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Rabea F, El Naofal M, Chekroun I, Khalaf M, Zaabi NA, AlZaabi K, ElHalik M, Dash S, El Saba Y, Ali A, Abraham S, Fathi K, Shekhy J, Aswad SG, Elbashir H, Alkuraya F, Loney T, Alsheikh-Ali A, Khayat AA, Abou Tayoun A. Spinal muscular atrophy genetic epidemiology and the case for premarital genomic screening in Arab populations. COMMUNICATIONS MEDICINE 2024; 4:119. [PMID: 38879606 PMCID: PMC11180197 DOI: 10.1038/s43856-024-00548-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/07/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a fatal autosomal recessive disorder for which several treatment options, including a gene therapy, have become available. SMA incidence has not been well-characterized in most Arab countries where rates of consanguinity are high. Understanding SMA disease epidemiology has important implications for screening, prevention, and treatment in those populations. METHODS We perform SMA diagnostic testing in a clinical multi-national patient cohort (N = 171) referred for hypotonia and/or muscle weakness. In addition, we carry out genetic newborn screening for SMA on 1502 healthy Emirati newborns to estimate the carrier frequency and incidence of the disease in the United Arab Emirates. RESULTS Patients referred for SMA genetic testing are mostly Arabs (82%) representing 18 countries. The overall diagnostic yield is 33.9%, which is higher (>50%) for certain nationalities. Most patients (71%) has two SMN2 copies and earlier disease onset. For the first time, we estimate SMA carrier frequency (1.3%) and incidence of the disease (1 in 7122 live births) in the United Arab Emirates. Using birth and marriage rates in two Arab populations (United Arab Emirates and Saudi Arabia), as well as disease incidence in both countries, we show that, besides preventing new cases, premarital genetic screening could potentially result in around $8 to $324 million annual cost savings, respectively, relative to postnatal treatment. CONCLUSIONS The SMA carrier frequency and incidence we document suggests high potential benefit for universal implementation of premarital genomic screening for a wide range of recessive disorders in Arab populations.
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Affiliation(s)
- Fatma Rabea
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Maha El Naofal
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Ikram Chekroun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Mona Khalaf
- Neonatology Department, Al Qassimi Women's & Children's Hospital, Emirates Health Services, Sharjah, UAE
| | - Nuha Al Zaabi
- Pediatric Department, Fujairah Hospital, Emirates Health Services, Fujairah, UAE
| | - Khawla AlZaabi
- Pediatric Department, Kalba Hospital, Emirates Health Services, Sharjah, UAE
| | - Mahmoud ElHalik
- Neonatal Section, Latifa Women & Children Hospital, Dubai Health, Dubai, UAE
| | - Swarup Dash
- Neonatal Section, Latifa Women & Children Hospital, Dubai Health, Dubai, UAE
| | - Yaser El Saba
- Department of Neonatology, Dubai Hospital, Dubai Health, Dubai, UAE
| | - Azhari Ali
- Neonatology Department, Umm Al Quwain Hospital, Emirates Health Services, Umm Al Quwain, UAE
| | - Smitha Abraham
- Department of Neonatology, Abdullah Bin Omran Hospital, Emirates Health Services, Ras Al Khaimah, UAE
| | - Khansa Fathi
- Neonatology Department, Al Dhaid Hospital, Emirates Health Services, Sharjah, UAE
| | - Jwan Shekhy
- Neonatology Department, Khorfakkan Hospital, Emirates Health Services, Sharjah, UAE
| | - Saad G Aswad
- General-Obs/Gyno Clinic, Tawam Hospital, Al Ain City, Abu Dhabi, UAE
| | - Haitham Elbashir
- Neurosceince Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Fowzan Alkuraya
- Departement of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | | | - Ahmad Abou Tayoun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE.
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Milibari D, Nowilaty SR, Ba-Abbad R. The Clinical and Mutational Spectrum of Bardet-Biedl Syndrome in Saudi Arabia. Genes (Basel) 2024; 15:762. [PMID: 38927698 PMCID: PMC11202873 DOI: 10.3390/genes15060762] [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: 04/11/2024] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The retinal features of Bardet-Biedl syndrome (BBS) are insufficiently characterized in Arab populations. This retrospective study investigated the retinal features and genotypes of BBS in Saudi patients managed at a single tertiary eye care center. Data analysis of the identified 46 individuals from 31 families included visual acuity (VA), systemic manifestations, multimodal retinal imaging, electroretinography (ERG), family pedigrees, and genotypes. Patients were classified to have cone-rod, rod-cone, or generalized photoreceptor dystrophy based on the pattern of macular involvement on the retinal imaging. Results showed that nyctalopia and subnormal VA were the most common symptoms with 76% having VA ≤ 20/200 at the last visit (age: 5-35). Systemic features included obesity 91%, polydactyly 56.5%, and severe cognitive impairment 33%. The predominant retinal phenotype was cone-rod dystrophy 75%, 10% had rod-cone dystrophy and 15% had generalized photoreceptor dystrophy. ERGs were undetectable in 95% of patients. Among the 31 probands, 61% had biallelic variants in BBSome complex genes, 32% in chaperonin complex genes, and 6% had biallelic variants in ARL6; including six previously unreported variants. Interfamilial and intrafamilial variabilities were noted, without a clear genotype-phenotype correlation. Most BBS patients had advanced retinopathy and were legally blind by early adulthood, indicating a narrow therapeutic window for rescue strategies.
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Affiliation(s)
- Doaa Milibari
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh 12211, Saudi Arabia; (D.M.); (S.R.N.)
- Department of Ophthalmology, King Abdullah Medical City, Makkah 24211, Saudi Arabia
| | - Sawsan R. Nowilaty
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh 12211, Saudi Arabia; (D.M.); (S.R.N.)
| | - Rola Ba-Abbad
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh 12211, Saudi Arabia; (D.M.); (S.R.N.)
- Ocular Genetics Services, King Khaled Eye Specialist Hospital, Riyadh 12211, Saudi Arabia
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3
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Marafi D. Founder mutations and rare disease in the Arab world. Dis Model Mech 2024; 17:dmm050715. [PMID: 38922202 PMCID: PMC11225585 DOI: 10.1242/dmm.050715] [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] [Indexed: 06/27/2024] Open
Abstract
Founder mutations are disease-causing variants that occur frequently in geographically or culturally isolated groups whose shared ancestor(s) carried the pathogenic variant. While some disease alleles may vanish from the genetic pool due to natural selection, variants with weaker effects may survive for a long time, thereby enhancing the prevalence of some rare diseases. These are predominantly autosomal recessive diseases but can also be autosomal dominant traits with late-onset or mild phenotypes. Cultural practices, such as endogamy and consanguinity, in these isolated groups lead to higher prevalence of such rare diseases compared to the rest of the population and worldwide. In this Perspective, we define population isolates and the underlying genetic mechanisms for accumulating founder mutations. We also discuss the current and potential scientific, clinical and public-health implications of studying founder mutations in population isolates around the world, with a particular focus on the Arab population.
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Affiliation(s)
- Dana Marafi
- Department of Pediatrics, College of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
- Section of Child Neurology, Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya 52700, Kuwait
- Kuwait Medical Genetics Centre, Ministry of Health, Sulaibikhat 80901, Kuwait
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Al-Saei O, Malka S, Owen N, Aliyev E, Vempalli FR, Ocieczek P, Al-Khathlan B, Fakhro K, Moosajee M. Increasing the diagnostic yield of childhood glaucoma cases recruited into the 100,000 Genomes Project. BMC Genomics 2024; 25:484. [PMID: 38755526 PMCID: PMC11097485 DOI: 10.1186/s12864-024-10353-8] [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: 12/22/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Childhood glaucoma (CG) encompasses a heterogeneous group of genetic eye disorders that is responsible for approximately 5% of childhood blindness worldwide. Understanding the molecular aetiology is key to improving diagnosis, prognosis and unlocking the potential for optimising clinical management. In this study, we investigated 86 CG cases from 78 unrelated families of diverse ethnic backgrounds, recruited into the Genomics England 100,000 Genomes Project (GE100KGP) rare disease cohort, to improve the genetic diagnostic yield. Using the Genomics England/Genomic Medicine Centres (GE/GMC) diagnostic pipeline, 13 unrelated families were solved (13/78, 17%). Further interrogation using an expanded gene panel yielded a molecular diagnosis in 7 more unrelated families (7/78, 9%). This analysis effectively raises the total number of solved CG families in the GE100KGP to 26% (20/78 families). Twenty-five percent (5/20) of the solved families had primary congenital glaucoma (PCG), while 75% (15/20) had secondary CG; 53% of this group had non-acquired ocular anomalies (including iris hypoplasia, megalocornea, ectopia pupillae, retinal dystrophy, and refractive errors) and 47% had non-acquired systemic diseases such as cardiac abnormalities, hearing impairment, and developmental delay. CYP1B1 was the most frequently implicated gene, accounting for 55% (11/20) of the solved families. We identified two novel likely pathogenic variants in the TEK gene, in addition to one novel pathogenic copy number variant (CNV) in FOXC1. Variants that passed undetected in the GE100KGP diagnostic pipeline were likely due to limitations of the tiering process, the use of smaller gene panels during analysis, and the prioritisation of coding SNVs and indels over larger structural variants, CNVs, and non-coding variants.
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Affiliation(s)
- Omayma Al-Saei
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Samantha Malka
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Nicholas Owen
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | | | - Paulina Ocieczek
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | | | - Khalid Fakhro
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
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Goljan E, Abouelhoda M, Tahir A, ElKalioby M, Meyer B, Monies D. Large-scale next generation sequencing based analysis of SLCO1B1 pharmacogenetics variants in the Saudi population. Hum Genomics 2024; 18:30. [PMID: 38523294 PMCID: PMC10962151 DOI: 10.1186/s40246-024-00594-9] [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: 10/12/2023] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND SLCO1B1 plays an important role in mediating hepatic clearance of many different drugs including statins, angiotensin-converting enzyme inhibitors, chemotherapeutic agents and antibiotics. Several variants in SLCO1B1 have been shown to have a clinically significant impact, in relation to efficacy of these medications. This study provides a comprehensive overview of SLCO1B1 variation in Saudi individuals, one of the largest Arab populations in the Middle East. METHODS The dataset of 11,889 (9,961 exomes and 1,928 pharmacogenetic gene panel) Saudi nationals, was used to determine the presence and frequencies of SLCO1B1 variants, as described by the Clinical Pharmacogenetic Implementation Consortium (CPIC). RESULTS We identified 141 previously described SNPs, of which rs2306283 (50%) and rs4149056 (28%), were the most common. In addition, we observed six alleles [*15 (24.7%) followed by *20 (8.04%), *14 (5.86%), *5 (3.84%), *31 (0.21%) and *9 (0.03%)] predicted to be clinically actionable. Allele diplotype to phenotype conversion revealed 41 OATP1B1 diplotypes. We estimated the burden of rare, and novel predicted deleterious variants, resulting from 17 such alterations. CONCLUSIONS The data we present, from one of the largest Arab cohorts studied to date, provides the most comprehensive overview of SLCO1B1 variants, and the subsequent OATP1B1 activity of this ethnic group, which thus far remains relatively underrepresented in available international genomic databases. We believe that the presented data provides a basis for further clinical investigations and the application of personalized statin drug therapy guidance in Arabs.
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Affiliation(s)
- Ewa Goljan
- Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Mohammed Abouelhoda
- Computational Biosciences, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Asma Tahir
- Computational Biosciences, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohamed ElKalioby
- Computational Biosciences, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Brian Meyer
- Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Dorota Monies
- Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia.
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Binobaid L, As Sobeai HM, Alhazzani K, AlAbdi L, Alwazae MM, Alotaibi M, Parrington J, Alhoshani A. Whole-exome sequencing identifies cancer-associated variants of the endo-lysosomal ion transport channels in the Saudi population. Saudi Pharm J 2024; 32:101961. [PMID: 38313820 PMCID: PMC10832475 DOI: 10.1016/j.jsps.2024.101961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024] Open
Abstract
Background Although national efforts are underway to document the genomic variability of the Saudi population relative to other populations, such variability remains largely unexplored. Genetic variability is known to impact the fate of cells and increase or decrease the risk of a variety of complex diseases including cancer forms. Therefore, the identification of variants associated with cancer susceptibility in Saudi population may protect individuals from cancer or aid in patient-tailored therapies. The endo-lysosomal ion transport genes responsible for cationic ion homeostasis within the cell. We screened 703 single-nucleotide polymorphisms (SNPs) of the endo-lysosomal ion transporter genes in the Saudi population and identified cancer-associated variants that have been reported in other populations. Methods Utilizing previously derived local data of Whole-Exome Sequencing (WES), we examined SNPs of TPCN1, TPCN2, P2RX4, TRPM7, TRPV4, TRPV4, and TRPV6 genes. The SNPs were identified for those genes by our in-house database. We predicted the pathogenicity of these variants using in silico tools CADD, Polyphen-2, SIFT, PrimateAI, and FATHMM-XF. Then, we validated our findings by exploring the genetics database (VarSome, dbSNP NCB, OMIM, ClinVar, Ensembl, and GWAS Catalog) to further link cancer risk. Results The WES database yielded 703 SNPs found in TPCN2, P2RX4, TRPM7, TRPV4, and TRPV6 genes in 1,144 subjects. The number of variants that were found to be common in our population was 150 SNPs. We identified 13 coding-region non-synonymous variants of the endo-lysosomal genes that were most common with a minor allele frequency (MAF) of ≥ 1 %. Twelve of these variants are rs2376558, rs3750965, rs61746574, rs35264875, rs3829241, rs72928978, rs25644, rs8042919, rs17881456, rs4987682, rs4987667, and rs4987657 that were classified as cancer-associated genes. Conclusion Our study highlighted cancer-associated SNPs in the endo-lysosomal genes among Saudi individuals. The allelic frequencies on polymorphic variants confer susceptibility to complex diseases that are comparable to other populations. There is currently insufficient clinical data supporting the link between these SNPs and cancer risk in the Saudi population. Our data argues for initiating future cohort studies in which individuals with the identified SNPs are monitored and assessed for their likelihood of developing malignancies and therapy outcomes.
