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Fattahi Z, Shokouhian E, Peymani F, Babanejad M, Beheshtian M, Edizadeh M, Molaei N, Alagha P, Ghodratpour F, Keshavarzi F, Moghadam MG, Arzhangi S, Kahrizi K, Najmabadi H. Improved Diagnostic Yield in Recessive Intellectual Disability Utilizing Systematic Whole Exome Sequencing Data Reanalysis. Clin Genet 2025; 107:612-619. [PMID: 39748273 DOI: 10.1111/cge.14692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Revised: 12/13/2024] [Accepted: 12/19/2024] [Indexed: 01/04/2025]
Abstract
Recent advances in next generation sequencing (NGS) have positioned whole exome sequencing (WES) as an efficient first-tier method in genetic diagnosis. However, despite the diagnostic yield of 35%-50% in intellectual disability (ID) many patients still remain undiagnosed due to inherent limitations and bioinformatic short-comings. In this study, we reanalyzed WES data from 159 Iranian families showing recessively inherited ID. The reanalysis was conducted with an initial clinical re-evaluation of the patients and their families, followed by data reanalysis using two updated bioinformatic pipelines. In the first phase, the BWA-GATK pipeline was utilized for alignment and variant calling, with subsequent variant annotation by the ANNOVAR tool. This approach yielded causative variants in 17 families (10.6%). Among these, six genes (MAZ, ACTR5, AKTIP, MIX23, SERPINB12, and CDC25B) were identified as novel candidates potentially associated with ID, supported by bioinformatics functional annotation and segregation analysis. In the second phase, families with negative results were reassessed using the Illumina DRAGEN Bio-IT platform for variant-calling, and Ilyome, a newly developed web-based tool, for annotation. The second phase identified likely pathogenic variants in two additional families, increasing the total diagnostic yield to 11.9% which is consistent with other studies conducted on cohorts of patients with ID. In conclusion, identification of co-segregating variants in six novel candidate genes in this study, emphasizes once more on the potential of WES reanalysis to uncover previously unknown gene-disease associations. Notably, it demonstrates that systematic reanalysis of WES data using updated bioinformatic tools and a thorough review of the literature for new gene-disease associations while performing phenotypic re-evaluation, can improve diagnostic outcome of WES in recessively inherited ID. Consequently, if performed within a 1-3 year period, it can reduce the number of cases that may require other costly diagnostic methods such as whole genome sequencing.
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Affiliation(s)
- Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ebrahim Shokouhian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Peymani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Masoud Edizadeh
- Department of Bioinformatics, Genoks Genetic Diagnosis Center, Ankara, Turkey
| | - Negar Molaei
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Parnian Alagha
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Keshavarzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Zhang Y, Xie Y, Hu X, Wei A. Identification of POLA1 gene deep intronic mutation confirms diagnosis of X-linked reticulate pigmentary disorder in a Chinese patient. Indian J Dermatol Venereol Leprol 2024; 0:1-4. [PMID: 39635787 DOI: 10.25259/ijdvl_623_2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 09/12/2024] [Indexed: 12/07/2024]
Affiliation(s)
- Yingzi Zhang
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yutong Xie
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xuyun Hu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Aihua Wei
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Zhang Y, Bi C, Nadeef S, Maddirevula S, Alqahtani M, Alkuraya FS, Li M. NanoRanger enables rapid single-base-pair resolution of genomic disorders. MED 2024; 5:1307-1325.e3. [PMID: 39047733 DOI: 10.1016/j.medj.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/13/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Delineating base-resolution breakpoints of complex rearrangements is crucial for an accurate clinical understanding of pathogenic variants and for carrier screening within family networks or the broader population. However, despite advances in genetic testing using short-read sequencing (SRS), this task remains costly and challenging. METHODS This study addresses the challenges of resolving missing disease-causing breakpoints in complex genomic disorders with suspected homozygous rearrangements by employing multiple long-read sequencing (LRS) strategies, including a novel and efficient strategy named nanopore-based rapid acquisition of neighboring genomic regions (NanoRanger). NanoRanger does not require large amounts of ultrahigh-molecular-weight DNA and stands out for its ease of use and rapid acquisition of large genomic regions of interest with deep coverage. FINDINGS We describe a cohort of 16 familial cases, each harboring homozygous rearrangements that defied breakpoint determination by SRS and optical genome mapping (OGM). NanoRanger identified the breakpoints with single-base-pair resolution, enabling accurate determination of the carrier status of unaffected family members as well as the founder nature of these genomic lesions and their frequency in the local population. The resolved breakpoints revealed that repetitive DNA, gene regulatory elements, and transcription activity contribute to genome instability in these novel recessive rearrangements. CONCLUSIONS Our data suggest that NanoRanger greatly improves the success rate of resolving base-resolution breakpoints of complex genomic disorders and expands access to LRS for the benefit of patients with Mendelian disorders. FUNDING M.L. is supported by KAUST Baseline Award no. BAS/1/1080-01-01 and KAUST Research Translation Fund Award no. REI/1/4742-01.
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Affiliation(s)
- Yingzi Zhang
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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4
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Sedlackova L, Sterbova K, Vlckova M, Seeman P, Zarubova J, Marusic P, Krsek P, Krijtova H, Musilova A, Lassuthova P. Yield of exome sequencing in patients with developmental and epileptic encephalopathies and inconclusive targeted gene panel. Eur J Paediatr Neurol 2024; 48:17-29. [PMID: 38008000 DOI: 10.1016/j.ejpn.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 10/25/2023] [Accepted: 10/28/2023] [Indexed: 11/28/2023]
Abstract
OBJECTIVE Developmental and epileptic encephalopathies (DEEs) are a group of severe, early-onset epilepsies characterised by refractory seizures, developmental delay, or regression and generally poor prognosis. DEE are now known to have an identifiable molecular genetic basis and are usually examined using a gene panel. However, for many patients, the genetic cause has still not been identified. The aims of this study were to identify causal variants for DEE in patients for whom the previous examination with a gene panel did not determine their genetic diagnosis. It also aims for a detailed description and broadening of the phenotypic spectrum of several rare DEEs. METHODS In the last five years (2015-2020), 141 patients from all over the Czech Republic were referred to our department for genetic testing in association with their diagnosis of epilepsy. All patients underwent custom-designed gene panel testing prior to enrolment into the study, and their results were inconclusive. We opted for whole exome sequencing (WES) to identify the cause of their disorder. If a causal or potentially causal variant was identified, we performed a detailed clinical evaluation and phenotype-genotype correlation study to better describe the specific rare subtypes. RESULTS Explanatory causative variants were detected in 20 patients (14%), likely pathogenic variants that explain the epilepsy in 5 patients (3.5%) and likely pathogenic variants that do not fully explain the epilepsy in 11 patients (7.5%), and variants in candidate genes in 4 patients (3%). Variants were mostly de novo 29/40 (72.5%). SIGNIFICANCE WES enables us to identify the cause of the disease in additional patients, even after gene panel testing. It is very important to perform a WES in DEE patients as soon as possible, since it will spare the patients and their families many years of a diagnostic odyssey. In particular, patients with rare epilepsies might significantly benefit from this approach, and we propose using WES as a new standard in the diagnosis of DEE instead of targeted gene panel testing.
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Affiliation(s)
- Lucie Sedlackova
- Neurogenetic Laboratory, Department of Paediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Katalin Sterbova
- Department of Paediatric Neurology, Second Faculty of Medicine, Motol Epilepsy Center, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Marketa Vlckova
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Pavel Seeman
- Neurogenetic Laboratory, Department of Paediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic; Department of Medical Genetics, Masaryk Hospital, Ústí nad Labem, Czech Republic.
| | - Jana Zarubova
- Department of Neurology, Motol Epilepsy Center, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Petr Marusic
- Department of Neurology, Motol Epilepsy Center, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Pavel Krsek
- Department of Paediatric Neurology, Second Faculty of Medicine, Motol Epilepsy Center, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Hana Krijtova
- Department of Neurology, Motol Epilepsy Center, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Alena Musilova
- Neurogenetic Laboratory, Department of Paediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
| | - Petra Lassuthova
- Neurogenetic Laboratory, Department of Paediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Full Member of the ERN EpiCARE, Czech Republic.
