin Building, Gower Street, London, WC1E, 6BT, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, Rockefeller Building, 21 University Street, London WC1E 6BT, UK
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Al Eissa MM, Fiorentino A, Sharp SI, O'Brien NL, Wolfe K, Giaroli G, Curtis D, Bass NJ, McQuillin A. Exome sequence analysis and follow up genotyping implicates rare ULK1 variants to be involved in susceptibility to schizophrenia. Ann Hum Genet 2017; 82:88-92. [PMID: 29148569 PMCID: PMC5813151 DOI: 10.1111/ahg.12226] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/18/2017] [Accepted: 09/22/2017] [Indexed: 01/31/2023]
Abstract
Schizophrenia (SCZ) is a severe, highly heritable psychiatric disorder. Elucidation of the genetic architecture of the disorder will facilitate greater understanding of the altered underlying neurobiological mechanisms. The aim of this study was to identify likely aetiological variants in subjects affected with SCZ. Exome sequence data from a SCZ cas–control sample from Sweden was analysed for likely aetiological variants using a weighted burden test. Suggestive evidence implicated the UNC‐51‐like kinase (ULK1) gene, and it was observed that four rare variants that were more common in the Swedish SCZ cases were also more common in UK10K SCZ cases, as compared to obesity cases. These three missense variants and one intronic variant were genotyped in the University College London cohort of 1304 SCZ cases and 1348 ethnically matched controls. All four variants were more common in the SCZ cases than controls and combining them produced a result significant at P = 0.02. The results presented here demonstrate the importance of following up exome sequencing studies using additional datasets. The roles of ULK1 in autophagy and mTOR signalling strengthen the case that these pathways may be important in the pathophysiology of SCZ. The findings reported here await independent replication.
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Affiliation(s)
- Mariam M Al Eissa
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Alessia Fiorentino
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK.,Current address: Institute of Opthalmology, University College London, London, UK
| | - Sally I Sharp
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Niamh L O'Brien
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Kate Wolfe
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Giovanni Giaroli
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - David Curtis
- University College London Genetics Institute, University College London, London, UK
| | - Nicholas J Bass
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
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Leonenko G, Richards AL, Walters JT, Pocklington A, Chambert K, Al Eissa MM, Sharp SI, O'Brien NL, Curtis D, Bass NJ, McQuillin A, Hultman C, Moran JL, McCarroll SA, Sklar P, Neale BM, Holmans PA, Owen MJ, Sullivan PF, O'Donovan MC. Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2017; 174:724-731. [PMID: 28719003 PMCID: PMC5669020 DOI: 10.1002/ajmg.b.32560] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/19/2017] [Indexed: 12/24/2022]
Abstract
Risk of schizophrenia is conferred by alleles occurring across the full spectrum of frequencies from common SNPs of weak effect through to ultra rare alleles, some of which may be moderately to highly penetrant. Previous studies have suggested that some of the risk of schizophrenia is attributable to uncommon alleles represented on Illumina exome arrays. Here, we present the largest study of exomic variation in schizophrenia to date, using samples from the United Kingdom and Sweden (10,011 schizophrenia cases and 13,791 controls). Single variants, genes, and gene sets were analyzed for association with schizophrenia. No single variant or gene reached genome-wide significance. Among candidate gene sets, we found significant enrichment for rare alleles (minor allele frequency [MAF] < 0.001) in genes intolerant of loss-of-function (LoF) variation and in genes whose messenger RNAs bind to fragile X mental retardation protein (FMRP). We further delineate the genetic architecture of schizophrenia by excluding a role for uncommon exomic variants (0.01 ≤ MAF ≥ 0.001) that confer a relatively large effect (odds ratio [OR] > 4). We also show risk alleles within this frequency range exist, but confer smaller effects and should be identified by larger studies.
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Affiliation(s)
- Ganna Leonenko
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Alexander L. Richards
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - James T. Walters
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Andrew Pocklington
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Kimberly Chambert
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts
| | - Mariam M. Al Eissa
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | - Sally I. Sharp
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | - Niamh L. O'Brien
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | | | - Nicholas J. Bass
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | - Andrew McQuillin
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | - Christina Hultman
- Department of Medical Epidemiology and BiostatisticsKarolinska InstituteStockholmSweden
| | - Jennifer L. Moran
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts
| | - Steven A. McCarroll
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts
- Department of GeneticsHarvard Medical SchoolBostonMassachusetts
| | - Pamela Sklar
- Icahn School of Medicine at Mount SinaiNew YorkNew York
| | - Benjamin M. Neale
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts
- Analytical and Translational Genetics UnitMassachusetts General HospitalBostonMassachusetts
| | - Peter A. Holmans
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Michael J. Owen
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and BiostatisticsKarolinska InstituteStockholmSweden
- Departments of Genetics and PsychiatryUniversity of North CarolinaChapel HillNorth Carolina
| | - Michael C. O'Donovan
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
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