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Affiliation(s)
- Lama Binobaid
- Dept. of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11454, Saudi Arabia
| | - Homood M. As Sobeai
- Dept. of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11454, Saudi Arabia
| | - Khalid Alhazzani
- Dept. of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11454, Saudi Arabia
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2457, Riyadh 11454, Saudi Arabia
| | - Meshari M. Alwazae
- Computational Sciences Department, Center of Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Moureq Alotaibi
- Dept. of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11454, Saudi Arabia
| | - John Parrington
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, United Kingdom
| | - Ali Alhoshani
- Dept. of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11454, Saudi Arabia
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Muthaffar OY, Abdulkareem AA, Ashi A, Naseer MI. A novel homozygous splice donor variant in the LRPPRC gene causing Leigh syndrome with epilepsy, a French-Canadian disorder in a Saudi family: case report. Front Pediatr 2023; 11:1288542. [PMID: 38046674 PMCID: PMC10690952 DOI: 10.3389/fped.2023.1288542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/24/2023] [Indexed: 12/05/2023] Open
Abstract
Background The mitochondria are a cellular power house. Tissues are involved in frequent energy consumption, and any failure or irregularity in the continuous energy production could lead to abnormalities. The leucine-rich pentatricopeptide repeat (LRPPRC) gene is one of the mitochondrial-related functions genes; variations in these genes are responsible for complex phenotypes that affect many organs such as the brain, liver, and muscles. Materials and methods This study enrolled a family with Leigh syndrome-like phenotype. The molecular diagnosis was conducted by first performing whole exome sequencing (WES), followed by Sanger sequencing. Results A novel splice-site variant (c.469 + 2T > A) at the exon-intron boundary in the LRPPRC gene was identified using the WES data analysis. Sanger validation confirmed the autosomal recessive inheritance of the identified variant. Based on the ACMG criteria for variant classification, PVS1 and PM2 suggest that the identified variant in the LRPPRC gene is likely to be pathogenic. Conclusion To the best of our knowledge, there have been no previous reports of this variant in the LRPPRC gene. Our research not only identifies a novel variant in the LRPPRC gene, but also confirms the unresolved molecular diagnosis of the family. WES can be used as a first-line diagnostic tool in familial cases, particularly in those cases when detailed clinical phenotyping is not possible. Once the molecular diagnosis is confirmed in a family, it is necessary to conduct a thorough re-evaluation of the patients' specific clinical phenotypes in order to establish a clear genotype-phenotype correlation.
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Affiliation(s)
- Osama Y. Muthaffar
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Angham Abdulrhman Abdulkareem
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abrar Ashi
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Alqahtani MA, Al-Qahtani SM, Al-Falki YH, Alharby E, Albulym OM, Almontashiri NAM. Biallelic loss of function variant in ZNF808 is associated with non-syndromic neonatal diabetes. Clin Genet 2023; 104:497-498. [PMID: 37308312 DOI: 10.1111/cge.14389] [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: 04/25/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/14/2023]
Abstract
A Loss-of-function variant in ZNF808 is associated with non-syndromic neonatal diabetes in a consanguineous family with three affected siblings.
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Affiliation(s)
| | - Saleh M Al-Qahtani
- Department of Child Health, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Yahya H Al-Falki
- Ophthalmology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Essa Alharby
- Center for Genetics and Inherited Diseases, Taibah University, Al Madinah Al Munawwarah, Saudi Arabia
| | | | - Naif A M Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, Al Madinah Al Munawwarah, Saudi Arabia
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9
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Wang J, Li S, Jiang Y, Wang Y, Ouyang J, Yi Z, Sun W, Jia X, Xiao X, Wang P, Zhang Q. Pathogenic Variants in CEP290 or IQCB1 Cause Earlier-Onset Retinopathy in Senior-Loken Syndrome Compared to Those in INVS, NPHP3, or NPHP4. Am J Ophthalmol 2023; 252:188-204. [PMID: 36990420 DOI: 10.1016/j.ajo.2023.03.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE Senior-Loken syndrome (SLSN) is an autosomal recessive disorder characterized by retinopathy and nephronophthisis. This study aimed to evaluate whether different phenotypes are associated with different variants or subsets of 10 SLSN-associated genes based on an in-house data set and a literature review. DESIGN Retrospective case series. METHODS Patients with biallelic variants in SLSN-associated genes, including NPHP1, INVS, NPHP3, NPHP4, IQCB1, CEP290, SDCCAG8, WDR19, CEP164, and TRAF3IP1, were recruited. Ocular phenotypes and nephrology medical records were collected for comprehensive analysis. RESULTS Variants in 5 genes were identified in 74 patients from 70 unrelated families, including CEP290 (61.4%), IQCB1 (28.6%), NPHP1 (4.2%), NPHP4 (2.9%), and WDR19 (2.9%). The median age at the onset of retinopathy was approximately 1 month (since birth). Nystagmus was the most common initial sign in patients with CEP290 (28 of 44, 63.6%) or IQCB1 (19 of 22, 86.4%) variants. Cone and rod responses were extinguished in 53 of 55 patients (96.4%). Characteristic fundus changes were observed in CEP290- and IQCB1-associated patients. During follow-up, 70 of the 74 patients were referred to nephrology, among whom nephronophthisis was not detected in 62 patients (88.6%) at a median age of 6 years but presented in 8 patients (11.4%) aged approximately 9 years. CONCLUSIONS Patients with pathogenic variants in CEP290 or IQCB1 presented early with retinopathy, whereas other patients with INVS, NPHP3, or NPHP4 variants first developed nephropathy. Therefore, awareness of the genetic and clinical features may facilitate the clinical management of SLSN, especially early intervention of kidney problems for patients with eyes affected first.
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Affiliation(s)
- Junwen Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Shiqiang Li
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yi Jiang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yingwei Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jiamin Ouyang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zhen Yi
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Wenmin Sun
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xiaoyun Jia
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xueshan Xiao
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Panfeng Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Qingjiong Zhang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China.
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10
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Almahmoud R, Mekki M, El-Hattab AW. Cerebral folate deficiency: A report of two affected siblings. Mol Genet Metab Rep 2023; 35:100975. [PMID: 37101857 PMCID: PMC10123369 DOI: 10.1016/j.ymgmr.2023.100975] [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: 03/08/2023] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023] Open
Abstract
Cerebral folate deficiency (CFD) is a rare progressive neurological condition characterized by normal blood folate level and low 5-methyltetrahydrofolate (5-MTHF) levels in the cerebrospinal fluid. Patients present with different neurological findings including hypotonia and microcephaly. Later, patients develop ataxia, seizures, para or quadri-plagia. Herein, we report two siblings; born to consanguineous parents; who had normal neurological development in early childhood. Subsequently they developed drug-resistant seizures, neurological regression, and spastic quadriplegia. After thorough investigations patients had brain MRI which showed abnormal white matter signals and ventricular dilatation, CSF with low 5-MTHF, and whole exome sequencing (WES) revealed a novel homozygous variant in FOLR1 (c.245A > G; p.Tyr82Cys) consistent with the diagnosis of cerebral folate deficiency. They were treated with folinic acid in addition to standard anti-seizure medications. WES aids in reaching CFD diagnosis due to FOLR1 pathogenic variants. These results can be used for future counselling to prevent recurrence in future pregnancies by preimplantation genetic testing prior to implanting the embryo in the uterus. Treatment with folinic acid was shown to improve the neurological symptoms namely reduced the seizures and spasticity.
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Affiliation(s)
- Rabah Almahmoud
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Corresponding author at: College of Medicine, University of Sharjah, PO BOX 27272, Sharjah, United Arab Emirates.
| | - Mohammed Mekki
- Department of Pediatrics, AlQassimi Women and Children Hospital, Sharjah, United Arab Emirates
| | - Ayman W. El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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Alsini H, Alghamdi A, Alshafi S, Hundallah K, Almehmadi S, Alsowat D, Al-Yamani S, Almuzaini H, Alwadie A, Al-Otaibi A, Jad L, Almadhi A, Bashiri F, Kentab A, Hamad MH, Baarmah D, Alrifaie M, Almuqbel M, Baradie RA, Meer A, Jan M, Muthaffar O, Aljabri M, Ali E, Saeed M, Matar A, Tabarki B. Developmental and/or epileptic encephalopathy with spike-and-wave activation in sleep in Saudi Arabia: Electroclinical, etiologic, genetic, and outcome multicenter study. Seizure 2023; 107:146-154. [PMID: 37062196 DOI: 10.1016/j.seizure.2023.04.013] [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: 01/12/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/18/2023] Open
Abstract
OBJECTIVES To investigate the clinical features of developmental and/or epileptic encephalopathy with spike-and-wave activation in sleep (D/EE-SWAS), its electrographic characteristics, and etiology and to compare the effects of different treatment strategies on the outcomes using a Saudi Arabian database. METHODS This multicenter study included children with D/EE-SWAS who were evaluated between 2010 and 2020 at 11 tertiary centers. Data were collected on their baseline clinical features, etiologies, and treatment modalities. Seizure reduction, spike-wave index, and cognitive state were examined as potential therapeutic outcomes. RESULTS Ninety-one children were diagnosed with D/EE-SWAS, with a median age of 7 years (IQR: 3-5) and an almost equal sex distribution. The average age at which epilepsy was diagnosed was 3 years (IQR: 5-2). A genetic/metabolic etiology was found in 35.1% of the patients, and a structural etiology was found in 27.4%. Children with underlying genetic/metabolic diseases exhibited an earlier seizure onset (P = 0.001) than children with other etiologies. Benzodiazepines (76.6%) were the most common treatment, followed by steroids (51.9%). Sodium valproate (75%) was the most frequently used antiseizure medication, followed by levetiracetam (64.9%). Children with a later seizure onset were more likely to have better clinical responses (P = 0.046), EEG responses (P = 0.012), and cognitive outcomes (P = 0.006) than children with an earlier onset. Moreover, better seizure response and electrographic response were seen in patients with bilateral interictal discharges on the EEG than otherwise. Children had a higher likelihood of both clinical and electrographic improvement with combination therapy of benzodiazepines (P = 0.001) and steroids (P = 0.001) than with other therapies. SIGNIFICANCE This study shows a higher prevalence of genetic/metabolic causes and suggests the superior efficacy of combination therapy with steroids and benzodiazepines in D/EE-SWAS. Prospective studies that strictly assess the treatment protocols and outcomes are needed.
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Affiliation(s)
- Hanin Alsini
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, PO Box 7889, Riyadh 11159, Saudi Arabia.
| | - Abdulaziz Alghamdi
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, PO Box 7889, Riyadh 11159, Saudi Arabia
| | - Shatha Alshafi
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, PO Box 7889, Riyadh 11159, Saudi Arabia
| | - Khalid Hundallah
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, PO Box 7889, Riyadh 11159, Saudi Arabia
| | - Sameer Almehmadi
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, PO Box 7889, Riyadh 11159, Saudi Arabia
| | - Daad Alsowat
- Division of Pediatric Neurology, Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Suad Al-Yamani
- Division of Pediatric Neurology, Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanin Almuzaini
- Division of Pediatric Neurology, Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ali Alwadie
- Department of Pediatric Neurology, National Neurosciences Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Al-Otaibi
- Department of Pediatric Neurology, National Neurosciences Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Lamyaa Jad
- Department of Pediatric Neurology, National Neurosciences Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Asma Almadhi
- Department of Pediatric Neurology, National Neurosciences Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fahad Bashiri
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Amal Kentab
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Muddathir H Hamad
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Duaa Baarmah
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Mohammed Alrifaie
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Mohammed Almuqbel
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; Division of Pediatric Neurology, King Abdullah Specialist Children's Hospital (KASCH), National Guard Health Affairs (NGHA), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard, Riyadh, Saudi Arabia
| | - Raidah Al Baradie
- Department of Pediatrics, University of Dammam and King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Ali Meer
- Department of Pediatrics, University of Dammam and King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Mohammed Jan
- Department of Pediatrics, College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Osama Muthaffar
- Department of Pediatrics, College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Aljabri
- Pediatric Neurology Unit and Neurophysiology Department, Alhada Armed Forces Hospital, Taif, Saudi Arabia
| | - Elsayed Ali
- Department of Clinical Neurosciences, King Fahad Military Medical Complex, Dhahran, Saudi Arabia
| | - Mohammed Saeed
- Division of Pediatric Neurology, Department of Pediatrics, Armed Forces Hospital Khamis Mashayt Southern Region, Saudi Arabia
| | - Abeer Matar
- Department of pediatrics, Maternity and Children Hospital, Makkah, Saudi Arabia
| | - Brahim Tabarki
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, PO Box 7889, Riyadh 11159, Saudi Arabia
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12
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Lecca M, Pehlivan D, Suñer DH, Weiss K, Coste T, Zweier M, Oktay Y, Danial-Farran N, Rosti V, Bonasoni MP, Malara A, Contrò G, Zuntini R, Pollazzon M, Pascarella R, Neri A, Fusco C, Marafi D, Mitani T, Posey JE, Bayramoglu SE, Gezdirici A, Hernandez-Rodriguez J, Cladera EA, Miravet E, Roldan-Busto J, Ruiz MA, Bauzá CV, Ben-Sira L, Sigaudy S, Begemann A, Unger S, Güngör S, Hiz S, Sonmezler E, Zehavi Y, Jerdev M, Balduini A, Zuffardi O, Horvath R, Lochmüller H, Rauch A, Garavelli L, Tournier-Lasserve E, Spiegel R, Lupski JR, Errichiello E. Bi-allelic variants in the ESAM tight-junction gene cause a neurodevelopmental disorder associated with fetal intracranial hemorrhage. Am J Hum Genet 2023; 110:681-690. [PMID: 36996813 PMCID: PMC10119151 DOI: 10.1016/j.ajhg.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
The blood-brain barrier (BBB) is an essential gatekeeper for the central nervous system and incidence of neurodevelopmental disorders (NDDs) is higher in infants with a history of intracerebral hemorrhage (ICH). We discovered a rare disease trait in thirteen individuals, including four fetuses, from eight unrelated families associated with homozygous loss-of-function variant alleles of ESAM which encodes an endothelial cell adhesion molecule. The c.115del (p.Arg39Glyfs∗33) variant, identified in six individuals from four independent families of Southeastern Anatolia, severely impaired the in vitro tubulogenic process of endothelial colony-forming cells, recapitulating previous evidence in null mice, and caused lack of ESAM expression in the capillary endothelial cells of damaged brain. Affected individuals with bi-allelic ESAM variants showed profound global developmental delay/unspecified intellectual disability, epilepsy, absent or severely delayed speech, varying degrees of spasticity, ventriculomegaly, and ICH/cerebral calcifications, the latter being also observed in the fetuses. Phenotypic traits observed in individuals with bi-allelic ESAM variants overlap very closely with other known conditions characterized by endothelial dysfunction due to mutation of genes encoding tight junction molecules. Our findings emphasize the role of brain endothelial dysfunction in NDDs and contribute to the expansion of an emerging group of diseases that we propose to rename as "tightjunctionopathies."