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AlAbdi L, Shamseldin HE, Khouj E, Helaby R, Aljamal B, Alqahtani M, Almulhim A, Hamid H, Hashem MO, Abdulwahab F, Abouyousef O, Jaafar A, Alshidi T, Al-Owain M, Alhashem A, Al Tala S, Khan AO, Mardawi E, Alkuraya H, Faqeih E, Afqi M, Alkhalifi S, Rahbeeni Z, Hagos ST, Al-Ahmadi W, Nadeef S, Maddirevula S, Khabar KSA, Putra A, Angelov A, Park C, Reyes-Ramos AM, Umer H, Ullah I, Driguez P, Fukasawa Y, Cheung MS, Gallouzi IE, Alkuraya FS. Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases. Genome Med 2023; 15:114. [PMID: 38098057 PMCID: PMC10720148 DOI: 10.1186/s13073-023-01270-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bayan Aljamal
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Pediatric Department, Division of Genetic and Metabolic Medicine, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Pediatric Department, Neonatal Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Elham Mardawi
- Maternal Fetal Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery and Ocular Genetics, Global Eye Care/Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Manal Afqi
- Metabolic and Genetic Center, King Salman Bin Abdulaziz Medical City, Almadinah Almunwarah, Saudi Arabia
| | - Salwa Alkhalifi
- Newborn Screening, Ministry of Health, Eastern Province, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wijdan Al-Ahmadi
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alexander Putra
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Angel Angelov
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Changsook Park
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ana M Reyes-Ramos
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Husen Umer
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ikram Ullah
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Patrick Driguez
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ming Sin Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Imed Eddine Gallouzi
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Bartolomaeus T, Hentschel J, Jamra RA, Popp B. Re-evaluation and re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 18. Eur J Hum Genet 2023; 31:1154-1164. [PMID: 37460657 PMCID: PMC10545662 DOI: 10.1038/s41431-023-01425-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
Iterative re-analysis of NGS results is not well investigated for published research cohorts of rare diseases. We revisited a cohort of 152 consanguineous families with developmental disorders (NDD) reported five years ago. We re-evaluated all reported variants according to diagnostic classification guidelines or our candidate gene scoring system (AutoCaSc) and systematically scored the validity of gene-disease associations (GDA). Sequencing data was re-processed using an up-to-date pipeline for case-level re-analysis. In 28/152 (18%) families, we identified a clinically relevant change. Ten previously reported (likely) pathogenic variants were re-classified as VUS/benign. In one case, the GDA (TSEN15) validity was judged as limited, and in five cases GDAs are meanwhile established. We identified 12 new disease causing variants. Two previously reported variants were missed by our updated pipeline due to alignment or reference issues. Our results support the need to re-evaluate screening studies, not only the negative cases but including supposedly solved ones. This also applies in a diagnostic setting. We highlight that the complexity of computational re-analysis for old data should be weighed against the decreasing re-testing costs. Since extensive re-analysis per case is beyond the resources of most institutions, we recommend a screening procedure that would quickly identify the majority (83%) of new variants.
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Affiliation(s)
- Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Functional Genomics, Hessische Straße 4A, 10115, Berlin, Germany.
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7
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AlAbdi L, Maddirevula S, Shamseldin HE, Khouj E, Helaby R, Hamid H, Almulhim A, Hashem MO, Abdulwahab F, Abouyousef O, Alqahtani M, Altuwaijri N, Jaafar A, Alshidi T, Alzahrani F, Alkuraya FS. Diagnostic implications of pitfalls in causal variant identification based on 4577 molecularly characterized families. Nat Commun 2023; 14:5269. [PMID: 37644014 PMCID: PMC10465531 DOI: 10.1038/s41467-023-40909-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Despite large sequencing and data sharing efforts, previously characterized pathogenic variants only account for a fraction of Mendelian disease patients, which highlights the need for accurate identification and interpretation of novel variants. In a large Mendelian cohort of 4577 molecularly characterized families, numerous scenarios in which variant identification and interpretation can be challenging are encountered. We describe categories of challenges that cover the phenotype (e.g. novel allelic disorders), pedigree structure (e.g. imprinting disorders masquerading as autosomal recessive phenotypes), positional mapping (e.g. double recombination events abrogating candidate autozygous intervals), gene (e.g. novel gene-disease assertion) and variant (e.g. complex compound inheritance). Overall, we estimate a probability of 34.3% for encountering at least one of these challenges. Importantly, our data show that by only addressing non-sequencing-based challenges, around 71% increase in the diagnostic yield can be expected. Indeed, by applying these lessons to a cohort of 314 cases with negative clinical exome or genome reports, we could identify the likely causal variant in 54.5%. Our work highlights the need to have a thorough approach to undiagnosed diseases by considering a wide range of challenges rather than a narrow focus on sequencing technologies. It is hoped that by sharing this experience, the yield of undiagnosed disease programs globally can be improved.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Norah Altuwaijri
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
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8
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Wormser O, Perez Y, Dolgin V, Kamali B, Tangeman JA, Gradstein L, Yogev Y, Hadar N, Freund O, Drabkin M, Halperin D, Irron I, Grajales-Esquivel E, Del Rio-Tsonis K, Birnbaum RY, Akler G, Birk OS. IHH enhancer variant within neighboring NHEJ1 intron causes microphthalmia anophthalmia and coloboma. NPJ Genom Med 2023; 8:22. [PMID: 37580330 PMCID: PMC10425348 DOI: 10.1038/s41525-023-00364-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1. The human NHEJ1 intronic variant lies within a known specifically limb-development enhancer of a neighboring gene, Indian hedgehog (Ihh), known to be involved in eye development in mice and chickens. Through mouse and chicken molecular development studies, we demonstrated that this variant is within an Ihh enhancer that drives gene expression in the developing eye and that the identified variant affects this eye-specific enhancer activity. We thus delineate an Ihh enhancer active in mammalian eye development whose variant causes human microphthalmia, anophthalmia and ocular coloboma. The findings highlight disease causation by an intronic variant affecting the expression of a neighboring gene, delineating molecular pathways of eye development.
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Affiliation(s)
- Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Vadim Dolgin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bahman Kamali
- Medical Advisory Committee, United Mashhadi Jewish Community of America, 54 Steamboat Rd., Great Neck, NY, 11024, USA
| | - Jared A Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noam Hadar
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ofek Freund
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Inbar Irron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Ramon Y Birnbaum
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gidon Akler
- TOVANA Health, Houston, TX, USA.
- Precision Medicine Insights, P.C., Great Neck, NY, USA.
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Genetics Institute, Soroka Medical Center affiliated to Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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9
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Al-Kouatly HB, Shivashankar K, Mossayebi MH, Makhamreh M, Critchlow E, Gao Z, Fasehun LK, Alkuraya FS, Ryan EE, Hegde M, Wodoslawsky S, Hughes J, Berger SI. Diagnostic yield from prenatal exome sequencing for non-immune hydrops fetalis: A systematic review and meta-analysis. Clin Genet 2023; 103:503-512. [PMID: 36757664 DOI: 10.1111/cge.14309] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Non-immune hydrops fetalis (NIHF) has multiple genetic etiologies diagnosable by exome sequencing (ES). We evaluated the yield of prenatal ES for NIHF, and the contribution of additional clinical findings and history. Systematic review was performed with PROSPERO tag 232951 using CINAHL, PubMed, and Ovid MEDLINE from January 1, 2000 through December 1, 2021. Selected studies performed ES to augment standard prenatal diagnostic approaches. Cases meeting a strict NIHF phenotype were tabulated with structured data imputed from papers or requested from authors. Genetic variants and diagnostic outcomes were harmonized across studies using current ACMG and ClinGen variant classification guidelines. Thirty-one studies reporting 445 NIHF cases had a 37% (95% CI: 32%-41%) diagnostic rate. There was no significant difference between isolated NIHF and NIHF with fetal malformations or between recurrent and simplex cases. Diagnostic rate was higher for consanguineous than non-consanguineous cases. Disease categories included RASopathies (24%), neuromuscular (21%), metabolic (17%), lymphatic (13%), other syndromes (9%), cardiovascular (5%), hematologic (2%), skeletal (2%), and other categories (7%). Inheritance patterns included recessive (55%), dominant (41%), and X-linked (4%). ES should be considered in the diagnostic workup of NIHF with and without associated ultrasound findings regardless of history of recurrence or consanguinity.
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Affiliation(s)
- Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Matthew H Mossayebi
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mona Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Zimeng Gao
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Luther-King Fasehun
- Department of Epidemiology and Biostatistics, College of Public Health, Temple University, Philadelphia, Pennsylvania, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Erin E Ryan
- Genomic Data / Genetic Counseling, GeneDx, Gaithersburg, Maryland, USA
| | - Madhuri Hegde
- Global Lab Services, PerkinElmer Genomics, Atlanta, Georgia, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joel Hughes
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
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10
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Khouj E, Bohlega S, Alkuraya FS. Cerebrotendinous xanthomatosis: A candidate for ACMG list of secondary findings? Clin Genet 2023; 103:125-126. [PMID: 36129065 DOI: 10.1111/cge.14230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saeed Bohlega
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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11
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Five years' experience of the clinical exome sequencing in a Spanish single center. Sci Rep 2022; 12:19209. [PMID: 36357507 PMCID: PMC9649665 DOI: 10.1038/s41598-022-23786-6] [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: 05/19/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Nowadays, exome sequencing is a robust and cost-efficient genetic diagnostic tool already implemented in many clinical laboratories. Despite it has undoubtedly improved our diagnostic capacity and has allowed the discovery of many new Mendelian-disease genes, it only provides a molecular diagnosis in up to 25-30% of cases. Here, we comprehensively evaluate the results of a large sample set of 4974 clinical exomes performed in our laboratory over a period of 5 years, showing a global diagnostic rate of 24.62% (1391/4974). For the evaluation we establish different groups of diseases and demonstrate how the diagnostic rate is not only dependent on the analyzed group of diseases (43.12% in ophthalmological cases vs 16.61% in neurological cases) but on the specific disorder (47.49% in retinal dystrophies vs 24.02% in optic atrophy; 18.88% in neuropathies/paraparesias vs 11.43% in dementias). We also detail the most frequent mutated genes within each group of disorders and discuss, on our experience, further investigations and directions needed for the benefit of patients.
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12
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Koh K, Shimazaki H, Ogawa M, Takiyama Y. A heterozygous GRID2 mutation in autosomal dominant cerebellar ataxia. Hum Genome Var 2022; 9:27. [PMID: 35882834 PMCID: PMC9325744 DOI: 10.1038/s41439-022-00204-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 01/12/2023] Open
Abstract
A heterozygous mutation in GRID2 that causes SCAR18 was first reported in an Algerian family with autosomal dominant cerebellar ataxia (ADCA). We identified the second ADCA family with a heterozygous GRID2 mutation. The Algerian family had cognitive impairment and hearing loss associated with cerebellar ataxia. However, the Japanese family presented here showed pure cerebellar ataxia. Therefore, we should also screen for the GRID2 mutation in ADCA families with pure cerebellar ataxia.
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Affiliation(s)
- Kishin Koh
- grid.267500.60000 0001 0291 3581Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, 409-3898 Japan
| | - Haruo Shimazaki
- grid.410802.f0000 0001 2216 2631Faculty of Health & Medical Care, Saitama Medical University, Saitama, 350-1241 Japan
| | | | - Yoshihisa Takiyama
- grid.267500.60000 0001 0291 3581Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, 409-3898 Japan
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13
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Kumari R, Grzywa TM, Małecka-Giełdowska M, Tyszkowska K, Wrzesień R, Ciepiela O, Nowis D, Kaźmierczak P. Ablation of Tmcc2 Gene Impairs Erythropoiesis in Mice. Int J Mol Sci 2022; 23:ijms23095263. [PMID: 35563652 PMCID: PMC9102901 DOI: 10.3390/ijms23095263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 12/23/2022] Open
Abstract
(1) Background: Transcriptomic and proteomic studies provide a wealth of new genes potentially involved in red blood cell (RBC) maturation or implicated in the pathogenesis of anemias, necessitating validation of candidate genes in vivo; (2) Methods: We inactivated one such candidate, transmembrane and coiled-coil domain 2 (Tmcc2) in mice, and analyzed the erythropoietic phenotype by light microscopy, transmission electron microscopy (TEM), and flow cytometry of erythrocytes and erythroid precursors; (3) Results: Tmcc2−/− pups presented pallor and reduced body weight due to the profound neonatal macrocytic anemia with numerous nucleated RBCs (nRBCs) and occasional multinucleated RBCs. Tmcc2−/− nRBCs had cytoplasmic intrusions into the nucleus and double membranes. Significantly fewer erythroid cells were enucleated. Adult knockouts were normocytic, mildly polycythemic, with active extramedullary erythropoiesis in the spleen. Altered relative content of different stage CD71+TER119+ erythroid precursors in the bone marrow indicated a severe defect of erythroid maturation at the polychromatic to orthochromatic transition stage; (4) Conclusions: Tmcc2 is required for normal erythropoiesis in mice. While several phenotypic features resemble congenital dyserythropoietic anemias (CDA) types II, III, and IV, the involvement of TMCC2 in the pathogenesis of CDA in humans remains to be determined.
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Affiliation(s)
- Ranju Kumari
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland;
- School of Molecular Medicine, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Tomasz M. Grzywa
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland; (T.M.G.); (D.N.)
- Doctoral School, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland
- Laboratory of Experimental Medicine, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland
| | - Milena Małecka-Giełdowska
- Department of Laboratory Medicine, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland; (M.M.-G.); (O.C.)
| | - Karolina Tyszkowska
- Central Laboratory of Experimental Animal, Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland; (K.T.); (R.W.)
| | - Robert Wrzesień
- Central Laboratory of Experimental Animal, Centre for Preclinical Research, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland; (K.T.); (R.W.)
| | - Olga Ciepiela
- Department of Laboratory Medicine, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland; (M.M.-G.); (O.C.)
| | - Dominika Nowis
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland; (T.M.G.); (D.N.)
- Laboratory of Experimental Medicine, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland
| | - Piotr Kaźmierczak
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland;
- Correspondence: or
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14
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Robertson AJ, Tan NB, Spurdle AB, Metke-Jimenez A, Sullivan C, Waddell N. Re-analysis of genomic data: An overview of the mechanisms and complexities of clinical adoption. Genet Med 2022; 24:798-810. [PMID: 35065883 DOI: 10.1016/j.gim.2021.12.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Re-analyzing genomic information from a patient suspected of having an underlying genetic condition can improve the diagnostic yield of sequencing tests, potentially providing significant benefits to the patient and to the health care system. Although a significant number of studies have shown the clinical potential of re-analysis, less work has been performed to characterize the mechanisms responsible for driving the increases in diagnostic yield. Complexities surrounding re-analysis have also emerged. The terminology itself represents a challenge because "re-analysis" can refer to a range of different concepts. Other challenges include the increased workload that re-analysis demands of curators, adequate reimbursement pathways for clinical and diagnostic services, and the development of systems to handle large volumes of data. Re-analysis also raises ethical implications for patients and families, most notably when re-classification of a variant alters diagnosis, treatment, and prognosis. This review highlights the possibilities and complexities associated with the re-analysis of existing clinical genomic data. We propose a terminology that builds on the foundation presented in a recent statement from the American College of Medical Genetics and Genomics and describes each re-analysis process. We identify mechanisms for increasing diagnostic yield and provide perspectives on the range of challenges that must be addressed by health care systems and individual patients.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; The Genomic Institute, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Natalie B Tan
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Clair Sullivan
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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15
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Romero R, de la Fuente L, Del Pozo-Valero M, Riveiro-Álvarez R, Trujillo-Tiebas MJ, Martín-Mérida I, Ávila-Fernández A, Iancu IF, Perea-Romero I, Núñez-Moreno G, Damián A, Rodilla C, Almoguera B, Cortón M, Ayuso C, Mínguez P. An evaluation of pipelines for DNA variant detection can guide a reanalysis protocol to increase the diagnostic ratio of genetic diseases. NPJ Genom Med 2022; 7:7. [PMID: 35087072 PMCID: PMC8795168 DOI: 10.1038/s41525-021-00278-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/09/2021] [Indexed: 01/01/2023] Open
Abstract
Clinical exome (CE) sequencing has become a first-tier diagnostic test for hereditary diseases; however, its diagnostic rate is around 30-50%. In this study, we aimed to increase the diagnostic yield of CE using a custom reanalysis algorithm. Sequencing data were available for three cohorts using two commercial protocols applied as part of the diagnostic process. Using these cohorts, we compared the performance of general and clinically relevant variant calling and the efficacy of an in-house bioinformatic protocol (FJD-pipeline) in detecting causal variants as compared to commercial protocols. On the whole, the FJD-pipeline detected 99.74% of the causal variants identified by the commercial protocol in previously solved cases. In the unsolved cases, FJD-pipeline detects more INDELs and non-exonic variants, and is able to increase the diagnostic yield in 2.5% and 3.2% in the re-analysis of 78 cancer and 62 cardiovascular cases. These results were considered to design a reanalysis, filtering and prioritization algorithm that was tested by reassessing 68 inconclusive cases of monoallelic autosomal recessive retinal dystrophies increasing the diagnosis by 4.4%. In conclusion, a guided NGS reanalysis of unsolved cases increases the diagnostic yield in genetic disorders, making it a useful diagnostic tool in medical genetics.
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Affiliation(s)
- Raquel Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Bioinformatics Unit, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Riveiro-Álvarez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - María José Trujillo-Tiebas
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada Martín-Mérida
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Almudena Ávila-Fernández
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ionut-Florin Iancu
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gonzalo Núñez-Moreno
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Bioinformatics Unit, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Alejandra Damián
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Rodilla
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Berta Almoguera
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Cortón
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
| | - Pablo Mínguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Bioinformatics Unit, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.
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16
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Beshlawy AE, Zekri AER, Ramadan MS, Selim YMM, Abdel-Salam A, Hegazy MT, Ragab L, Gaggiano C, Cantarini L, Ragab G. Genotype-phenotype associations in familial Mediterranean fever: a study of 500 Egyptian pediatric patients. Clin Rheumatol 2022; 41:1511-1521. [PMID: 34988684 DOI: 10.1007/s10067-021-06006-w] [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] [Received: 09/13/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/03/2022]
Abstract
INTRODUCTION Familial Mediterranean fever (FMF) is the most prevalent monogenic autoinflammatory disease, caused by recessively inherited MEFV gene mutations. The most frequent MEFV mutations differ in penetrance and disease severity. We investigated the genotype-phenotype associations of the three most frequent MEFV gene mutations (M680I, M694V, and V726A) in Egyptian FMF children, regarding clinical features, severity, and colchicine response. METHODS We conducted a retrospective analysis of the medical registries of 500 FMF pediatric patients from Metropolitan Cairo between 2010 and 2015. The diagnosis was based on the Tel-Hashomer clinical diagnostic criteria. Clinical data and baseline investigations were collected. Mutation analysis was performed by the amplification-refractory mutation system (ARMS)-PCR method. RESULTS Males represented 54% and ages ranged from 2 to 18 years. The most frequent symptoms were abdominal pain, fever, and arthralgia. Clinical features mostly associated with M694V mutation either homozygous or heterozygous whether simple, double, or triple. Of the patients, 94.6% completely responded to colchicine. Among patients benefiting from colchicine, 42.5% had M694V/V726A, 21.6% had M694V/V726A/M680I, and 21.1% had M694V genotype. Simple heterozygous M694V or V726A mutations conveyed a moderate phenotype in 57.1% and 50% of cases, respectively. Homozygous M694V mutation showed moderate and severe phenotypes in 21.7% and 65.2% of cases, respectively. Compound M694V/V726A mutation associated with moderate or severe disease in 48.3% and 33.8% of cases, respectively. CONCLUSION This study encompasses the largest group of Egyptian pediatric FMF up to date to explore their genotype-phenotype associations. Our results support the notion that the genotype influences the phenotype as regards clinical manifestations, disease severity, and colchicine response. KEY POINTS • This study encompasses the largest group of Egyptian pediatric patients affected by FMF up to date to explore their genotype-phenotype associations. • Our results support the notion that the genotype influences the phenotype as regards the clinical manifestations, the disease severity, and the response to colchicine treatment.