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Affiliation(s)
- Mauro Lecca
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Damià Heine Suñer
- Molecular Diagnostics and Clinical Genetics Unit, Hospital Universitari Son Espases, Palma, Illes Balears, Spain; Genomics of Health, Institute of Health Research of the Balearic Islands, Palma, Illes Balears, Spain
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Thibault Coste
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France; Université de Paris, INSERM UMR-1141 Neurodiderot, Paris, France
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey; Department of Medical Biology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | | | - Vittorio Rosti
- Center for the Study of Myelofibrosis, Laboratory of Biochemistry, Biotechnology and Advanced Diagnosis, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | | | - Alessandro Malara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Laboratory of Biochemistry-Biotechnology and Advanced Diagnostics, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Gianluca Contrò
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Marzia Pollazzon
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Rosario Pascarella
- Neuroradiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alberto Neri
- Ophthalmology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Carlo Fusco
- Child Neurology and Psychiatry Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer Ellen Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sadik Etka Bayramoglu
- Tertiary ROP Center, Health Science University Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | | | - Emilia Amengual Cladera
- Genomics of Health, Institute of Health Research of the Balearic Islands, Palma, Illes Balears, Spain
| | - Elena Miravet
- Metabolic Pathologies and Pediatric Neurology Unit, Pediatric Service, Hospital Universitari Son Espases, Palma, Illes Balears, Spain
| | - Jorge Roldan-Busto
- Pediatric Radiology Unit, Radiology Service, Hospital Universitari Son Espases, Palma, Illes Balears, Spain
| | - María Angeles Ruiz
- Metabolic Pathologies and Pediatric Neurology Unit, Pediatric Service, Hospital Universitari Son Espases, Palma, Illes Balears, Spain
| | - Cristofol Vives Bauzá
- Neurobiology, Institute of Health Research of the Balearic Islands, Palma, Illes Balears, Spain
| | - Liat Ben-Sira
- Department of Radiology, Division of Pediatric Radiology, Dana Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel; Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Sabine Sigaudy
- AP-HM, Service de Génétique, Hôpital de la Timone, Marseille, France
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Sheila Unger
- Medical Genetics Service, CHUV, University of Lausanne, Lausanne, Switzerland
| | - Serdal Güngör
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Pediatric Neurology, Malatya, Turkey
| | - Semra Hiz
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey; Department of Pediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir 35340, Turkey
| | - Ece Sonmezler
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Yoav Zehavi
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel; Department of Pediatrics B, Emek Medical Center, Afula, Israel
| | - Michael Jerdev
- Poriya Medical Center and the Azrieli Faculty of Medicine, Bar-Ilan University, Ramat-Gan, Israel
| | - Alessandra Balduini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PY, UK; Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0PY, UK
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada; Brain and Mind Research Institute, University of Ottawa, Ottawa ON K1H 8L1, Canada; Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON K1H 8L1, Canada
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Elisabeth Tournier-Lasserve
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France; Université de Paris, INSERM UMR-1141 Neurodiderot, Paris, France
| | - Ronen Spiegel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel; Department of Pediatrics B, Emek Medical Center, Afula, Israel
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Edoardo Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy.
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Ahmad S, Ali MZ, Abbasi SW, Abbas S, Ahmed I, Abbas S, Nawaz S, Ziab M, Ahmed I, Fakhro KA, Khan MA, Akil AAS. A GHRHR founder mutation causes isolated growth hormone deficiency type IV in a consanguineous Pakistani family. Front Endocrinol (Lausanne) 2023; 14:1066182. [PMID: 36960394 PMCID: PMC10029353 DOI: 10.3389/fendo.2023.1066182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/23/2023] [Indexed: 03/09/2023] Open
Abstract
Background Isolated growth hormone deficiency (IGHD) is caused by a severe shortage or absence of growth hormone (GH), which results in aberrant growth and development. Patients with IGHD type IV (IGHD4) have a short stature, reduced serum GH levels, and delayed bone age. Objectives To identify the causative mutation of IGHD in a consanguineous family comprising four affected patients with IGHD4 (MIM#618157) and explore its functional impact in silico. Methods Clinical and radiological studies were performed to determine the phenotypic spectrum and hormonal profile of the disease, while whole-exome sequencing (WES) and Sanger sequencing were performed to identify the disease-causing mutation. In-silico studies involved protein structural modeling and docking, and molecular dynamic simulation analyses using computational tools. Finally, data from the Qatar Genome Program (QGP) were screened for the presence of the founder variant in the Qatari population. Results All affected individuals presented with a short stature without gross skeletal anomalies and significantly reduced serum GH levels. Genetic mapping revealed a homozygous nonsense mutation [NM_000823:c.G214T:p.(Glu72*)] in the third exon of the growth-hormone-releasing hormone receptor gene GHRHR (MIM#139191) that was segregated in all patients. The substituted amber codon (UAG) seems to truncate the protein by deleting the C-terminus GPCR domain, thus markedly disturbing the GHRHR receptor and its interaction with the growth hormone-releasing hormone. Conclusion These data support that a p.Glu72* founder mutation in GHRHR perturbs growth hormone signaling and causes IGHD type IV. In-silico and biochemical analyses support the pathogenic effect of this nonsense mutation, while our comprehensive phenotype and hormonal profiling has established the genotype-phenotype correlation. Based on the current study, early detection of GHRHR may help in better therapeutic intervention.
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Affiliation(s)
- Safeer Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Zeeshan Ali
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Punjab, Pakistan
| | - Safdar Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Iftikhar Ahmed
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Shakil Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Shoaib Nawaz
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
| | - Mubarak Ziab
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
| | - Ikhlak Ahmed
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
| | - Khalid A. Fakhro
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College-Doha, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Ammira Al-Shabeeb Akil
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
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14
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Choi YJ, Joo K, Lim HT, Kim SS, Han J, Woo SJ. Clinical and Genetic Features of Korean Patients with Achromatopsia. Genes (Basel) 2023; 14:519. [PMID: 36833446 PMCID: PMC9957537 DOI: 10.3390/genes14020519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
This multicenter study aimed to characterize Korean patients with achromatopsia. The patients' genotypes and phenotypes were retrospectively evaluated. Twenty-one patients (with a mean age at the baseline of 10.9 years) were enrolled and followed up for a mean of 7.3 years. A targeted gene panel or exome sequencing was performed. The pathogenic variants of the four genes and their frequencies were identified. CNGA3 and PDE6C were equally the most prevalent genes: CNGA3 (N = 8, 38.1%), PDE6C (N = 8, 38.1%), CNGB3 (N = 3, 14.3%), and GNAT2 (N = 2, 9.5%). The degree of functional and structural defects varied among the patients. The patients' age exhibited no significant correlation with structural defects. During the follow-up, the visual acuity and retinal thickness did not change significantly. In CNGA3-achromatopsia patients, a proportion of patients with a normal foveal ellipsoid zone on the OCT was significantly higher than that of patients with other causative genes (62.5% vs. 16.7%; p = 0.023). In PDE6C-achromatopsia patients, the same proportion was significantly lower than that of patients with other causative genes (0% vs. 58.3%; p = 0.003). Korean patients with achromatopsia showed similar clinical features but a higher prevalence of PDE6C variants than those of other ethnic groups. The retinal phenotypes of the PDE6C variants were more likely to be worse than those of other genes.
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Affiliation(s)
- Yong Je Choi
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Hyun Taek Lim
- Department of Ophthalmology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea
- Orthopia Eye Clinic, Seoul 06162, Republic of Korea
| | - Sung Soo Kim
- Institute of Vision Research, Department of Ophthalmology, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Republic of Korea
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
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15
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Ohno K, Ohkawara B, Shen XM, Selcen D, Engel AG. Clinical and Pathologic Features of Congenital Myasthenic Syndromes Caused by 35 Genes-A Comprehensive Review. Int J Mol Sci 2023; 24:ijms24043730. [PMID: 36835142 PMCID: PMC9961056 DOI: 10.3390/ijms24043730] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Congenital myasthenic syndromes (CMS) are a heterogeneous group of disorders characterized by impaired neuromuscular signal transmission due to germline pathogenic variants in genes expressed at the neuromuscular junction (NMJ). A total of 35 genes have been reported in CMS (AGRN, ALG14, ALG2, CHAT, CHD8, CHRNA1, CHRNB1, CHRND, CHRNE, CHRNG, COL13A1, COLQ, DOK7, DPAGT1, GFPT1, GMPPB, LAMA5, LAMB2, LRP4, MUSK, MYO9A, PLEC, PREPL, PURA, RAPSN, RPH3A, SCN4A, SLC18A3, SLC25A1, SLC5A7, SNAP25, SYT2, TOR1AIP1, UNC13A, VAMP1). The 35 genes can be classified into 14 groups according to the pathomechanical, clinical, and therapeutic features of CMS patients. Measurement of compound muscle action potentials elicited by repetitive nerve stimulation is required to diagnose CMS. Clinical and electrophysiological features are not sufficient to identify a defective molecule, and genetic studies are always required for accurate diagnosis. From a pharmacological point of view, cholinesterase inhibitors are effective in most groups of CMS, but are contraindicated in some groups of CMS. Similarly, ephedrine, salbutamol (albuterol), amifampridine are effective in most but not all groups of CMS. This review extensively covers pathomechanical and clinical features of CMS by citing 442 relevant articles.
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Affiliation(s)
- Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Correspondence: (K.O.); (A.G.E.)
| | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Xin-Ming Shen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | - Duygu Selcen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | - Andrew G. Engel
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: (K.O.); (A.G.E.)
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16
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Kohil A, Abdallah AM, Hussain K, Al-Shafai M. Genetic epidemiology of Woodhouse-Sakati Syndrome in the Greater Middle East region and beyond: a systematic review. Orphanet J Rare Dis 2023; 18:22. [PMID: 36721231 PMCID: PMC9887781 DOI: 10.1186/s13023-023-02614-8] [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: 05/25/2022] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Woodhouse-Sakati syndrome (WSS) is a rare, autosomal recessive genetic disorder with variable clinical manifestations mainly affecting the endocrine and nervous systems. The aim of this study was to systematically review the genetic basis of WSS and report the genetic variants and clinical phenotypes associated with the disease. METHODS PubMed, Science Direct, Scopus, and Web of Science databases were searched from the time of inception until June 2022. Broad search terms were used to capture the literature describing all genetic variants associated with WSS. The search keywords used are "Woodhouse Sakati" along with the term "mutation" OR "gene" OR "variant" OR "polymorphism". RESULTS Twenty-five eligible studies were included in this study. One hundred and eighty-five patients in 97 families from 12 different countries were diagnosed with WSS. In patients from the Greater Middle East (GME) region, consanguineous marriages were common (67%). Thirteen different DCAF17 variants were associated with WSS development (including 8 identified in the GME region). The most frequent variant was a frameshift deletion variant (c.436delC, p.Ala147Hisfs*9) unique to Arabs that was reported in 11 cases from Tunisia, Kuwait, Qatar, Bahrain, and Saudi Arabia. There were no clear genotype-phenotype correlations for the different variants. CONCLUSIONS This systematic review highlights the molecular basis and clinical manifestations of WSS globally, including the GME region, where the disease is prevalent due to consanguinity. Additional studies are now needed to understand the genotype-phenotype correlation for different DCAF17 variants and their impact on the phenotypic heterogeneity observed in WSS patients.
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Affiliation(s)
- Amira Kohil
- grid.412603.20000 0004 0634 1084Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713 Doha, Qatar
| | - Atiyeh M. Abdallah
- grid.412603.20000 0004 0634 1084Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713 Doha, Qatar
| | - Khalid Hussain
- grid.467063.00000 0004 0397 4222Department of Pediatrics, Division of Endocrinology, Sidra Medicine, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713, Doha, Qatar.