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Affiliation(s)
- Amal El Beshlawy
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Abd El Rahman Zekri
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Manal S Ramadan
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Yasmeen M M Selim
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Amina Abdel-Salam
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Tharwat Hegazy
- Internal Medicine Department, Rheumatology and Clinical Immunology Unit, Faculty of Medicine, Cairo University, Cairo, Egypt.,Newgiza University (NGU), Giza, Egypt
| | | | - Carla Gaggiano
- Department of Medical Sciences, Surgery, and Neurosciences, Rheumatology Unit, University of Siena, Policlinico "Le Scotte", Siena, Italy
| | - Luca Cantarini
- Department of Medical Sciences, Surgery, and Neurosciences, Rheumatology Unit, University of Siena, Policlinico "Le Scotte", Siena, Italy
| | - Gaafar Ragab
- Internal Medicine Department, Rheumatology and Clinical Immunology Unit, Faculty of Medicine, Cairo University, Cairo, Egypt. .,Newgiza University (NGU), Giza, Egypt.
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17
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AlQudairy H, AlDhalaan H, AlRuways S, AlMutairi N, AlNakiyah M, AlGhofaili R, AlBakheet A, Alomrani A, Alharbi OA, Tous E, AlSayed M, AlZaidan H, AlRasheed MM, AlOdaib A, Kaya N. Clinical, radiological, and genetic characterization of SLC13A5 variants in Saudi families: Genotype phenotype correlation and brief review of the literature. Front Pediatr 2022; 10:1051534. [PMID: 36923948 PMCID: PMC10008858 DOI: 10.3389/fped.2022.1051534] [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: 09/22/2022] [Accepted: 12/14/2022] [Indexed: 03/03/2023] Open
Abstract
Background SLC13A5 (solute carrier family 13, member 5) encodes sodium/citrate cotransporter, which mainly localizes in cellular plasma membranes in the frontal cortex, retina, and liver. Pathogenic variants of the gene cause an autosomal recessive syndrome known as "developmental and epileptic encephalopathy 25 with amelogenesis imperfecta." Results Here, we have investigated six patients from three different consanguineous Saudi families. The affected individuals presented with neonatal seizures, developmental delay, and significant defects in tooth development. Some patients showed other clinical features such as muscle weakness, motor difficulties, intellectual disability, microcephaly, and speech problems in addition to additional abnormalities revealed by electroencephalography (EEGs) and magnetic resonance imaging (MRI). One of the MRI findings was related to cortical thickening in the frontal lobe. To diagnose and study the genetic defects of the patients, whole exome sequencing (WES) coupled with confirmatory Sanger sequencing was utilized. Iterative filtering identified two variants of SLC13A5, one of which is novel, in the families. Families 1 and 2 had the same insertion (a previously reported mutation), leading to a frameshift and premature stop codon. The third family had a novel splice site variant. Confirmatory Sanger sequencing corroborated WES results and indicated full segregation of the variants in the corresponding families. The patients' conditions were poorly controlled by multiple antiepileptics as they needed constant care. Conclusion Considering that recessive mutations are common in the Arab population, SLC13A5 screening should be prioritized in future patients harboring similar symptoms including defects in molar development.
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Affiliation(s)
- Hanan AlQudairy
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia
| | | | - Sarah AlRuways
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Nouf AlMutairi
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Maha AlNakiyah
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Reema AlGhofaili
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | | | | | - Omar A Alharbi
- Department of Neurosciences, KFSHRC, Riyadh, Saudi Arabia
| | - Ehab Tous
- Department of Neurosciences, KFSHRC, Riyadh, Saudi Arabia
| | - Moeen AlSayed
- Department of Medical Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Hamad AlZaidan
- Department of Medical Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Maha M AlRasheed
- College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia.,Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali AlOdaib
- Training and Education Department, Research Centre, KFSHRC, Riyadh, Saudi Arabia
| | - Namik Kaya
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia
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18
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Ceylan AC, Acar Arslan E, Erdem HB, Kavus H, Arslan M, Topaloğlu H. Autosomal recessive spinocerebellar ataxia 18 caused by homozygous exon 14 duplication in GRID2 and review of the literature. Acta Neurol Belg 2021; 121:1457-1462. [PMID: 32170608 DOI: 10.1007/s13760-020-01328-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/29/2020] [Indexed: 01/19/2023]
Abstract
Autosomal recessive cerebellar ataxias (ARCA) are characterized by the abnormal structure of the cerebellum and spinal cord. Spinocerebellar ataxia type 18 (MIM 616204), one of the ARCA, is caused by the loss-of-function mutations of the GRID2 gene due to deletions. Missense mutations in the GRID2 cause ataxia with the gain-of-function mechanism. We report a homozygous GRID2 duplication in childhood-onset ataxia in two siblings. The clinical exome sequencing was performed on one of the siblings. No disease-causing mutations were reported as a result of the clinical exome test. Chromosomal microarray analysis was performed on the entire family using Affymetrix Optima® chips. Chromosomal microarray analysis showed a ~ 121-kb homozygous duplication of GRID2 (arr[GRCh37]4q22.2(94426536_94613158) × 4), including exon 14, in both siblings. Previously, GRID2 has been associated with an autosomal recessive (loss-of-function) and autosomal semi-dominant (gain-of-function) forms of ataxia. To the best of our knowledge, this is the first study to identify a homozygous duplication of GRID2 causing loss of function of the GluRD2 protein. These findings provide us with the conclusion that copy number variation analyses should be in the diagnostic process of autosomal recessive ataxia types.
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19
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Abdel-Salam GMH, Duan R, Abdel-Hamid MS, Sayed ISM, Jhangiani SN, Khan Z, Du H, Gibbs RA, Posey JE, Marafi D, Lupski JR. Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait. Am J Med Genet A 2021; 188:648-657. [PMID: 34761517 DOI: 10.1002/ajmg.a.62561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/03/2021] [Accepted: 10/22/2021] [Indexed: 11/06/2022]
Abstract
SMG8 (MIM *617315) is a regulatory subunit involved in nonsense-mediated mRNA decay (NMD), a cellular protective pathway that regulates mRNA transcription, transcript stability, and degrades transcripts containing premature stop codons. SMG8 binds SMG9 and SMG1 to form the SMG1C complex and inhibit the kinase activity of SMG1. Biallelic deleterious variants in SMG9 are known to cause a heart and brain malformation syndrome (HBMS; MIM #616920), whereas biallelic deleterious variants in SMG8 were recently described to cause a novel neurodevelopmental disorder (NDD) with dysmorphic facies and cataracts, now defined as Alzahrani-Kuwahara syndrome (ALKUS: MIM #619268). Only eight subjects from four families with ALKUS have been described to date. Through research reanalysis of a nondiagnostic clinical exome, we identified a subject from a fifth unrelated family with a homozygous deleterious variant in SMG8 and features consistent with ALKUS. Interestingly, the subject also had unilateral microphthalmia, a clinical feature that has been described in SMG9-related disorder. Our study expands the phenotypic spectrum of SMG8-related disorder, demonstrates an overlapping phenotype between SMG8- and SMG9-related rare disease traits, provides further evidence for the SMG8 and SMG9 protein interactions, and highlights the importance of revisiting nondiagnostic exome data to identify and affirm emerging novel genes for rare disease traits.
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Affiliation(s)
- Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National ResearchCentre, Cairo, Egypt
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Mohamed S Abdel-Hamid
- Medical Molecular Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Inas S M Sayed
- Orodental Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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20
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Schymick J, Leahy P, Cowan T, Ruzhnikov MRZ, Gates R, Fernandez L, Pramanik G, Yarlagadda V, Wheeler M, Bernstein JA, Enns GM, Lee C. Variable clinical severity in TANGO2 deficiency: Case series and literature review. Am J Med Genet A 2021; 188:473-487. [PMID: 34668327 DOI: 10.1002/ajmg.a.62543] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 11/10/2022]
Abstract
Biallelic pathogenic variants in the TANGO2 (transport and Golgi organization 2 homolog) gene have been identified as causing a rare metabolic disorder characterized by susceptibility to recurrent rhabdomyolysis, lactic acidosis, encephalopathy, and life-threatening tachyarrhythmias. Recently published reports suggest variable clinical severity and phenotypes. This study details five new patients from two families with biallelic pathogenic variants in the TANGO2 gene identified by whole exome sequencing and includes the largest number of affected individuals from a single family reported to date. We document significant intrafamilial variability and highlight that milder phenotypes may be underrecognized. We present biochemical and clinical data to help highlight the features that aid in consideration of this condition in the differential with disorders of fatty acid oxidation. We also present a comprehensive literature review summarizing the molecular, clinical, and biochemical findings for 92 individuals across 13 publications. Of the 27 pathogenic variants reported to date, the recurrent exons 3-9 deletion represents the most common variant seen in 42% of individuals with TANGO2 deficiency. Common clinical features seen in >70% of all individuals include acute metabolic crisis, rhabdomyolysis, neurologic abnormalities, developmental delay, and intellectual disability. Findings such as elevated creatine kinase, hypothyroidism, ketotic hypoglycemia, QT prolongation, or abnormalities of long-chain acylcarnitines and urine dicarboxylic acids should raise clinical suspicion for this life-threatening condition.