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17
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Sobahy TM, Motwalli O, Alazmi M. AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:796-801. [PMID: 35239491 DOI: 10.1109/tcbb.2022.3155659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND & OBJECTIVE Genomic medicine stands to be revolutionized by understanding single nucleotide variants (SNVs) and their expression in single-gene disorders (Mendelian diseases). Computational tools can play a vital role in the exploration of such variations and their pathogenicity. Consequently, we developed the ensemble prediction tool AllelePred to identify deleterious SNVs and disease causative genes. RESULTS The model utilizes different population genetics backgrounds and restricted criteria for features selection to help generate high accuracy results. In comparison to other tools, such as Eigen, PROVEAN, and fathmm-MKL our classifier achieves higher accuracy (98%), precision (96%), F1 score (93%), and coverage (100%) for different types of coding variants. The new method was also compared against a bioinformatics analytical workflow, which uses gnomAD overall AFs (less than 1%) and CADD (scaled C-score of at least 15). Furthermore, this research highlights the stature of genetic variant sharing and curation. We accumulated a list of highly probable deleterious variants and recommended further experimental validation before medical diagnostic usage. CONCLUSIONS The ensemble prediction tool AllelePred enables increased accuracy in recognizing deleterious SNVs and the genetic determinants in real clinical data.
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18
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Alhaidari AI, Albakri AS, Alhumaidi SS. A Novel PGAP3 Gene Mutation-Related Megalocornea Can Be Misdiagnosed as Primary Congenital Glaucoma. Cureus 2022; 14:e29387. [PMID: 36304370 PMCID: PMC9585391 DOI: 10.7759/cureus.29387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Hyperphosphatasia with mental retardation syndrome 4 (HPMRS4) is a rare autosomal recessive disorder caused by glycosylphosphatidylinositol (GPI) deficiency. GPI deficiency results from a mutation in one of six known genes. Mutation in post-GPI attachment to protein phospholipase 3 gene (PGAP3) is linked to HPMRS4. Patients usually present with dysmorphic features, developmental delay, central hypotonia, and seizure. However, in our case, we report a novel homozygous missense mutation of PGAP3 gene in a female child who presented with megalocornea, which is an unusual clinical presentation for HPMRS4. Megalocornea, in her first days of life, led to a misdiagnosis of primary congenital glaucoma. Later, other common clinical features of HPMRS4 became apparent.
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19
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Park S, Jang SS, Lee S, Kim M, Sim H, Jeon H, Hong SE, Lee J, Lee J, Jeon EY, Lee J, Lee CR, Kim SY, Kim MJ, Yoon JG, Lim BC, Kim WJ, Kim KJ, Ko JM, Cho A, Lee JS, Choi M, Chae JH. Systematic analysis of inheritance pattern determination in genes that cause rare neurodevelopmental diseases. Front Genet 2022; 13:990015. [PMID: 36212160 PMCID: PMC9533195 DOI: 10.3389/fgene.2022.990015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Despite recent advancements in our understanding of genetic etiology and its molecular and physiological consequences, it is not yet clear what genetic features determine the inheritance pattern of a disease. To address this issue, we conducted whole exome sequencing analysis to characterize genetic variants in 1,180 Korean patients with neurological symptoms. The diagnostic yield for definitive pathogenic variant findings was 50.8%, after including 33 cases (5.9%) additionally diagnosed by reanalysis. Of diagnosed patients, 33.4% carried inherited variants. At the genetic level, autosomal recessive-inherited genes were characterized by enrichments in metabolic process, muscle organization and metal ion homeostasis pathways. Transcriptome and interactome profiling analyses revealed less brain-centered expression and fewer protein-protein interactions for recessive genes. The majority of autosomal recessive genes were more tolerant of variation, and functional prediction scores of recessively-inherited variants tended to be lower than those of dominantly-inherited variants. Additionally, we were able to predict the rates of carriers for recessive variants. Our results showed that genes responsible for neurodevelopmental disorders harbor different molecular mechanisms and expression patterns according to their inheritance patterns. Also, calculated frequency rates for recessive variants could be utilized to pre-screen rare neurodevelopmental disorder carriers.
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Affiliation(s)
- Soojin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Se Song Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Seungbok Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Minsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyungtai Sim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeongseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jean Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongeun Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Eun Young Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Cho-Rong Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,Rare Disease Center, Seoul National University Hospital, Seoul, South Korea
| | - Jihoon G. Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Woo Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Anna Cho
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jin Sook Lee
- Department of Pediatrics, Seoul National University Hospital Child Cancer and Rare Disease Administration, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
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20
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Aldhilan A, Alhakeem A, Al Hajjaj S, Abukhalid M, Aldhalaan H, Salah E, Saeed M, Tabassum S, El Khashab HY, Aljabri M, Ali ES, Alwadei A, Hundallah K, Alghamdi A, Hakami W, AlShafi S, Alkuraya FS, Alanazy N, Seidahmed MZ, Alfadhel M, Tabarki B. Hereditary Hyperekplexia in Saudi Arabia. Pediatr Neurol 2022; 134:78-82. [PMID: 35841715 DOI: 10.1016/j.pediatrneurol.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/07/2022] [Accepted: 06/17/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Hyperekplexia is a rare disorder characterized by exaggerated startle responses to unexpected sensory stimuli, recurrent apneas, and stiffness. Only few studies have been published on this disorder in populations with high rates of consanguinity. METHODS We retrospectively reviewed Saudi patients with genetically confirmed hereditary hyperekplexia using a standard questionnaire that was sent to nine major referral hospitals in Saudi Arabia. RESULTS A total of 22 Saudi patients (11 males, 11 females) from 20 unrelated families who had hereditary hyperekplexia were included. Based on molecular studies, they were classified into different subtypes: SLC6A5 variant (12 patients, 54.5%), GLRB variant (seven patients, 31.8%), and GLRA1 variant (three patients, 13.7%). All patients were homozygous for the respective causal variant. The combined carrier frequency of hereditary hyperekplexia for the encountered founder mutations in the Saudi population is 10.9 per 10,000, which translates to a minimum disease burden of 13 patients per 1,000,000. CONCLUSION Our study provides comprehensive epidemiologic information, prevalence figures, and clinical characteristics of a large cohort of patients with hereditary hyperekplexia.
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Affiliation(s)
- Amal Aldhilan
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Afnan Alhakeem
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Sumayah Al Hajjaj
- Division of Pediatric Neurology, Department of Pediatrics, King Abdulaziz Hospital of National Guard, Al Ahsa, Saudi Arabia
| | - Musaad Abukhalid
- Division of Pediatric Neurology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hisham Aldhalaan
- Division of Pediatric Neurology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ehab Salah
- Division of Pediatric Neurology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Muhammed Saeed
- Department of Pediatrics, Armed Forces Hospital Southern Region, Khamis Mushayt, Saudi Arabia
| | - Sadia Tabassum
- Division of Pediatric Neurology, Department of Pediatrics, King Fahd Medical City, Riyadh, Saudi Arabia
| | - Heba Y El Khashab
- Department of Neurology, Dr. Sulimann Al Habib Medical Group, Riyadh, Saudi Arabia; Division of Pediatric Neurology, Department of Pediatrics, Children Hospital, Ain Shams University, Cairo, Egypt
| | - Mohammed Aljabri
- Department of Pediatrics, Alhada Military Hospital, Taif, Saudi Arabia
| | - El-Sayed Ali
- Department of Pediatrics, King Fahad Military Medical Complex, Dhahran, Saudi Arabia
| | - Ali Alwadei
- Division of Pediatric Neurology, Department of Pediatrics, King Fahd Medical City, Riyadh, Saudi Arabia
| | - Khalid Hundallah
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Abdulaziz Alghamdi
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Wejdan Hakami
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Shatha AlShafi
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Naif Alanazy
- Division of Pediatric Neurology, Department of Pediatrics, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Mohammed Zain Seidahmed
- Division of Neonatal Intensive Care, Department of Pediatrics, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia; King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia; Genetics and Precision Medicine Department (GPM), King Abdullah Specialized, Children's Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard, Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
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21
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Boonsawat P, Horn AHC, Steindl K, Baumer A, Joset P, Kraemer D, Bahr A, Ivanovski I, Cabello EM, Papik M, Zweier M, Oneda B, Sirleto P, Burkhardt T, Sticht H, Rauch A. Assessing clinical utility of preconception expanded carrier screening regarding residual risk for neurodevelopmental disorders. NPJ Genom Med 2022; 7:45. [PMID: 35906228 PMCID: PMC9338263 DOI: 10.1038/s41525-022-00316-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/15/2022] [Indexed: 11/10/2022] Open
Abstract
The magnitude of clinical utility of preconception expanded carrier screening (ECS) concerning its potential to reduce the risk of affected offspring is unknown. Since neurodevelopmental disorders (NDDs) in their offspring is a major concern of parents-to-be, we addressed the question of residual risk by assessing the risk-reduction potential for NDDs in a retrospective study investigating ECS with different criteria for gene selection and definition of pathogenicity. We used exome sequencing data from 700 parents of children with NDDs and blindly screened for carrier-alleles in up to 3046 recessive/X-linked genes. Depending on variant pathogenicity thresholds and gene content, NDD-risk-reduction potential was up to 43.5% in consanguineous, and 5.1% in nonconsanguineous couples. The risk-reduction-potential was compromised by underestimation of pathogenicity of missense variants (false-negative-rate 4.6%), inherited copy-number variants and compound heterozygosity of one inherited and one de novo variant (0.9% each). Adherence to the ACMG recommendations of restricting ECS to high-frequency genes in nonconsanguineous couples would more than halve the detectable inherited NDD-risk. Thus, for optimized clinical utility of ECS, screening in recessive/X-linked genes regardless of their frequency (ACMG Tier-4) and sensible pathogenicity thresholds should be considered for all couples seeking ECS.
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Affiliation(s)
| | - Anselm H C Horn
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.,Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Pascal Joset
- Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Dennis Kraemer
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Elena M Cabello
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Michael Papik
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Pietro Sirleto
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Tilo Burkhardt
- University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland. .,University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
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22
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Owen MJ, Lefebvre S, Hansen C, Kunard CM, Dimmock DP, Smith LD, Scharer G, Mardach R, Willis MJ, Feigenbaum A, Niemi AK, Ding Y, Van Der Kraan L, Ellsworth K, Guidugli L, Lajoie BR, McPhail TK, Mehtalia SS, Chau KK, Kwon YH, Zhu Z, Batalov S, Chowdhury S, Rego S, Perry J, Speziale M, Nespeca M, Wright MS, Reese MG, De La Vega FM, Azure J, Frise E, Rigby CS, White S, Hobbs CA, Gilmer S, Knight G, Oriol A, Lenberg J, Nahas SA, Perofsky K, Kim K, Carroll J, Coufal NG, Sanford E, Wigby K, Weir J, Thomson VS, Fraser L, Lazare SS, Shin YH, Grunenwald H, Lee R, Jones D, Tran D, Gross A, Daigle P, Case A, Lue M, Richardson JA, Reynders J, Defay T, Hall KP, Veeraraghavan N, Kingsmore SF. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13:4057. [PMID: 35882841 PMCID: PMC9325884 DOI: 10.1038/s41467-022-31446-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/08/2022] [Indexed: 12/31/2022] Open
Abstract
While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.
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Affiliation(s)
- Mallory J. Owen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sebastien Lefebvre
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Christian Hansen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Chris M. Kunard
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David P. Dimmock
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Laurie D. Smith
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Gunter Scharer
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Rebecca Mardach
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mary J. Willis
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Annette Feigenbaum
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Anna-Kaisa Niemi
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Yan Ding
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Luca Van Der Kraan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Katarzyna Ellsworth
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Lucia Guidugli
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Bryan R. Lajoie
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | | | - Kevin K. Chau
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Yong H. Kwon
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zhanyang Zhu
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sergey Batalov
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Shimul Chowdhury
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Seema Rego
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - James Perry
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Speziale
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Nespeca
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Neuroscience, University of California San Diego, San Diego, CA 92093 USA
| | - Meredith S. Wright
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | | | | | - Joe Azure
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | | | - Sandy White
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Charlotte A. Hobbs
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Sheldon Gilmer
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Gail Knight
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Albert Oriol
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Jerica Lenberg
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Shareef A. Nahas
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Kate Perofsky
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Kyu Kim
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jeanne Carroll
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Nicole G. Coufal
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Erica Sanford
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Kristen Wigby
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jacqueline Weir
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Vicki S. Thomson
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Louise Fraser
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Seka S. Lazare
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Yoon H. Shin
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - Richard Lee
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David Jones
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Duke Tran
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Andrew Gross
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Patrick Daigle
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Anne Case
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Marisa Lue
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - John Reynders
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Thomas Defay
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Kevin P. Hall
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Narayanan Veeraraghavan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Stephen F. Kingsmore
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
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23
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Solaki M, Baumann B, Reuter P, Andreasson S, Audo I, Ayuso C, Balousha G, Benedicenti F, Birch D, Bitoun P, Blain D, Bocquet B, Branham K, Català-Mora J, De Baere E, Dollfus H, Falana M, Giorda R, Golovleva I, Gottlob I, Heckenlively JR, Jacobson SG, Jones K, Jägle H, Janecke AR, Kellner U, Liskova P, Lorenz B, Martorell-Sampol L, Messias A, Meunier I, Belga Ottoni Porto F, Papageorgiou E, Plomp AS, de Ravel TJL, Reiff CM, Renner AB, Rosenberg T, Rudolph G, Salati R, Sener EC, Sieving PA, Stanzial F, Traboulsi EI, Tsang SH, Varsanyi B, Weleber RG, Zobor D, Stingl K, Wissinger B, Kohl S. Comprehensive variant spectrum of the CNGA3 gene in patients affected by achromatopsia. Hum Mutat 2022; 43:832-858. [PMID: 35332618 DOI: 10.1002/humu.24371] [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: 08/13/2021] [Revised: 02/23/2022] [Accepted: 03/22/2022] [Indexed: 11/06/2022]
Abstract
Achromatopsia (ACHM) is a congenital cone photoreceptor disorder characterized by impaired color discrimination, low visual acuity, photosensitivity, and nystagmus. To date, six genes have been associated with ACHM (CNGA3, CNGB3, GNAT2, PDE6C, PDE6H, and ATF6), the majority of these being implicated in the cone phototransduction cascade. CNGA3 encodes the CNGA3 subunit of the cyclic nucleotide-gated ion channel in cone photoreceptors and is one of the major disease-associated genes for ACHM. Herein, we provide a comprehensive overview of the CNGA3 variant spectrum in a cohort of 1060 genetically confirmed ACHM patients, 385 (36.3%) of these carrying "likely disease-causing" variants in CNGA3. Compiling our own genetic data with those reported in the literature and in public databases, we further extend the CNGA3 variant spectrum to a total of 316 variants, 244 of which we interpreted as "likely disease-causing" according to ACMG/AMP criteria. We report 48 novel "likely disease-causing" variants, 24 of which are missense substitutions underlining the predominant role of this mutation class in the CNGA3 variant spectrum. In addition, we provide extensive in silico analyses and summarize reported functional data of previously analyzed missense, nonsense and splicing variants to further advance the pathogenicity assessment of the identified variants.
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Affiliation(s)
- Maria Solaki
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Britta Baumann
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Peggy Reuter
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Sten Andreasson
- Department of Ophthalmology, University Hospital Lund, Lund, Sweden
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- CHNO des Quinze-Vingts, Centre de Référence Maladies Rares REFERET, and INSERM-DGOS CIC1423, Paris, France
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Ghassan Balousha
- Department of Pathology and Histology, Faculty of Medicine, Al-Quds University, Eastern Jerusalem, Palestine
| | - Francesco Benedicenti
- Clinical Genetics Service and South Tyrol Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - David Birch
- Retina Foundation of the Southwest, Dallas, Texas, USA
| | - Pierre Bitoun
- Genetique Medicale, CHU Paris Nord, Hopital Jean Verdier, Bondy Cedex, France
| | | | - Beatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Kari Branham
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Jaume Català-Mora
- Unitat de Distròfies Hereditàries de Retina Hospital Sant Joan de Déu, Barcelona, Esplugues de Llobregat, Spain
| | - Elfride De Baere
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Helene Dollfus
- CARGO, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- U-1112, Inserm, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Mohammed Falana
- Department of Pathology and Histology, Faculty of Medicine, Al-Quds University, Eastern Jerusalem, Palestine
| | - Roberto Giorda
- Molecular Biology Laboratory, Scientific Institute IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Irina Golovleva
- Department of Medical Biosciences/Medical and Clinical Genetics, University of Umea, Umea, Sweden
| | - Irene Gottlob
- The University of Leicester Ulverscroft Eye Unit, Leicester Royal Infirmary, Leicester, UK
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Samuel G Jacobson
- Department of Ophthalmology, Perelman School of Medicine, Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kaylie Jones
- Retina Foundation of the Southwest, Dallas, Texas, USA
| | - Herbert Jägle
- Department of Ophthalmology, University of Regensburg, Regensburg, Germany
| | - Andreas R Janecke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Ulrich Kellner
- Zentrum für Seltene Netzhauterkrankungen, AugenZentrum Siegburg, MVZ Augenärztliches Diagnostik- und Therapiecentrum Siegburg GmbH, Siegburg, Germany
- RetinaScience, Bonn, 53192, Germany
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig University Giessen, Giessen, Germany
- Department of Ophthalmology, Universitaetsklinikum Bonn, Bonn, Germany
| | | | - André Messias
- Department of Ophthalmology, Otorhinolaryngology, and Head and Neck Surgery, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, Montpellier University Hospital, University of Montpellier, Montpellier, France
- Sensgene Care Network, France
| | | | - Eleni Papageorgiou
- Department of Ophthalmology, University Hospital of Larissa, Mezourlo, Larissa, Greece
| | - Astrid S Plomp
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomy J L de Ravel
- Centre for Medical Genetics, University Hospital Brussels, Brussels, Belgium
| | | | | | - Thomas Rosenberg
- Department of Ophthalmology, National Eye Clinic, Glostrup Hospital, Glostrup, Denmark
| | - Günther Rudolph
- University Eye Hospital, Ludwig Maximilians University, Munich, Germany
| | - Roberto Salati
- Scientific Institute, IRCCS Eugenio Medea, Pediatric Ophthalmology Unit, Bosisio Parini, Lecco, Italy
| | - E Cumhur Sener
- Strabismus and Pediatric Ophthalmology, Private Practice, Ankara, Turkey
| | - Paul A Sieving
- Center for Ocular Regenerative Therapy, School of Medicine, University of California Davis, Sacramento, USA
| | - Franco Stanzial
- Clinical Genetics Service and South Tyrol Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Elias I Traboulsi
- Center for Genetic Eye Diseases, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York City, New York, USA
| | - Balázs Varsanyi
- Department of Ophthalmology, Medical School, University of Pécs and Ganglion Medical Center, Pécs, Pécs, Hungary
| | - Richard G Weleber
- Oregon Health & Science University, Ophthalmic Genetics Service of the Casey Eye Institute, 515 SW Campus Drive, 97239, Portland, Oregon, USA
| | - Ditta Zobor
- Centre for Ophthalmology, Institute for Ophthalmic Research, University Hospital Tübingen, Tübingen, Germany
- Department of Ophthalmology, Semmelweis University Budapest, Budapest, Hungary
| | - Katarina Stingl
- Center for Ophthalmology, University Eye Hospital, University of Tübingen, Tübingen, Germany
- Center for Rare Eye Diseases, University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
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24
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Schmidtke J, Krawczak M. Carrier detection probabilities for autosomal recessive variants in unrelated and consanguineous couples - an evaluation of the 86 genes of the ACMG 'Tier 3' panel. J Community Genet 2022; 13:399-401. [PMID: 35661981 PMCID: PMC9314508 DOI: 10.1007/s12687-022-00593-0] [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: 03/29/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022] Open
Abstract
Carrier screening for autosomal recessive variants has become a cornerstone of community and public health genetics. While the first carrier screening programs were confined to conditions with relatively high prevalence, and hence well-known carrier frequency, the number of candidate genes has increased greatly since the advent of high-throughput DNA sequencing technologies. The epidemiological database of the ensuing gene panels is mostly sparse, and judgement of their performance is, therefore, anything but straightforward. We therefore derived estimates of the carrier detection probabilities among non-consanguineous and consanguineous couples as expected using the ‘Tier 3’ carrier screening gene panel recently recommended by the American College of Medical Genetics (ACMG). For non-Finnish Europeans, the respective estimate for unrelated couples equals 0.63%, implying that the ACMG Tier 3 panel accounts for over 90% of the genetic load for autosomal recessive diseases in this population. Among the offspring of first cousins, the corresponding incidence is expected to be tenfold higher, an increase still consistent with previous estimates of the overall risk of birth defects for this type of mating. Our considerations are intended to aid the implementation of carrier screening programs and to provide additional support to reproductive counselling and to obtaining informed consent.
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Affiliation(s)
- Jörg Schmidtke
- Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany. .,Amedes MVZ Wagnerstibbe, Georgstrasse 50, 30159, Hannover, Germany.
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Medical Centre Schleswig-Holstein Campus Kiel, Brunswiker Strasse 10, 24105, Kiel, Germany
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25
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Lynch MT, Maloney KA, Pollin TI, Streeten EA, Puffenberger EG, Strauss KA, Shuldiner AR, Mitchell BD. Impact of parental relatedness on reproductive outcomes among the Old Order Amish of Lancaster County. Am J Med Genet A 2022; 188:2119-2128. [PMID: 35442562 DOI: 10.1002/ajmg.a.62757] [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: 10/26/2021] [Revised: 02/01/2022] [Accepted: 03/18/2022] [Indexed: 11/06/2022]
Abstract
Genetically isolated populations that arise due to recent bottleneck events have reduced genetic variation reflecting the common set of founders. Increased genetic relatedness among members of isolated populations puts them at increased risk for some recessive disorders that are rare in outbred populations. To assess the burden on reproductive health, we compared frequencies of adverse reproductive outcomes between Amish couples who were both heterozygous carriers of a highly penetrant pathogenic or likely pathogenic variant and noncarrier couples from the same Amish community. In addition, we evaluated whether overall genetic relatedness of parents was associated with reproductive outcomes. Of the 1824 couples included in our study, 11.1% were at risk of producing a child with an autosomal recessive disorder. Carrier couples reported a lower number of miscarriages compared to noncarrier couples (p = 0.02), although the number of stillbirths (p = 0.3), live births (p = 0.9), and number of pregnancies (p = 0.9) did not differ significantly between groups. In contrast, higher overall relatedness between spouses was positively correlated with number of live births (p < 0.0001), pregnancies (p < 0.0001), and stillbirths (p = 0.03), although not with the number of miscarriages (p = 0.4). These results highlight a complex association between relatedness of parents and reproductive health outcomes in this community.
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Affiliation(s)
- Megan T Lynch
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kristin A Maloney
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Toni I Pollin
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth A Streeten
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
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- Regeneron Genetics Center LLC, Tarrytown, New York, USA
| | | | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
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26
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González-Iglesias E, López-Vázquez A, Noval S, Nieves-Moreno M, Granados-Fernández M, Arruti N, Rosa-Pérez I, Pacio-Míguez M, Montaño VEF, Rodríguez-Solana P, del Pozo A, Santos-Simarro F, Vallespín E. Next-Generation Sequencing Screening of 43 Families with Non-Syndromic Early-Onset High Myopia: A Clinical and Genetic Study. Int J Mol Sci 2022; 23:ijms23084233. [PMID: 35457050 PMCID: PMC9031962 DOI: 10.3390/ijms23084233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/04/2022] [Indexed: 02/01/2023] Open
Abstract
Early-onset high myopia (EoHM) is a disease that causes a spherical refraction error of ≥-6 diopters before 10 years of age, with potential multiple ocular complications. In this article, we report a clinical and genetic study of 43 families with EoHM recruited in our center. A complete ophthalmological evaluation was performed, and a sample of peripheral blood was obtained from proband and family members. DNA was analyzed using a customized next-generation sequencing panel that included 419 genes related to ophthalmological disorders with a suspected genetic cause, and genes related to EoHM pathogenesis. We detected pathogenic and likely pathogenic variants in 23.9% of the families and detected variants of unknown significance in 76.1%. Of these, 5.7% were found in genes related to non-syndromic EoHM, 48.6% in genes associated with inherited retinal dystrophies that can include a syndromic phenotype, and 45.7% in genes that are not directly related to EoHM or retinal dystrophy. We found no candidate genes in 23% of the patients, which suggests that further studies are needed. We propose a systematic genetic analysis for patients with EoHM because it helps with follow-up, prognosis and genetic counseling.
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Affiliation(s)
- Eva González-Iglesias
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
| | - Ana López-Vázquez
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Susana Noval
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - María Nieves-Moreno
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - María Granados-Fernández
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Natalia Arruti
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Irene Rosa-Pérez
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Marta Pacio-Míguez
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Neurodevelopmental Disorders, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Victoria E. F. Montaño
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
| | - Patricia Rodríguez-Solana
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
| | - Angela del Pozo
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Clinical Bioinformatics, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Fernando Santos-Simarro
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Clinical Genetics, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Elena Vallespín
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Correspondence:
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27
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Identification of pharmacogenetic variants from large scale next generation sequencing data in the Saudi population. PLoS One 2022; 17:e0263137. [PMID: 35089958 PMCID: PMC8797234 DOI: 10.1371/journal.pone.0263137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/12/2022] [Indexed: 11/19/2022] Open
Abstract
It is well documented that drug responses are related to Absorption, Distribution, Metabolism, and Excretion (ADME) characteristics of individual patients. Several studies have identified genetic variability in pharmacogenes, that are either directly responsible for or are associated with ADME, giving rise to individualized treatments. Our objective was to provide a comprehensive overview of pharmacogenetic variation in the Saudi population. We mined next generation sequencing (NGS) data from 11,889 unrelated Saudi nationals, to determine the presence and frequencies of known functional SNP variants in 8 clinically relevant pharmacogenes (CYP2C9, CYP2C19, CYP3A5, CYP4F2, VKORC1, DPYD, TPMT and NUDT15), recommended by the Clinical Pharmacogenetics Implementation Consortium (CPIC), and collectively identified 82 such star alleles. Functionally significant pharmacogenetic variants were prevalent especially in CYP genes (excluding CYP3A5), with 10-44.4% of variants predicted to be inactive or to have decreased activity. In CYP3A5, inactive alleles (87.5%) were the most common. Only 1.8%, 0.7% and 0.7% of NUDT15, TPMT and DPYD variants respectively, were predicted to affect gene activity. In contrast, VKORC1 was found functionally, to be highly polymorphic with 53.7% of Saudi individuals harboring variants predicted to result in decreased activity and 31.3% having variants leading to increased metabolic activity. Furthermore, among the 8 pharmacogenes studied, we detected six rare variants with an aggregated frequency of 1.1%, that among several other ethnicities, were uniquely found in Saudi population. Similarly, within our cohort, the 8 pharmacogenes yielded forty-six novel variants predicted to be deleterious. Based upon our findings, 99.2% of individuals from the Saudi population carry at least one actionable pharmacogenetic variant.