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Affiliation(s)
- Jennifer Schymick
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Department of Pediatrics, Santa Clara Valley Health and Hospital System, San Jose, California, USA
| | - Peter Leahy
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Cook Children's Medical Center, Fort Worth, Texas, USA
| | - Tina Cowan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Maura R Z Ruzhnikov
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Stanford Center for Undiagnosed Diseases, Stanford, California, USA
| | - Ryan Gates
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | | | - Gopal Pramanik
- Stanford Center for Undiagnosed Diseases, Stanford, California, USA
| | | | - Vamsi Yarlagadda
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford, California, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.,Stanford Center for Undiagnosed Diseases, Stanford, California, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Chung Lee
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
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21
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Shamseldin HE, AlAbdi L, Maddirevula S, Alsaif HS, Alzahrani F, Ewida N, Hashem M, Abdulwahab F, Abuyousef O, Kuwahara H, Gao X, Alkuraya FS. Lethal variants in humans: lessons learned from a large molecular autopsy cohort. Genome Med 2021; 13:161. [PMID: 34645488 PMCID: PMC8511862 DOI: 10.1186/s13073-021-00973-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Molecular autopsy refers to DNA-based identification of the cause of death. Despite recent attempts to broaden its scope, the term remains typically reserved to sudden unexplained death in young adults. In this study, we aim to showcase the utility of molecular autopsy in defining lethal variants in humans. METHODS We describe our experience with a cohort of 481 cases in whom the cause of premature death was investigated using DNA from the index or relatives (molecular autopsy by proxy). Molecular autopsy tool was typically exome sequencing although some were investigated using targeted approaches in the earlier stages of the study; these include positional mapping, targeted gene sequencing, chromosomal microarray, and gene panels. RESULTS The study includes 449 cases from consanguineous families and 141 lacked family history (simplex). The age range was embryos to 18 years. A likely causal variant (pathogenic/likely pathogenic) was identified in 63.8% (307/481), a much higher yield compared to the general diagnostic yield (43%) from the same population. The predominance of recessive lethal alleles allowed us to implement molecular autopsy by proxy in 55 couples, and the yield was similarly high (63.6%). We also note the occurrence of biallelic lethal forms of typically non-lethal dominant disorders, sometimes representing a novel bona fide biallelic recessive disease trait. Forty-six disease genes with no OMIM phenotype were identified in the course of this study. The presented data support the candidacy of two other previously reported novel disease genes (FAAH2 and MSN). The focus on lethal phenotypes revealed many examples of interesting phenotypic expansion as well as remarkable variability in clinical presentation. Furthermore, important insights into population genetics and variant interpretation are highlighted based on the results. CONCLUSIONS Molecular autopsy, broadly defined, proved to be a helpful clinical approach that provides unique insights into lethal variants and the clinical annotation of the human genome.
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Affiliation(s)
- Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Center of Excellence for Biomedicine, King Abdulaziz City for Science and Technology, Riyadh, 12354, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abuyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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22
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Arteche-López A, Álvarez-Mora MI, Sánchez Calvin MT, Lezana Rosales JM, Palma Milla C, Gómez Rodríguez MJ, Gomez Manjón I, Blázquez A, Juarez Rufián A, Ramos Gómez P, Sierra Tomillo O, Hidalgo Mayoral I, Pérez de la Fuente R, Posada Rodríguez IJ, González Granado LI, Martin MA, Quesada-Espinosa JF, Moreno-García M. Biallelic variants in genes previously associated with dominant inheritance: CACNA1A, RET and SLC20A2. Eur J Hum Genet 2021; 29:1520-1526. [PMID: 34267336 PMCID: PMC8484357 DOI: 10.1038/s41431-021-00919-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 05/12/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
A subset of families with co-dominant or recessive inheritance has been described in several genes previously associated with dominant inheritance. Those recessive families displayed similar, more severe, or even completely different phenotypes to their dominant counterparts. We report the first patients harboring homozygous disease-related variants in three genes that were previously associated with dominant inheritance: a loss-of-function variant in the CACNA1A gene and two missense variants in the RET and SLC20A2 genes, respectively. All patients presented with a more severe clinical phenotype than the corresponding typical dominant form. We suggest that co-dominant or recessive inheritance for these three genes could explain the phenotypic differences from those documented in their cognate dominant phenotypes. Our results reinforce that geneticists should be aware of the possible different forms of inheritance in genes when WES variant interpretation is performed. We also evidence the need to refine phenotypes and inheritance patterns associated with genes in order to avoid failures during WES analysis and thus, raising the WES diagnostic capacity in the benefit of patients.
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Affiliation(s)
- A. Arteche-López
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - MI. Álvarez-Mora
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain ,grid.428756.a0000 0004 0412 0974Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona and Fundació Clínic per la Recerca Biomèdica, Barcelona, Spain
| | - MT. Sánchez Calvin
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - JM. Lezana Rosales
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - C. Palma Milla
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - M. J. Gómez Rodríguez
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - I. Gomez Manjón
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - A. Blázquez
- Mitochondrial and Neurometabolic Diseases Lab. Biochemistry Department, ‘12 de Octubre’ Research Institute (imas12), Madrid, Spain ,grid.413448.e0000 0000 9314 1427Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - A. Juarez Rufián
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - P. Ramos Gómez
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - O. Sierra Tomillo
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - I. Hidalgo Mayoral
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - R. Pérez de la Fuente
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - IJ. Posada Rodríguez
- grid.144756.50000 0001 1945 5329Neurology Department, University Hospital 12 de Octubre, Madrid, Spain
| | - LI. González Granado
- grid.144756.50000 0001 1945 5329Pediatrics Department, Immunodeficiency Unit, University Hospital 12 de Octubre, Madrid, Spain ,grid.4795.f0000 0001 2157 7667Complutense University School of Medicine. Madrid, Spain and ‘12 de Octubre’ Research Institute (imas12), Madrid, Spain
| | - Miguel A. Martin
- Mitochondrial and Neurometabolic Diseases Lab. Biochemistry Department, ‘12 de Octubre’ Research Institute (imas12), Madrid, Spain ,grid.413448.e0000 0000 9314 1427Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - JF. Quesada-Espinosa
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
| | - M. Moreno-García
- grid.144756.50000 0001 1945 5329Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
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23
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Zhu Q, Zhou Y, Ding J, Chen L, Liu J, Zhou T, Bian W, Ding G, Li G. Screening of Candidate Pathogenic Genes for Spontaneous Abortion using Whole Exome Sequencing. Comb Chem High Throughput Screen 2021; 25:1462-1473. [PMID: 34225611 DOI: 10.2174/1386207324666210628115715] [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: 01/05/2021] [Revised: 04/19/2021] [Accepted: 05/10/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Spontaneous abortion is a common disease in obstetrics and reproduction. OBJECTIVE This study aimed to screen candidate pathogenic genes for spontaneous abortion using whole-exome sequencing. METHODS Genomic DNA was extracted from abortion tissues of spontaneous abortion patients and sequenced using the Illumina HiSeq2500 high-throughput sequencing platform. Whole exome sequencing was performed to select harmful mutations, including SNP and insertion and deletion sites, associated with spontaneous abortion. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and gene fusion analyses were performed. MUC3A and PDE4DIP were two novel mutation genes that were screened and verified by PCR in abortion tissues of patients. RESULTS A total of 83,633 SNPs and 13,635 Indel mutations were detected, of which 29172 SNPs and 3093 Indels were screened as harmful mutations. The 7 GO-BP, 4 GO-CC, 9 GO-MF progress, and 3 KEGG pathways were enriched in GO and KEGG pathway analyses. A total of 746 gene fusion mutations were obtained, involving 492 genes. MUC3A and PDE4DIP were used for PCR verification because of their high number of mutation sites in all samples. CONCLUSION There are extensive SNPs and Indel mutations in the genome of spontaneous abortion tissues, and the effect of these gene mutations on spontaneous abortion needs further experimental verification.