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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] [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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Genetic Insights into the Middle East Respiratory Syndrome Coronavirus Infection among Saudi People. Vaccines (Basel) 2021; 9:vaccines9101193. [PMID: 34696302 PMCID: PMC8539242 DOI: 10.3390/vaccines9101193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Middle East respiratory syndrome coronavirus (MERS-CoV) was isolated for the first time in Saudi Arabia from a patient suffering from atypical pneumonia. The Saudi Genome database was built by King Abdulaziz Medical City via the next-generation sequencing of 7000 candidates. METHOD A large list of point mutations were reported in the region of the dipeptidyl peptidase 4 (DPP4) gene. The DPP4 amino acid residues correlated to MERS-CoV entry and the site of activity of DPP4 inhibitors was investigated. We retrieved the SNPs (Single-Nucleotide Polymorphism) with a variation frequency of >0.05. RESULTS SNP 2:162,890,175 and SNP 2:162,891,848 in the intronic region were located within 50 bp of amino acid residues responsible for MERS-CoV entry, amino acids 259-296 and 205-258, respectively. The variation frequency of SNP 2:162,890,175 was 2321 out of 2379 screened individuals. Moreover, mutation of SNP 2:162,891,848, which is located near amino acid residues E205 and E206 (crucial for the activity of DPP4 inhibitors), occurred in 76 out of 2379 screened individuals. CONCLUSIONS Our study shows high variation frequency in the DPP4 region reported in the Saudi Genome database. The identified SNPs are of high significance for MERS-CoV infection in better understanding disease pathogenesis.
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Chen Y, Fang B, Hu X, Guo R, Guo J, Fang K, Ni J, Li W, Qian S, Hao C. Identification and functional analysis of novel SLC25A19 variants causing thiamine metabolism dysfunction syndrome 4. Orphanet J Rare Dis 2021; 16:403. [PMID: 34587972 PMCID: PMC8480130 DOI: 10.1186/s13023-021-02028-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background Thiamine metabolism dysfunction syndrome 4 (THMD4, OMIM #613710) is an autosomal recessive inherited disease caused by the deficiency of SLC25A19 that encodes the mitochondrial thiamine pyrophosphate (TPP) transporter. This disorder is characterized by bilateral striatal degradation and progressive polyneuropathy with the onset of fever of unknown origin. The limited number of reported cases and lack of functional annotation of related gene variants continue to limit diagnosis. Results We report three cases of encephalopathy from two unrelated pedigrees with basal ganglia signal changes after fever of unknown origin. To distinguish this from other types of encephalopathy, such as acute necrotizing encephalopathy, exome sequencing was performed, and four novel heterozygous variations, namely, c.169G>A (p.Ala57Thr), c.383C>T (p.Ala128Val), c.76G>A (p.Gly26Arg), and c.745T>A (p.Phe249Ile), were identified in SLC25A19. All variants were confirmed using Sanger sequencing. To determine the pathogenicity of these variants, functional studies were performed. We found that mitochondrial TPP levels were significantly decreased in the presence of SLC25A19 variants, indicating that TPP transport activities of mutated SLC25A19 proteins were impaired. Thus, combining clinical phenotype, genetic analysis, and functional studies, these variants were deemed as likely pathogenic. Conclusions Exome sequencing analysis enables molecular diagnosis as well as provides potential etiology. Further studies will enable the elucidation of SLC25A19 protein function. Our investigation supplied key molecular evidence for the precise diagnosis of and clinical decision-making for a rare disease.
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Affiliation(s)
- Yuanying Chen
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Boliang Fang
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xuyun Hu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Ruolan Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Jun Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Kenan Fang
- Pediatric Intensive Care Unit, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Jingwen Ni
- Pediatric Intensive Care Unit, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Suyun Qian
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China. .,Henan Key Laboratory of Pediatric Inherited and Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China.
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31
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Alsaleem BM, Hasosah M, Ahmed ABM, Al Hatlani MM, Alanazi AH, Al-Hussaini A, Asery AT, Alghamdi KA, AlRuwaithi MM, Khormi MAM, Al Sarkhy A, Alshamrani AS. Tricho-hepato-enteric syndrome: Retrospective multicenter experience in Saudi Arabia. Saudi J Gastroenterol 2021; 28:135-142. [PMID: 34414925 PMCID: PMC9007078 DOI: 10.4103/sjg.sjg_200_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Trichohepatoenteric syndrome (THES) is a very rare disorder that is characterized by intractable congenital diarrhea, woolly hair, intrauterine growth restriction, facial dysmorphism, and short stature. Our knowledge of THES is limited due to the small number of reported cases. METHODS Thirty patients diagnosed with THES, all molecularly confirmed by whole exome sequencing (WES) to have biallelic variants in TTC37 or SKIV2L, were included in the study. Clinical, biochemical, and nutritional phenotypes and outcome data were collected from all participants. RESULTS The median age of THES patients was 3.7 years (0.9-23 years). Diarrhea and malnutrition were the most common clinical features (100%). Other common features included hair abnormalities (96%), skin hyperpigmentation (87%), facial dysmorphic abnormalities (73%), psychomotor retardation (57%), and hepatic abnormalities (30%). Twenty-five patients required parenteral nutrition (83%) with a mean duration of 13.34 months, and nearly half were eventually weaned off. Parenteral nutrition was associated with a poor prognosis. The vast majority of cases (89.6%) had biallelic variants in SKIV2L, with biallelic variants in TTC37 accounting for the remaining cases. A total of seven variants were identified in TTC37 (n = 3) and SKIV2L (n = 4). The underlying genotype influenced some phenotypic aspects, especially liver involvement, which was more common in TTC37-related THES. CONCLUSION Our data helps define the natural history of THES and provide clinical management guidelines.
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Affiliation(s)
- Badr M. Alsaleem
- Department of Pediatric Gastroenterology, Intestinal Failure Program, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia,Address for correspondence: Dr. Badr M. Alsaleem, Pediatric Consultant Gastroenterologist, King Fahad Medical City, Children's Hospital, Intestinal Failure Program, Riyadh, Saudi Arabia. E-mail:
| | - Mohammed Hasosah
- Department of Pediatric Gastroenterology, King Abdulaziz Medical City, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Amna Basheer M. Ahmed
- Department of Pediatric Gastroenterology, Intestinal Failure Program, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Maher M. Al Hatlani
- Department of Pediatric Gastroenterology, IABF Hospital of National Guard, Dammam, Saudi Arabia
| | - Aziz Helal Alanazi
- Department of Pediatric Gastroenterology, King Abdulaziz Medical City, Ministry of National Guard, Health Affairs, Riyadh, Saudi Arabia
| | - Abdulrahman Al-Hussaini
- The Division of Pediatric Gastroenterology, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia,Alfaisal University, College of Medicine, Riyadh, Saudi Arabia,Prince Abdullah bin Khalid Celiac Disease Research Chair, Department of Pediatrics, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ali T. Asery
- Department of Pediatric Gastroenterology, Intestinal Failure Program, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Khalid A. Alghamdi
- Department of Pediatric Gastroenterology, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Muhanad M. AlRuwaithi
- Department of Pediatric Gastroenterology, Intestinal Failure Program, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Musa Ali M. Khormi
- Department of Pediatric Gastroenterology, King Saud Medical City, Riyadh, Saudi Arabia
| | - Ahmed Al Sarkhy
- Department of Pediatric Gastroenterology, King Khalid University Hospital, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ali S. Alshamrani
- Department of Pediatric Gastroenterology, Maternity and Children's Hospital, Makkah, Saudi Arabia
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32
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Abouelhoda M, Mohty D, Alayary I, Meyer BF, Arold ST, Fadel BM, Monies D. Established and candidate transthyretin amyloidosis variants identified in the Saudi population by data mining. Hum Genomics 2021; 15:52. [PMID: 34380564 PMCID: PMC8359098 DOI: 10.1186/s40246-021-00351-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Familial transthyretin (TTR) amyloidosis (ATTR) is an autosomal dominant disease with significant phenotypic heterogeneity. Its prevalence in Saudi Arabia has not previously been investigated. An existing exome variant database of Saudi individuals, sequenced to globally investigate rare diseases in the population, was mined for TTR variants and filtered for missense mutations resulting in single amino acid changes. A total of 13,906 Saudi exomes from unrelated individuals were analyzed blindly. RESULTS Three TTR variants known to be associated with ATTR amyloidosis were identified. Additionally, three novel TTR mutations were identified. Structural analysis of the three novel variants suggests that at least two could be amyloidogenic. The most common variant associated with amyloidosis was p.Val142Ile (allele frequency 0.001). Further investigation of these variants and their translation to clinical practice may help to diagnose, monitor, and manage patients with ATTR amyloidosis. CONCLUSION Multiple TTR variants potentially associated with systemic ATTR amyloidosis were identified in the Saudi population. Early diagnosis and intervention, facilitated by familial genetic testing of patients with ATTR amyloidosis, may benefit in the management of this disease. Early diagnosis could be enhanced through inclusion of ATTR variants in existing population-based screening programs.
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Affiliation(s)
- Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Dania Mohty
- Heart Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
- Al-Faisal University, College of Medicine, Affiliate Harvard Medical School International, Riyadh, Saudi Arabia
| | | | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Bahaa M Fadel
- Heart Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
- Al-Faisal University, College of Medicine, Affiliate Harvard Medical School International, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia.
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Al Qahtani NH, AbdulAzeez S, Almandil NB, Fahad Alhur N, Alsuwat HS, Al Taifi HA, Al-Ghamdi AA, Rabindran Jermy B, Abouelhoda M, Subhani S, Al Asoom L, Borgio JF. Whole-Genome Sequencing Reveals Exonic Variation of ASIC5 Gene Results in Recurrent Pregnancy Loss. Front Med (Lausanne) 2021; 8:699672. [PMID: 34395479 PMCID: PMC8363113 DOI: 10.3389/fmed.2021.699672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/21/2021] [Indexed: 12/08/2022] Open
Abstract
Family trio next-generation sequencing-based variant analysis was done to identify the genomic reason on unexplained recurrent pregnancy loss (RPL). A family (dead fetus and parents) from Saudi Arabia with an earlier history of three unexplained RPLs at the ninth week of pregnancy was included in the study. Whole-genome sequencing (WGS) of a dead fetus and the parents was done to identify the pathogenic variation and confirmed through Sanger sequencing. WGS of dead fetus identifies a novel homozygous exonic variation (NM_017419.3:c.680G>T) in ASIC5 (acid-sensing ion channel subunit family member 5) gene; the parents are heterozygous. Newly designed ARMS PCR followed by direct sequencing confirms the presence of heterozygous in one subject and absence of homozygous novel mutation among randomly selected healthy Saudis. The second family with heterozygous was confirmed with three unexplained RPLs. Pathogenicity analysis of R227I amino acid substitution in ASIC5 protein through molecular docking and interaction analysis revealed that the mutations are highly pathogenic, decrease the stability of the protein, and prevent binding of amiloride, which is an activator to open the acid-sensing ion channel of ASIC5. The identified rare and novel autosomal recessive mutation, c.680G>T:p.R227I (ASIC5Saudi), in two families confirm the ASIC5 gene association with RPL and can be fatal to the fetus.
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Affiliation(s)
- Nourah H. Al Qahtani
- Department of Obstetrics and Gynaecology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Norah Fahad Alhur
- Department of Genetic Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Hind Saleh Alsuwat
- Department of Genetic Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Hatoon Ahmed Al Taifi
- Department of Obstetrics and Gynaecology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ahlam A. Al-Ghamdi
- Department of Obstetrics and Gynaecology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - B. Rabindran Jermy
- Department of Nanomedicine Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mohamed Abouelhoda
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shazia Subhani
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lubna Al Asoom
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Quaio CRDC, Chung CH, Perazzio SF, Dutra AP, Moreira CM, Filho GMN, Sacramento-Bobotis PR, Penna MG, de Souza RRF, Cintra VP, Carnavalli JEP, da Silva RA, Paixão D, Baratela WADR, Olivati C, Spolador GM, Santos MNP, Pintao MC, Fornari ARDS, Burger M, Ramalho RF, Pereira OJE, E Ferreira EN, Mitne-Neto M, Kim CA. Frequency of carriers for rare recessive Mendelian diseases in a Brazilian cohort of 320 patients. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2021; 187:364-372. [PMID: 34269512 DOI: 10.1002/ajmg.c.31932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/13/2021] [Accepted: 06/30/2021] [Indexed: 12/31/2022]
Abstract
Several Mendelian disorders follow an autosomal recessive inheritance pattern. Epidemiological information on many inherited disorders may be useful to guide health policies for rare diseases, but it is often inadequate, particularly in developing countries. We aimed to calculate the carrier frequencies of rare autosomal recessive Mendelian diseases in a cohort of Brazilian patients using whole exome sequencing (WES). We reviewed the molecular findings of WES from 320 symptomatic patients who had carrier status for recessive diseases. Using the Hardy-Weinberg equation, we estimated recessive disease frequencies (q2 ) considering the respective carrier frequencies (2pq) observed in our study. We calculated the sensitivity of carrier screening tests based on lists of genes from five different clinical laboratories that offer them in Brazil. A total of 425 occurrences of 351 rare variants were reported in 278 different genes from 230 patients (71.9%). Almost half (48.8%) were carriers of at least one heterozygous pathogenic/likely pathogenic variant for rare metabolic disorders, while 25.9% of epilepsy, 18.1% of intellectual disabilities, 15.6% of skeletal disorders, 10.9% immune disorders, and 9.1% of hearing loss. We estimated that an average of 67% of the variants would not have been detected by carrier screening panels. The combined frequencies of autosomal recessive diseases were estimated to be 26.39/10,000 (or ~0.26%). This study shows the potential research utility of WES to determine carrier status, which may be a possible strategy to evaluate the clinical and social burden of recessive diseases at the population level and guide the optimization of carrier screening panels.