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Affiliation(s)
- Qingwen Zhu
- Nantong Municipal Maternal and Child Health Hospital, Nantong, 226010, China
| | - Yiwen Zhou
- Shanghai Biological Information Research Center, Zhangjiang Hi-tech Park, Shanghai, 201203, China
| | - Jiayi Ding
- Reproductive Medicine Center, Nantong Municipal Maternal and Child Health Hospital, Nantong, 226010, China
| | - Li Chen
- Reproductive Medicine Center, Nantong Municipal Maternal and Child Health Hospital, Nantong, 226010, China
| | - Jia Liu
- Shanghai Biological Information Research Center, Zhangjiang Hi-tech Park, Shanghai, 201203, China
| | - Tao Zhou
- Reproductive Medicine Center, Nantong Municipal Maternal and Child Health Hospital, Nantong, 226010, China
| | - Wenjun Bian
- Prenatal Screening and Diagnosis Center, Nantong Municipal Maternal and Child Health Hospital, Nantong, 226010, China
| | - Guohui Ding
- Shanghai Biological Information Research Center, Zhangjiang Hi-tech Park, Shanghai, 201203, China
| | - Guang Li
- Shanghai Biological Information Research Center, Zhangjiang Hi-tech Park, Shanghai, 201203, China
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24
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Hildebrandt CC, Patel N, Graham JM, Bamshad M, Nickerson DA, White JJ, Marvin CT, Miller DE, Grand KL, Sanchez-Lara PA, Schweitzer D, Al-Zaidan HI, Al Masseri Z, Alkuraya FS, Lin AE. Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome. Am J Med Genet A 2021; 185:2136-2149. [PMID: 33783941 DOI: 10.1002/ajmg.a.62194] [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: 11/30/2020] [Revised: 02/18/2021] [Accepted: 02/27/2021] [Indexed: 12/29/2022]
Abstract
Van den Ende-Gupta syndrome (VDEGS) is a rare autosomal recessive condition characterized by distinctive facial and skeletal features, and in most affected persons, by biallelic pathogenic variants in SCARF2. We review the type and frequency of the clinical features in 36 reported individuals with features of VDEGS, 15 (42%) of whom had known pathogenic variants in SCARF2, 6 (16%) with negative SCARF2 testing, and 15 (42%) not tested. We also report three new individuals with pathogenic variants in SCARF2 and clinical features of VDEGS. Of the six persons without known pathogenic variants in SCARF2, three remain unsolved despite extensive genetic testing. Three were found to have pathogenic ABL1 variants using whole exome sequencing (WES) or whole genome sequencing (WGS). Their phenotype was consistent with the congenital heart disease and skeletal malformations syndrome (CHDSKM), which has been associated with ABL1 variants. Of the three unsolved cases, two were brothers who underwent WGS and targeted long-range sequencing of both SCARF2 and ABL1, and the third person who underwent WES and RNA sequencing for SCARF2. Because these affected individuals with classical features of VDEGS lacked a detectable pathogenic SCARF2 variant, genetic heterogeneity is likely. Our study shows the importance of performing genetic testing on individuals with the VDEGS "phenotype," either as a targeted gene analysis (SCARF2, ABL1) or WES/WGS. Additionally, individuals with the combination of arachnodactyly and blepharophimosis should undergo echocardiography while awaiting results of molecular testing due to the overlapping physical features of VDEGS and CHDSKM.
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Affiliation(s)
- Clara C Hildebrandt
- Genetics Unit, MassGeneral Hospital for Children, Massachusetts, USA.,Boston Children's Hospital Medical Biochemical Fellowship, Boston, Massachusetts, USA
| | - Nisha Patel
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - John M Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Michael Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute, Seattle, Washington, USA
| | | | - Colby T Marvin
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Katheryn L Grand
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Daniela Schweitzer
- Division of Pediatric Genetics, Department of Pediatrics, University of California Los Angeles, Los Angeles, California, USA
| | - Hamad I Al-Zaidan
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Zainab Al Masseri
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Angela E Lin
- Genetics Unit, MassGeneral Hospital for Children, Massachusetts, USA
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Alsaif HS, Alshehri A, Sulaiman RA, Al-Hindi H, Guzmán-Vega FJ, Arold ST, Alkuraya FS. MYH1 is a candidate gene for recurrent rhabdomyolysis in humans. Am J Med Genet A 2021; 185:2131-2135. [PMID: 33755318 DOI: 10.1002/ajmg.a.62188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/01/2021] [Accepted: 03/05/2021] [Indexed: 01/04/2023]
Abstract
Rhabdomyolysis is a serious medical condition characterized by muscle injury, and there are recognized genetic causes especially in recurrent forms. The majority of these cases, however, remain unexplained. Here, we describe a patient with recurrent rhabdomyolysis in whom extensive clinical testing failed to identify a likely etiology. Whole-exome sequencing revealed a novel missense variant in MYH1, which encodes a major adult muscle fiber protein. Structural biology analysis revealed that the mutated residue is extremely well conserved and is located in the actin binding cleft. Furthermore, immediately adjacent mutations in that cleft in other myosins are pathogenic in humans. Our results are consistent with the finding that MYH1 is mutated in rhabdomyolysis in horses and suggest that this gene should be investigated in cases with recurrent rhabdomyolysis.
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Affiliation(s)
- Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ali Alshehri
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Raashda A Sulaiman
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hindi Al-Hindi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Francisco J Guzmán-Vega
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia.,Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Riyadh, Saudi Arabia
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26
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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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27
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Panda PK, Dawman L, Sharawat IK. GRID2 Mutation-Related Spinocerebellar Ataxia Type 18: A New Report and Literature Review. J Pediatr Genet 2020; 11:99-109. [DOI: 10.1055/s-0040-1721084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/12/2020] [Indexed: 10/22/2022]
Abstract
AbstractSpinocerebellar ataxias (SCAs) are heterogeneous disorders with multiple genetic etiology. Mutations in the GRID2 gene are associated with spinocerebellar ataxia type 18 (SCA-18). We report the first Indian case of SCA-18. The proband is a 7-year-old boy with motor delay, cerebellar signs, and cerebellar atrophy. Whole exome and direct sequencing identified compound heterozygous mutations of the coding and noncoding regions of the GRID2 gene. A literature review of the published cases with pathogenic GRID2 variants was performed. Beside our patients, 32 cases were identified. The majority of reported cases were males, of consanguineous kindreds, with autosomal recessive inheritance. However, a proportion of cases (39%) had autosomal dominant/semidominant inheritance with heterozygous variants. In addition to childhood-onset cerebellar ataxia, other reported features were: early-onset dementia, complicated spastic paraparesis, retinal dystrophy, hearing loss, lower motor neuron signs, and severe global developmental delay in some homozygous cases. Cerebellar atrophy was the commonest neuroimaging finding, with few cases demonstrating brain stem, supratentorial, and white matter abnormalities. Although SCA-18 should be suspected in patients with early-onset cerebellar ataxia, eye movement abnormalities, and motor delay, clinicians should be aware of late-onset, variable presentations with pyramidal signs, dementia, and hearing loss. In suspected cases, if mutations were not detected by whole-exome sequencing, direct sequencing of noncoding regions and chromosomal microarray should be considered.
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Affiliation(s)
- Prateek Kumar Panda
- Division of Pediatric Neurology, Department of Pediatrics, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Lesa Dawman
- Department of Pediatrics, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Indar Kumar Sharawat
- Division of Pediatric Neurology, Department of Pediatrics, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
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28
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Cope H, Spillmann R, Rosenfeld JA, Brokamp E, Signer R, Schoch K, Kelley EG, Sullivan JA, Macnamara E, Lincoln S, Golden‐Grant K, Undiagnosed Diseases Network, Orengo JP, Clark G, Burrage LC, Posey JE, Punetha J, Robertson A, Cogan J, Phillips JA, Martinez‐Agosto J, Shashi V. Missed diagnoses: Clinically relevant lessons learned through medical mysteries solved by the Undiagnosed Diseases Network. Mol Genet Genomic Med 2020; 8:e1397. [PMID: 32730690 PMCID: PMC7549585 DOI: 10.1002/mgg3.1397] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Resources within the Undiagnosed Diseases Network (UDN), such as genome sequencing (GS) and model organisms aid in diagnosis and identification of new disease genes, but are currently difficult to access by clinical providers. While these resources do contribute to diagnoses in many cases, they are not always necessary to reach diagnostic resolution. The UDN experience has been that participants can also receive diagnoses through the thoughtful and customized application of approaches and resources that are readily available in clinical settings. METHODS The UDN Genetic Counseling and Testing Working Group collected case vignettes that illustrated how clinically available methods resulted in diagnoses. The case vignettes were classified into three themes; phenotypic considerations, selection of genetic testing, and evaluating exome/GS variants and data. RESULTS We present 12 participants that illustrate how clinical practices such as phenotype-driven genomic investigations, consideration of variable expressivity, selecting the relevant tissue of interest for testing, utilizing updated testing platforms, and recognition of alternate transcript nomenclature resulted in diagnoses. CONCLUSION These examples demonstrate that when a diagnosis is elusive, an iterative patient-specific approach utilizing assessment options available to clinical providers may solve a portion of cases. However, this does require increased provider time commitment, a particular challenge in the current practice of genomics.
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Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Rebecca Spillmann
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Jill A. Rosenfeld
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Rebecca Signer
- Department of Human GeneticsUniversity of CaliforniaLos AngelesCAUSA
| | - Kelly Schoch
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Emily G. Kelley
- Department of Biomedical InformaticsHarvard Medical SchoolBostonMAUSA
| | - Jennifer A. Sullivan
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Ellen Macnamara
- Undiagnosed Diseases ProgramCommon FundOffice of the DirectorNational Institutes of HealthNIHBethesdaMDUSA
| | - Sharyn Lincoln
- Division of Genetics and GenomicsDepartment of PediatricsBoston Children’s HospitalBostonMAUSA
| | | | | | - James P. Orengo
- Department of NeurologyBaylor College of MedicineHoustonTXUSA
| | - Gary Clark
- Department of NeurologyBaylor College of MedicineHoustonTXUSA
| | - Lindsay C. Burrage
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Jennifer E. Posey
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Jaya Punetha
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Amy Robertson
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Joy Cogan
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - John A. Phillips
- Division of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | | | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
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29
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Tan NB, Stapleton R, Stark Z, Delatycki MB, Yeung A, Hunter MF, Amor DJ, Brown NJ, Stutterd CA, McGillivray G, Yap P, Regan M, Chong B, Fanjul Fernandez M, Marum J, Phelan D, Pais LS, White SM, Lunke S, Tan TY. Evaluating systematic reanalysis of clinical genomic data in rare disease from single center experience and literature review. Mol Genet Genomic Med 2020; 8:e1508. [PMID: 32969205 PMCID: PMC7667328 DOI: 10.1002/mgg3.1508] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/15/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Our primary aim was to evaluate the systematic reanalysis of singleton exome sequencing (ES) data for unsolved cases referred for any indication. A secondary objective was to undertake a literature review of studies examining the reanalysis of genomic data from unsolved cases. Methods We examined data from 58 unsolved cases referred between June 2016 and March 2017. First reanalysis at 4–13 months after the initial report considered genes newly associated with disease since the original analysis; second reanalysis at 9–18 months considered all disease‐associated genes. At 25–34 months we reviewed all cases and the strategies which solved them. Results Reanalysis of existing ES data alone at two timepoints did not yield new diagnoses. Over the same timeframe, 10 new diagnoses were obtained (17%) from additional strategies, such as microarray detection of copy number variation, repeat sequencing to improve coverage, and trio sequencing. Twenty‐seven peer‐reviewed articles were identified on the literature review, with a median new diagnosis rate via reanalysis of 15% and median reanalysis timeframe of 22 months. Conclusion Our findings suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis. We also recommend a multi‐faceted strategy for cases remaining unsolved after singleton ES.
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Affiliation(s)
- Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rachel Stapleton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - David J Amor
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Patrick Yap
- Genetic Health Service NZ, Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Miriam Fanjul Fernandez
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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30
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Hartley T, Lemire G, Kernohan KD, Howley HE, Adams DR, Boycott KM. New Diagnostic Approaches for Undiagnosed Rare Genetic Diseases. Annu Rev Genomics Hum Genet 2020; 21:351-372. [DOI: 10.1146/annurev-genom-083118-015345] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate diagnosis is the cornerstone of medicine; it is essential for informed care and promoting patient and family well-being. However, families with a rare genetic disease (RGD) often spend more than five years on a diagnostic odyssey of specialist visits and invasive testing that is lengthy, costly, and often futile, as 50% of patients do not receive a molecular diagnosis. The current diagnostic paradigm is not well designed for RGDs, especially for patients who remain undiagnosed after the initial set of investigations, and thus requires an expansion of approaches in the clinic. Leveraging opportunities to participate in research programs that utilize new technologies to understand RGDs is an important path forward for patients seeking a diagnosis. Given recent advancements in such technologies and international initiatives, the prospect of identifying a molecular diagnosis for all patients with RGDs has never been so attainable, but achieving this goal will require global cooperation at an unprecedented scale.
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Affiliation(s)
- Taila Hartley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - Gabrielle Lemire
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
| | - Kristin D. Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Newborn Screening Ontario, CHEO, Ottawa, Ontario K1H 9M8, Canada
| | - Heather E. Howley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - David R. Adams
- Office of the Clinical Director, National Human Genome Research Institute and Undiagnosed Diseases Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kym M. Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
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31
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Chiu FPC, Doolan BJ, McGrath JA, Onoufriadis A. A decade of next-generation sequencing in genodermatoses: the impact on gene discovery and clinical diagnostics. Br J Dermatol 2020; 184:606-616. [PMID: 32628274 DOI: 10.1111/bjd.19384] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Discovering the genetic basis of inherited skin diseases is fundamental to improving diagnostic accuracy and genetic counselling. In the 1990s and 2000s, genetic linkage and candidate gene approaches led to the molecular characterization of several dozen genodermatoses, but over the past decade the advent of next-generation sequencing (NGS) technologies has accelerated diagnostic discovery and precision. OBJECTIVES This review examines the application of NGS technologies from 2009 to 2019 that have (i) led to the initial discovery of gene mutations in known or new genodermatoses and (ii) identified involvement of more than one contributing pathogenic gene in individuals with complex Mendelian skin disorder phenotypes. METHODS A comprehensive review of the PubMed database and dermatology conference abstracts was undertaken between January 2009 and December 2019. The results were collated and cross-referenced with OMIM. RESULTS We identified 166 new disease-gene associations in inherited skin diseases discovered by NGS. Of these, 131 were previously recognized, while 35 were brand new disorders. Eighty-five were autosomal dominant (with 43 of 85 mutations occurring de novo), 78 were autosomal recessive and three were X-linked. We also identified 63 cases harbouring multiple pathogenic mutations, either involving two coexisting genodermatoses (n = 13) or an inherited skin disorder in conjunction with other organ system phenotypes (n = 50). CONCLUSIONS NGS technologies have accelerated disease-gene discoveries in dermatology over the last decade. Moreover, the era of NGS has enabled clinicians to split complex Mendelian phenotypes into separate diseases. These genetic data improve diagnostic precision and make feasible accurate prenatal testing and better-targeted translational research.
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Affiliation(s)
- F P-C Chiu
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - B J Doolan
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - J A McGrath
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - A Onoufriadis
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
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32
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Hetzelt KLML, Kraus C, Kusnik S, Thiel CT, Uebe S, Ekici AB, Trollmann R, Reis A, Zweier C. A case of severe autosomal recessive spinocerebellar ataxia type 18 with a novel nonsense variant in GRID2. Eur J Med Genet 2020; 63:103998. [PMID: 32622959 DOI: 10.1016/j.ejmg.2020.103998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/12/2020] [Accepted: 06/28/2020] [Indexed: 12/20/2022]
Abstract
Autosomal-recessive spinocerebellar ataxia type 18 (SCAR18) is a rare neurologic disorder. It is caused by bi-allelic aberrations in the GRID2 gene, encoding an ionotropic glutamate receptor. In total, 20 affected individuals with mainly homozygous/compound heterozygous intragenic deletions/duplications, two different missense variants and one nonsense variant in GRID2 have been reported, so far. SCAR18 is characterized by delayed psychomotor development, intellectual disability, severely impaired gait due to cerebellar ataxia, ocular movement abnormalities, and cerebellar atrophy in brain imaging. By trio exome sequencing, we now identified a novel homozygous nonsense variant (c.568C > T; p.Gln190*) in GRID2 in a four year old female from a consanguineous family who presented with a particularly severe manifestation of SCAR18. The girl was born after an uneventful pregnancy and showed early-onset, profoundly delayed psychomotor development with no achieved psychomotor milestones at age 4 years. Additionally, she presented with severe muscular hypotonia, progressive truncal and appendicular ataxia, binocular vertical nystagmus, central hearing loss and incomplete loss of sight. She was dystrophic, interacted only very little and had behavioral anomalies such as eating hair and bruxism. Brain imaging showed cerebellar hypoplasia, extended cerebrospinal fluid spaces and beginning reduction of cerebral volume. Our findings further delineate the mutational and clinical spectrum of GRID2-associated spinocerebellar ataxia type 18 and indicate that homozygous nonsense variants are possibly associated with the severe end of the SCAR18 phenotypic spectrum.
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Affiliation(s)
- Katalin L M L Hetzelt
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Cornelia Kraus
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Stefan Kusnik
- Department of Pediatrics, Division of Pediatric Neurology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Christian T Thiel
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Regina Trollmann
- Department of Pediatrics, Division of Pediatric Neurology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany.
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33
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Maddirevula S, Kuwahara H, Ewida N, Shamseldin HE, Patel N, Alzahrani F, AlSheddi T, AlObeid E, Alenazi M, Alsaif HS, Alqahtani M, AlAli M, Al Ali H, Helaby R, Ibrahim N, Abdulwahab F, Hashem M, Hanna N, Monies D, Derar N, Alsagheir A, Alhashem A, Alsaleem B, Alhebbi H, Wali S, Umarov R, Gao X, Alkuraya FS. Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics. Genome Biol 2020; 21:145. [PMID: 32552793 PMCID: PMC7298854 DOI: 10.1186/s13059-020-02053-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/21/2020] [Indexed: 12/20/2022] Open
Abstract
Background At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fraction is unclear. Whole transcriptome sequencing is a promising supplement to WES, although empirical data on the contribution of RNA analysis to the diagnosis of Mendelian diseases on a large scale are scarce. Results Here, we describe our experience with transcript-deleterious variants (TDVs) based on a cohort of 5647 families with suspected Mendelian diseases. We first interrogate all families for which the respective Mendelian phenotype could be mapped to a single locus to obtain an unbiased estimate of the contribution of TDVs at 18.9%. We examine the entire cohort and find that TDVs account for 15% of all “solved” cases. We compare the results of RT-PCR to in silico prediction. Definitive results from RT-PCR are obtained from blood-derived RNA for the overwhelming majority of variants (84.1%), and only a small minority (2.6%) fail analysis on all available RNA sources (blood-, skin fibroblast-, and urine renal epithelial cells-derived), which has important implications for the clinical application of RNA-seq. We also show that RNA analysis can establish the diagnosis in 13.5% of 155 patients who had received “negative” clinical WES reports. Finally, our data suggest a role for TDVs in modulating penetrance even in otherwise highly penetrant Mendelian disorders. Conclusions Our results provide much needed empirical data for the impending implementation of diagnostic RNA-seq in conjunction with genome sequencing.