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Affiliation(s)
- Caio Robledo D'Angioli Costa Quaio
- Instituto da Crianca (Children's Hospital), Hospital das Clinicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Fleury Medicina e Saúde, São Paulo, Brazil.,Laboratório Clínico, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Sandro Felix Perazzio
- Fleury Medicina e Saúde, São Paulo, Brazil.,Division of Rheumatology, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | | | | | | | | | - Rafael Alves da Silva
- Fleury Medicina e Saúde, São Paulo, Brazil.,Laboratório de Hepatologia Molecular Aplicada (LHeMA), Escola Paulista de Medicina, Universidade Federal de São Paulo, Sao Paulo, Brazil
| | | | | | | | - Gustavo Marquezani Spolador
- Instituto da Crianca (Children's Hospital), Hospital das Clinicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Fleury Medicina e Saúde, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | - Chong Ae Kim
- Instituto da Crianca (Children's Hospital), Hospital das Clinicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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35
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Wang P, Jia X, Xiao X, Li S, Long Y, Liu M, Li Y, Li J, Xu Y, Zhang Q. An Early Diagnostic Clue for COL18A1- and LAMA1-Associated Diseases: High Myopia With Alopecia Areata in the Cranial Midline. Front Cell Dev Biol 2021; 9:644947. [PMID: 34249907 PMCID: PMC8267009 DOI: 10.3389/fcell.2021.644947] [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: 12/22/2020] [Accepted: 05/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background High myopia with alopecia areata in the occipital region has been observed in patients with Knobloch syndrome caused by COL18A1 mutations. This study investigated other possible genetic causes of high myopia in patients with alopecia areata in the cranial midline. Methods Six patients with early onset high myopia and alopecia areata in the cranial midline were recruited. Targeted high-throughput sequencing was performed on the proband’s DNA to detect potential pathogenic variants. Cosegregation analysis was performed for available family members. Minigene assay and RNA Sequencing were used to validate the abnormality of possible splicing change and gross deletion. Ophthalmological and neuroimaging examinations were performed. Results Eight novel and one known loss-of-function mutants were detected in all six patients, including a gross deletion detected by RNA sequencing. Four COL18A1 mutants in three patients with scalp leisure in the occipital region; and five LAMA1 mutations in three patients with scalp leisure in the parietal region. Further assessments indicated that patients with COL18A1 mutations had Knobloch syndrome, and the patients with LAMA1 mutations had Poretti–Boltshauser syndrome. Conclusion Our study found that early onset high myopia with midline alopecia areata could be caused not only by mutations of the COL18A1 gene but also by mutations in the LAMA1 gene. To our knowledge, we are the first to observe scalp defects in patients with LAMA1 mutations. High myopia with alopecia areata in the cranial midline could be treated as an early diagnostic clue for ophthalmologists to consider the two kinds of rare diseases.
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Affiliation(s)
- Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yuxi Long
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Mengchu Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yongyu Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jun Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yan Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Xiao Q, Lauschke VM. The prevalence, genetic complexity and population-specific founder effects of human autosomal recessive disorders. NPJ Genom Med 2021; 6:41. [PMID: 34078906 PMCID: PMC8172936 DOI: 10.1038/s41525-021-00203-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022] Open
Abstract
Autosomal recessive (AR) disorders pose a significant burden for public health. However, despite their clinical importance, epidemiology and molecular genetics of many AR diseases remain poorly characterized. Here, we analyzed the genetic variability of 508 genes associated with AR disorders based on sequencing data from 141,456 individuals across seven ethnogeographic groups by integrating variants with documented pathogenicity from ClinVar, with stringent functionality predictions for variants with unknown pathogenicity. We first validated our model using 85 diseases for which population-specific prevalence data were available and found that our estimates strongly correlated with the respective clinically observed disease frequencies (r = 0.68; p < 0.0001). We found striking differences in population-specific disease prevalence with 101 AR diseases (27%) being limited to specific populations, while an additional 305 diseases (68%) differed more than tenfold across major ethnogeographic groups. Furthermore, by analyzing genetic AR disease complexity, we confirm founder effects for cystic fibrosis and Stargardt disease, and provide strong evidences for >25 additional population-specific founder mutations. The presented analyses reveal the molecular genetics of AR diseases with unprecedented resolution and provide insights into epidemiology, complexity, and population-specific founder effects. These data can serve as a powerful resource for clinical geneticists to inform population-adjusted genetic screening programs, particularly in otherwise understudied ethnogeographic groups.
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Affiliation(s)
- Qingyang Xiao
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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Daich Varela M, Ullah E, Yousaf S, Brooks BP, Hufnagel RB, Huryn LA. PDE6C: Novel Mutations, Atypical Phenotype, and Differences Among Children and Adults. Invest Ophthalmol Vis Sci 2021; 61:1. [PMID: 33001157 PMCID: PMC7545085 DOI: 10.1167/iovs.61.12.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Purpose Genetic variation in PDE6C is associated with achromatopsia and cone dystrophy, with only a few reports of cone-rod dystrophy in the literature. We describe two pediatric and two adult patients with PDE6C related cone and cone-rod dystrophy and the first longitudinal data of a pediatric patient with PDE6C-related cone dystrophy. Methods This cohort of four patients underwent comprehensive ophthalmologic evaluation at the National Eye Institute's Ophthalmic Genetics clinic, including visual field testing, retinal imaging and electroretinogram (ERG). Next-generation sequencing-based genetic testing was performed and subsequent analysis of the variants was done through three-dimensional protein models generated by Phyre2 and Chimera. Results All cases shared decreased best-corrected visual acuity and poor color discrimination. Three of the four patients had a cone-rod dystrophy, presenting with an ERG showing decreased amplitude on both photopic and scotopic waveforms and a mild to moderately constricted visual field. One of the children was diagnosed with cone dystrophy, having a preserved peripheral field. The children had none to minor structural retinal changes, whereas the adults had clear macular dystrophy. Conclusions PDE6C-related cone-rod dystrophy consists of a severe phenotype characterized by early-onset nystagmus, decreased best-corrected visual acuity, poor color discrimination, progressive constriction of the visual field, and night blindness. Our work contributes with valuable information toward understanding the visual prognosis and allelic heterogeneity of PDE6C-related cone and cone-rod dystrophy.
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Affiliation(s)
- Malena Daich Varela
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Ehsan Ullah
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Sairah Yousaf
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Laryssa A Huryn
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
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Morton CC. ASHG 2020 Curt Stern Award introduction: Fowzan Sami Alkuraya. Am J Hum Genet 2021; 108:392-394. [PMID: 33667392 DOI: 10.1016/j.ajhg.2020.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
This article is based on the address given by the author at the 2020 virtual meeting of the American Society of Human Genetics (ASHG) on October 26, 2020. The video of the original address can be found at the ASHG website.
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Alkuraya FS. 2020 Curt Stern Award address: a more perfect clinical genome-how consanguineous populations contribute to the medical annotation of the human genome. Am J Hum Genet 2021; 108:395-399. [PMID: 33667393 DOI: 10.1016/j.ajhg.2020.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This article is based on the address given by the author at the 2020 virtual meeting of the American Society of Human Genetics (ASHG) on October 26, 2020. The video of the original address can be found at the ASHG website.
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Mann N, Mzoughi S, Schneider R, Kühl SJ, Schanze D, Klämbt V, Lovric S, Mao Y, Shi S, Tan W, Kühl M, Onuchic-Whitford AC, Treimer E, Kitzler TM, Kause F, Schumann S, Nakayama M, Buerger F, Shril S, van der Ven AT, Majmundar AJ, Holton KM, Kolb A, Braun DA, Rao J, Jobst-Schwan T, Mildenberger E, Lennert T, Kuechler A, Wieczorek D, Gross O, Ermisch-Omran B, Werberger A, Skalej M, Janecke AR, Soliman NA, Mane SM, Lifton RP, Kadlec J, Guccione E, Schmeisser MJ, Zenker M, Hildebrandt F. Mutations in PRDM15 Are a Novel Cause of Galloway-Mowat Syndrome. J Am Soc Nephrol 2021; 32:580-596. [PMID: 33593823 PMCID: PMC7920168 DOI: 10.1681/asn.2020040490] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Galloway-Mowat syndrome (GAMOS) is characterized by neurodevelopmental defects and a progressive nephropathy, which typically manifests as steroid-resistant nephrotic syndrome. The prognosis of GAMOS is poor, and the majority of children progress to renal failure. The discovery of monogenic causes of GAMOS has uncovered molecular pathways involved in the pathogenesis of disease. METHODS Homozygosity mapping, whole-exome sequencing, and linkage analysis were used to identify mutations in four families with a GAMOS-like phenotype, and high-throughput PCR technology was applied to 91 individuals with GAMOS and 816 individuals with isolated nephrotic syndrome. In vitro and in vivo studies determined the functional significance of the mutations identified. RESULTS Three biallelic variants of the transcriptional regulator PRDM15 were detected in six families with proteinuric kidney disease. Four families with a variant in the protein's zinc-finger (ZNF) domain have additional GAMOS-like features, including brain anomalies, cardiac defects, and skeletal defects. All variants destabilize the PRDM15 protein, and the ZNF variant additionally interferes with transcriptional activation. Morpholino oligonucleotide-mediated knockdown of Prdm15 in Xenopus embryos disrupted pronephric development. Human wild-type PRDM15 RNA rescued the disruption, but the three PRDM15 variants did not. Finally, CRISPR-mediated knockout of PRDM15 in human podocytes led to dysregulation of several renal developmental genes. CONCLUSIONS Variants in PRDM15 can cause either isolated nephrotic syndrome or a GAMOS-type syndrome on an allelic basis. PRDM15 regulates multiple developmental kidney genes, and is likely to play an essential role in renal development in humans.
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Affiliation(s)
- Nina Mann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Slim Mzoughi
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Susanne J Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Verena Klämbt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Svjetlana Lovric
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Youying Mao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shasha Shi
- Grenoble Alpes University, National Center for Scientific Research (CNRS), French Alternative Energies and Atomic Energy Commission (CEA), Institute of Structural Biology, Grenoble, France
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Ana C Onuchic-Whitford
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ernestine Treimer
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Thomas M Kitzler
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Franziska Kause
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sven Schumann
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Makiko Nakayama
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Florian Buerger
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amelie T van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Amy Kolb
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jia Rao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eva Mildenberger
- Division of Neonatology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Thomas Lennert
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Faculty of Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Oliver Gross
- Clinic of Nephrology and Rheumatology, University Medical Center Goettingen, University of Goettingen, Goettingen, Germany
| | - Beate Ermisch-Omran
- Department of Pediatric Nephrology, University Children's Hospital, Münster, Germany
| | - Anja Werberger
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Martin Skalej
- Institute of Neuroradiology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Andreas R Janecke
- Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
- The Egyption Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Jan Kadlec
- Grenoble Alpes University, National Center for Scientific Research (CNRS), French Alternative Energies and Atomic Energy Commission (CEA), Institute of Structural Biology, Grenoble, France
| | - Ernesto Guccione
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael J Schmeisser
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
- Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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Al-Fadhli FM, Afqi M, Sairafi MH, Almuntashri M, Alharby E, Alharbi G, Abdud Samad F, Hashmi JA, Zaytuni D, Bahashwan AA, Choi JH, Peake RWA, Beutler B, Almontashiri NAM. Biallelic loss of function variant in the unfolded protein response gene PDIA6 is associated with asphyxiating thoracic dystrophy and neonatal-onset diabetes. Clin Genet 2021; 99:694-703. [PMID: 33495992 DOI: 10.1111/cge.13930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/18/2022]
Abstract
Protein disulfide isomerase A6 (PDIA6) is an unfolded protein response (UPR)-regulating protein. PDIA6 regulates the UPR sensing proteins, Inositol requiring enzyme 1, and EIF2AK3. Biallelic inactivation of the two genes in mice and humans resulted in embryonic lethality, diabetes, skeletal defects, and renal insufficiency. We recently showed that PDIA6 inactivation in mice caused embryonic and early lethality, diabetes and immunodeficiency. Here, we present a case with asphyxiating thoracic dystrophy (ATD) syndrome and infantile-onset diabetes. Whole exome sequencing revealed a homozygous frameshift variant in the PDIA6 gene. RNA expression was reduced in a gene dosage-dependent manner, supporting a loss-of-function effect of this variant. Phenotypic correlation with the mouse model recapitulated the growth defect and delay, early lethality, coagulation, diabetes, immunological, and polycystic kidney disease phenotypes. In general, the phenotype of the current patient is consistent with phenotypes associated with the disruption of PDIA6 and the sensors of UPR in mice and humans. This is the first study to associate ATD to the UPR gene, PDIA6. We recommend screening ATD cases with or without insulin-dependent diabetes for variants in PDIA6.
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Affiliation(s)
- Fatima M Al-Fadhli
- Unit of Genetic Diseases, Department of Pediatrics, Maternity and Children's Hospital, Almadinah Almunwarah, Saudi Arabia
| | - Manal Afqi
- Unit of Genetic Diseases, Department of Pediatrics, Maternity and Children's Hospital, Almadinah Almunwarah, Saudi Arabia
| | - Mona Hamza Sairafi
- Department of Nephrology, Maternity and Children's Hospital, Almadinah Almunwarah, Saudi Arabia
| | - Makki Almuntashri
- Department of Radiology, King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Essa Alharby
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Ghadeer Alharbi
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Firoz Abdud Samad
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Jamil Amjad Hashmi
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Dimah Zaytuni
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Ahmed A Bahashwan
- Laboratory and Blood Bank Department, Maternity and Children's Hospital, Almadinah Almunwarah, Saudi Arabia
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Roy W A Peake
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Naif A M Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia.,Faculty of Applied Medical Sciences, Taibah University, Almadinah Almunwarah, Saudi Arabia
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Shamseldin HE, Al Mogarri I, Alqwaiee MM, Alharbi AS, Baqais K, AlSaadi M, AlAnzi T, Alhashem A, Saghier A, Ameen W, Ibrahim N, Yang J, Abdulwahab F, Hashem M, Chivukula RR, Alkuraya FS. An exome-first approach to aid in the diagnosis of primary ciliary dyskinesia. Hum Genet 2020; 139:1273-1283. [PMID: 32367404 DOI: 10.1007/s00439-020-02170-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/25/2020] [Indexed: 01/31/2023]
Abstract
Unlike disorders of primary cilium, primary ciliary dyskinesia (PCD) has a much narrower clinical spectrum consistent with the limited tissue distribution of motile cilia. Nonetheless, PCD diagnosis can be challenging due to the overlapping features with other disorders and the requirement for sophisticated tests that are only available in specialized centers. We performed exome sequencing on all patients with a clinical suspicion of PCD but for whom no nasal nitric oxide test or ciliary functional assessment could be ordered. Among 81 patients (56 families), in whom PCD was suspected, 68% had pathogenic or likely pathogenic variants in established PCD-related genes that fully explain the phenotype (20 variants in 11 genes). The major clinical presentations were sinopulmonary infections (SPI) (n = 58), neonatal respiratory distress (NRD) (n = 2), laterality defect (LD) (n = 6), and combined LD/SPI (n = 15). Biallelic likely deleterious variants were also encountered in AKNA and GOLGA3, which we propose as novel candidates in a lung phenotype that overlaps clinically with PCD. We also encountered a PCD phenocopy caused by a pathogenic variant in ITCH, and a pathogenic variant in CEP164 causing Bardet-Biedl syndrome and PCD presentation as a very rare example of the dual presentation of these two disorders of the primary and motile cilia. Exome sequencing is a powerful tool that can help "democratize" the diagnosis of PCD, which is currently limited to highly specialized centers.
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Affiliation(s)
- Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ibrahim Al Mogarri
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mansour M Alqwaiee
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Adel S Alharbi
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Khaled Baqais
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Muslim AlSaadi
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Talal AlAnzi
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Deparment of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Afaf Saghier
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Waleed Ameen
- Department of Pediatrics, King Saud Medical City, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jason Yang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Raghu R Chivukula
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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Kiseleva AV, Klimushina MV, Sotnikova EA, Divashuk MG, Ershova AI, Skirko OP, Kurilova OV, Zharikova AA, Khlebus EY, Efimova IA, Pokrovskaya MS, Slominsky PA, Shalnova SA, Meshkov AN, Drapkina OM. A Data-Driven Approach to Carrier Screening for Common Recessive Diseases. J Pers Med 2020; 10:E140. [PMID: 32971794 PMCID: PMC7563953 DOI: 10.3390/jpm10030140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic screening is an advanced tool for reducing recessive disease burden. Nowadays, it is still unclear as to the number of genes or their variants that are necessary for effective screening. This paper describes the development of a carrier screening custom panel for cystic fibrosis, phenylketonuria, alpha-1 antitrypsin deficiency, and sensorineural hearing loss consisting of 116 variants in the CFTR, PAH, SERPINA1, and GJB2 genes. The approach is based on the cheapest and fastest method, on using a small number of genes, and on the estimation of the effectiveness of carriers' detection. The custom panel was tested on a population-based cohort that included 1244 participants. Genotypes were determined by the TaqMan OpenArray Genotyping platform on the QuantStudio 12K Flex Real-Time PCR System. The frequency of heterozygotes in the Russian population was 16.87% or 1:6 (CI95%: 14.76-19.00% by Clopper-Pearson exact method): in CFTR-2.81% (1:36), PAH-2.33% (1:43), SERPINA1-4.90% (1:20), and GJB2-6.83% (1:15). The data on allele frequencies were obtained for the first time on a Russian population. The panel allows us to identify the vast majority of carriers of recessive diseases in the population. It is an effective approach to carrier screening for common recessive diseases.
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Affiliation(s)
- Anna V. Kiseleva
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Marina V. Klimushina
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Evgeniia A. Sotnikova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Mikhail G. Divashuk
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Alexandra I. Ershova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Olga P. Skirko
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Olga V. Kurilova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Anastasia A. Zharikova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 1-73, 119991 Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bol’shoi Karetnyi per., 19, 127051 Moscow, Russia
| | - Eleonora Yu. Khlebus
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Irina A. Efimova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Maria S. Pokrovskaya
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Petr A. Slominsky
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq., 2, 123182 Moscow, Russia;
| | - Svetlana A. Shalnova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Alexey N. Meshkov
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Oxana M. Drapkina
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
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45
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Ling C, Zhang D, Zhang J, Sun H, Du Q, Li X. Updates on the molecular genetics of primary congenital glaucoma (Review). Exp Ther Med 2020; 20:968-977. [PMID: 32742340 PMCID: PMC7388405 DOI: 10.3892/etm.2020.8767] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/01/2020] [Indexed: 12/14/2022] Open
Abstract
Primary congenital glaucoma (PCG) is one of the primary causes of blindness in children and is characterized by congenital trabecular meshwork and anterior chamber angle dysplasia. While being a rare condition, PCG severely impairs the quality of life of affected patients. However, the pathogenesis of PCG remains to be fully elucidated. It has previously been indicated that genetic factors serve a critical role in the pathogenesis of PCG, although patients with PCG exhibit significant genetic heterogeneity. Mutations in the cytochrome P450 family 1 subfamily B member 1 gene have been implicated in PCG and further genes that have been reported to be involved in PCG are myocilin, forkhead box C1, collagen type I α1 chain and latent transforming growth factor β binding protein 2. The present review aims to provide an up to date understanding of the genes associated with PCG and the use of molecular technologies in the identification of such genes and mutations. This may pave the way for the development of preventative methods, early diagnosis and improved therapeutic strategies in PCG.
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Affiliation(s)
- Chen Ling
- Sichuan Provincial Key Laboratory for Genetic Disease, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, P.R. China
| | - Dingding Zhang
- Sichuan Provincial Key Laboratory for Genetic Disease, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, P.R. China
| | - Jing Zhang
- Department of Thoracic Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Huanxin Sun
- Department of Immunology, North Sichuan Medical College, Nanchong, Sichuan 637100, P.R. China
| | - Qiu Du
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
| | - Xuefei Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
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46
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FitzPatrick DR, Firth HV. Genomically Aided Diagnosis of Severe Developmental Disorders. Annu Rev Genomics Hum Genet 2020; 21:327-349. [PMID: 32421356 DOI: 10.1146/annurev-genom-120919-082329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our ability to make accurate and specific genetic diagnoses in individuals with severe developmental disorders has been transformed by data derived from genomic sequencing technologies. These data reveal both the patterns and rates of different mutational mechanisms and identify regions of the human genome with fewer mutations than would be expected. In outbred populations, the most common identifiable cause of severe developmental disorders is de novo mutation affecting the coding region in one of approximately 500 different genes, almost universally showing constraint. Simply combining the location of a de novo genomic event with its predicted consequence on the gene product gives significant diagnostic power. Our knowledge of the diversity of phenotypic consequences associated with comparable diagnostic genotypes at each locus is improving. Computationally useful phenotype data will improve diagnostic interpretation of ultrarare genetic variants and, in the long run, indicate which specific embryonic processes have been perturbed.
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Affiliation(s)
- David R FitzPatrick
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom; .,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom.,Royal Hospital for Children and Young People, Edinburgh EH16 4SF, United Kingdom
| | - Helen V Firth
- Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; .,Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
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47
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El Bitar F, Qadi N, Al Rajeh S, Majrashi A, Abdulaziz S, Majrashi N, Al Inizi M, Taher A, Al Tassan N. Genetic Study of Alzheimer's Disease in Saudi Population. J Alzheimers Dis 2020; 67:231-242. [PMID: 30636737 DOI: 10.3233/jad-180415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is a chronic neurological disorder associated with mental decline and dementia. Several studies focused on investigating the molecular basis of the disease that led to the identification of several causative genes and risk associated alleles. Replication of these studies and findings from different populations is very important. OBJECTIVE Molecular assessment of a cohort of 117 familial and sporadic AD cases from Saudi Arabia. METHODS Comprehensive screening for point mutations was carried out by direct sequencing of coding regions in the three known AD causative genes: PSEN1, PSEN2, APP, as well as the AD associated gene SORL1. All patients were also genotyped for APOE alleles. In silico 3D protein structure analysis was performed for two novel SORL1 variants. RESULTS We identified a total of eight potential pathogenic missense variants in all studied genes. Five of these variants were not previously reported including four in SORL1 (p.Val297Met, p.Arg1084Cys, p.Asp1100Asn, and p.Pro1213Ser) and one in APP (p.Glu380Lys). The frequency of APOE-ɛ4 allele was 21.37% of total investigated cases. In silico 3D protein structure analysis of two SORL1 novel missense variants (p.Pro1213Ser and p.Arg1084Cys) suggested that these variants may affect the folding of the proteins and disturb their structure. CONCLUSIONS Our comprehensive analysis of the open reading frame of the known genes have identified potential pathogenic rare variants in 18/117 cases. We found that point mutations in AD main genes (PSEN1, PSEN2, and APP) were underrepresented in our cohort of patients. Our results confirm involvement of SORL1 in familial and sporadic AD cases.
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Affiliation(s)
- Fadia El Bitar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Najeeb Qadi
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Saad Al Rajeh
- Al Habib Medical Center, Riyadh, Kingdom of Saudi Arabia
| | - Amna Majrashi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Sara Abdulaziz
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Nada Majrashi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Maznah Al Inizi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Asma Taher
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Nada Al Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
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48
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Almannai M, Obaid O, Faqeih E, Alasmari A, Samman MM, Pinz H, Braddock SR, Alkuraya FS. Further delineation of METTL23-associated intellectual disability. Am J Med Genet A 2020; 182:785-791. [PMID: 32067349 DOI: 10.1002/ajmg.a.61503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/08/2019] [Accepted: 01/17/2020] [Indexed: 11/07/2022]
Abstract
METTL23 belongs to a family of methyltransferase like proteins (METTL) that transfer methyl group to various substrates. Recently, pathogenic homozygous variants in METTL23 were identified in patients from three families who presented with intellectual disability (ID) and variable dysmorphic features. In this report, we present unpublished phenotypic data from the original family as well as six new subjects from four families who also presented with mild to moderate ID and dysmorphic features, and were found to harbor four previously unpublished homozygous or compound heterozygous variants in METTL23. Our report further supports the role of this gene in autosomal recessive ID and emphasizes the mild but consistent facial features.
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Affiliation(s)
- Mohammed Almannai
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Osama Obaid
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Alasmari
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Manar M Samman
- Pathology and Clinical Laboratory Medicine Administration, Section of Molecular Pathology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hailey Pinz
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Medical Center, St. Louis, Missouri.,Department of Pediatrics, Saint Louis University Hospital, St. Louis, Missouri
| | - Stephen R Braddock
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Medical Center, St. Louis, Missouri.,Department of Pediatrics, Saint Louis University Hospital, St. Louis, Missouri
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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49
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Five Novel Mutations in LOXHD1 Gene Were Identified to Cause Autosomal Recessive Nonsyndromic Hearing Loss in Four Chinese Families. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1685974. [PMID: 32149082 PMCID: PMC7049443 DOI: 10.1155/2020/1685974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/17/2020] [Indexed: 01/31/2023]
Abstract
Hearing loss is one of the most common sensory disorders in newborns and is mostly caused by genetic factors. Autosomal recessive nonsyndromic hearing loss (ARNSHL) is usually characterized as a severe-to-profound congenital sensorineural hearing loss and later can cause various degrees of defect in the language and intelligent development of newborns. The mutations in LOXHD1 gene have been shown to cause DFNB77, a type of ARNSHL. To date, there are limited reports about the association between LOXHD1 gene and ARNSHL. In this study, we reported six patients from four Chinese families suffering from severe-to-profound nonsyndromic hearing loss. We performed targeted next generation sequencing in the six affected members and identified five novel pathogenic mutations in LOXHD1 including c.277G>A (p.D93N), c.611-2A>T, c.1255+3A>G, c.2329C>T (p.Q777 ∗ ), and c.5888delG (p.G1963Afs ∗ 136). These mutations were confirmed to be cosegregated with the hearing impairment in the families by Sanger sequencing and were inherited in an autosomal recessive pattern. All of the five mutations were absent in 200 control subjects. There were no symptoms of Fuchs corneal dystrophy in the probands and their blood-related relatives. We concluded that these five novel mutations could be involved in the underlying mechanism resulting in the hearing loss, and this discovery expands the genotypic spectrum of LOXHD1 mutations.
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50
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Huizing M, Malicdan MCV, Wang JA, Pri-Chen H, Hess RA, Fischer R, O'Brien KJ, Merideth MA, Gahl WA, Gochuico BR. Hermansky-Pudlak syndrome: Mutation update. Hum Mutat 2020; 41:543-580. [PMID: 31898847 DOI: 10.1002/humu.23968] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/06/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022]
Abstract
Hermansky-Pudlak syndrome (HPS) is a group of 10 autosomal recessive multisystem disorders, each defined by the deficiency of a specific gene. HPS-associated genes encode components of four ubiquitously expressed protein complexes: Adaptor protein-3 (AP-3) and biogenesis of lysosome-related organelles complex-1 (BLOC-1) through -3. All individuals with HPS exhibit albinism and a bleeding diathesis; additional features occur depending on the defective protein complex. Pulmonary fibrosis is associated with AP-3 and BLOC-3 deficiency, immunodeficiency with AP-3 defects, and gastrointestinal symptoms are more prevalent and severe in BLOC-3 deficiency. Therefore, identification of the HPS subtype is valuable for prognosis, clinical management, and treatment options. The prevalence of HPS is estimated at 1-9 per 1,000,000. Here we summarize 264 reported and novel variants in 10 HPS genes and estimate that ~333 Puerto Rican HPS subjects and ~385 with other ethnicities are reported to date. We provide pathogenicity predictions for missense and splice site variants and list variants with high minor allele frequencies. Current cellular and clinical aspects of HPS are also summarized. This review can serve as a manifest for molecular diagnostics and genetic counseling aspects of HPS.
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Affiliation(s)
- Marjan Huizing
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - May C V Malicdan
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Jennifer A Wang
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Hadass Pri-Chen
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Richard A Hess
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Roxanne Fischer
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Kevin J O'Brien
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Melissa A Merideth
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Bernadette R Gochuico
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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