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Affiliation(s)
- Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa AlSheddi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman AlObeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mona Alenazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha Alqahtani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha AlAli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hatoon Al Ali
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - 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
| | - Nadine Hanna
- Département de génétique, AP-HP, Hôpital Bichat, Université de Paris, LVTS INSERM U1148, Paris, France
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nada Derar
- Deparmtent of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Afaf Alsagheir
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Badr Alsaleem
- Division of Pediatric Gastroenterology, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hamoud Alhebbi
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Sami Wali
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ramzan Umarov
- Computational Bioscience Research Center (CBRC), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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34
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Lentini JM, Alsaif HS, Faqeih E, Alkuraya FS, Fu D. DALRD3 encodes a protein mutated in epileptic encephalopathy that targets arginine tRNAs for 3-methylcytosine modification. Nat Commun 2020; 11:2510. [PMID: 32427860 PMCID: PMC7237682 DOI: 10.1038/s41467-020-16321-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
In mammals, a subset of arginine tRNA isoacceptors are methylated in the anticodon loop by the METTL2 methyltransferase to form the 3-methylcytosine (m3C) modification. However, the mechanism by which METTL2 identifies specific tRNA arginine species for m3C formation as well as the biological role of m3C in mammals is unknown. Here, we show that human METTL2 forms a complex with DALR anticodon binding domain containing 3 (DALRD3) protein to recognize particular arginine tRNAs destined for m3C modification. DALRD3-deficient human cells exhibit nearly complete loss of the m3C modification in tRNA-Arg species. Notably, we identify a homozygous nonsense mutation in the DALRD3 gene that impairs m3C formation in human patients exhibiting developmental delay and early-onset epileptic encephalopathy. These findings uncover an unexpected function for the DALRD3 protein in the targeting of distinct arginine tRNAs for m3C modification and suggest a crucial biological role for DALRD3-dependent tRNA modification in proper neurological development.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - 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
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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35
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Borges MG, Rocha CS, Carvalho BS, Lopes-Cendes I. Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis. Genet Mol Biol 2020; 43:e20190270. [PMID: 32343762 PMCID: PMC7198014 DOI: 10.1590/1678-4685-gmb-2019-0270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/16/2020] [Indexed: 11/24/2022] Open
Abstract
For a better interpretation of variants, evidence-based databases, such as
ClinVar, compile data on the presumed relationships between variants and
phenotypes. In this study, we aimed to analyze the pattern of sequencing depth
in variants from whole-exome sequencing data in the 1000 Genomes project phase
3, focusing on the variants present in the ClinVar database that were predicted
to affect protein-coding regions. We demonstrate that the distribution of the
sequencing depth varies across different sequencing centers (pair-wise
comparison, p < 0.001). Most importantly, we found that the
distribution pattern of sequencing depth is specific to each facility, making it
possible to correctly assign 96.9% of the samples to their sequencing center.
Thus, indicating the presence of a systematic bias, related to the methods used
in the different facilities, which generates significant variations in breadth
and depth in whole-exome sequencing data in clinically relevant regions. Our
results show that methodological differences, leading to significant
heterogeneity in sequencing depth, may potentially influence the accuracy of
genetic diagnosis. Furthermore, our findings highlight how it is still
challenging to integrate results from different sequencing centers, which may
also have an impact on genomic research.
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Affiliation(s)
- Murilo G Borges
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil.,Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN), Campinas, SP, Brazil.,Universidade Estadual de Campinas (UNICAMP), Instituto de Física "Gleb Wataghin". Campinas, SP, Brazil
| | - Cristiane S Rocha
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil.,Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN), Campinas, SP, Brazil
| | - Benilton S Carvalho
- Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN), Campinas, SP, Brazil.,Universidade Estadual de Campinas (UNICAMP), Instituto de Matemática, Estatística e Computação Científica, Departamento de Estatística, Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Genética Médica e Medicina Genômica, Campinas, SP, Brazil.,Instituto Brasileiro de Neurociência e Neurotecnologia (BRAINN), Campinas, SP, Brazil
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36
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Boycott KM, Hartley T, Biesecker LG, Gibbs RA, Innes AM, Riess O, Belmont J, Dunwoodie SL, Jojic N, Lassmann T, Mackay D, Temple IK, Visel A, Baynam G. A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers. Cell 2020; 177:32-37. [PMID: 30901545 DOI: 10.1016/j.cell.2019.02.040] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The introduction of exome sequencing in the clinic has sparked tremendous optimism for the future of rare disease diagnosis, and there is exciting opportunity to further leverage these advances. To provide diagnostic clarity to all of these patients, however, there is a critical need for the field to develop and implement strategies to understand the mechanisms underlying all rare diseases and translate these to clinical care.
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Affiliation(s)
- Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - John Belmont
- Illumina, Madison, WI, USA; Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | | | - Timo Lassmann
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Deborah Mackay
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
| | - I Karen Temple
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, CA, USA; DOE Joint Genome Institute, CA, USA; The University of California at Merced, CA, USA
| | - Gareth Baynam
- Faculty of Health and Medical Sciences, University of Western Australia Medical School, Perth, WA, Australia; Western Australian Register of Developmental Anomalies, Genetic Services of Western Australia, Perth, WA, Australia; Office of Population Health Genomics, Western Australian Department of Health, Perth, WA, Australia
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37
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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: 62] [Impact Index Per Article: 12.4] [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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38
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Greenbaum L, Barel O, Nikitin V, Hersalis-Eldar A, Kol N, Reznik-Wolf H, Dominissini D, Pras E, Dori A. Identification of a homozygous VRK1 mutation in two patients with adult-onset distal hereditary motor neuropathy. Muscle Nerve 2020; 61:395-400. [PMID: 31837156 DOI: 10.1002/mus.26779] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/04/2019] [Accepted: 12/07/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Adult-onset hereditary motor neuropathies are caused by mutations in multiple genes. Mutations within the vaccinia-related kinase 1 (VRK1) gene were associated with a wide spectrum of recessively inherited motor neuropathies, characterized by childhood to early adulthood age of onset and an occasionally non-lower motor neuron involvement. METHODS We describe two patients with adult-onset (aged 48 and 40 years) length-dependent motor neuropathy from unrelated consanguineous families of Moroccan Jewish descent. One also demonstrated mild nocturnal respiratory difficulty and sensory symptoms. Whole-exome sequencing (WES) was performed. RESULTS A homozygous mutation in VRK1 (c.1160G>A (p.Arg387His)), shared by both patients, was identified. This rare mutation segregated with the disease in the two families, and was absent in 120 controls of Jewish Moroccan origin. CONCLUSIONS Our findings support VRK1 as a causative gene for adult-onset distal hereditary motor neuropathy, and indicate its relevance for evaluation of individuals with similar motor impairment.
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Affiliation(s)
- Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ortal Barel
- Cancer Research Center and Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Vera Nikitin
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
| | | | - Nitzan Kol
- Cancer Research Center and Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Haike Reznik-Wolf
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Dan Dominissini
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Cancer Research Center and Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Elon Pras
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amir Dori
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
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39
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Bruel AL, Nambot S, Quéré V, Vitobello A, Thevenon J, Assoum M, Moutton S, Houcinat N, Lehalle D, Jean-Marçais N, Chevarin M, Jouan T, Poë C, Callier P, Tisserand E, Philippe C, Them FTM, Duffourd Y, Faivre L, Thauvin-Robinet C. Increased diagnostic and new genes identification outcome using research reanalysis of singleton exome sequencing. Eur J Hum Genet 2019; 27:1519-1531. [PMID: 31231135 PMCID: PMC6777617 DOI: 10.1038/s41431-019-0442-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/30/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022] Open
Abstract
In clinical exome sequencing (cES), the American College of Medical Genetics and Genomics recommends limiting variant interpretation to established human-disease genes. The diagnostic yield of cES in intellectual disability and/or multiple congenital anomalies (ID/MCA) is currently about 30%. Though the results may seem acceptable for rare diseases, they mean that 70% of affected individuals remain genetically undiagnosed. Further analysis extended to all mutated genes in a research environment is a valuable strategy for improving diagnostic yields. This study presents the results of systematic research reanalysis of negative cES in a cohort of 313 individuals with ID/MCA. We identified 17 new genes not related to human disease, implicated 22 non-OMIM disease-causing genes recently or previously rarely related to disease, and described 1 new phenotype associated with a known gene. Twenty-six candidate genes were identified and are waiting for future recurrence. Overall, we diagnose 15% of the individuals with initial negative cES, increasing the diagnostic yield from 30% to more than 40% (or 46% if strong candidate genes are considered). This study demonstrates the power of such extended research reanalysis to increase scientific knowledge of rare diseases. These novel findings can then be applied in the field of diagnostics.
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Affiliation(s)
- Ange-Line Bruel
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France.
| | - Sophie Nambot
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Virginie Quéré
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Antonio Vitobello
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Julien Thevenon
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Mirna Assoum
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Sébastien Moutton
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Nada Houcinat
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Daphné Lehalle
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Nolwenn Jean-Marçais
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Martin Chevarin
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Thibaud Jouan
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Charlotte Poë
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Patrick Callier
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Emilie Tisserand
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Christophe Philippe
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Frédéric Tran Mau Them
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Yannis Duffourd
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
- Centre de Référence Maladies Rares "Déficiences Intellectuelles de causes rares", FHU-TRANSLAD, CHU Dijon Bourgogne, France
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40
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Schmitz-Abe K, Li Q, Rosen SM, Nori N, Madden JA, Genetti CA, Wojcik MH, Ponnaluri S, Gubbels CS, Picker JD, O'Donnell-Luria AH, Yu TW, Bodamer O, Brownstein CA, Beggs AH, Agrawal PB. Unique bioinformatic approach and comprehensive reanalysis improve diagnostic yield of clinical exomes. Eur J Hum Genet 2019; 27:1398-1405. [PMID: 30979967 PMCID: PMC6777619 DOI: 10.1038/s41431-019-0401-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/11/2019] [Accepted: 03/26/2019] [Indexed: 01/30/2023] Open
Abstract
Clinical exome sequencing (CES) is increasingly being utilized; however, a large proportion of patients remain undiagnosed, creating a need for a systematic approach to increase the diagnostic yield. We have reanalyzed CES data for a clinically heterogeneous cohort of 102 probands with likely Mendelian conditions, including 74 negative cases and 28 cases with candidate variants, but reanalysis requested by clinicians. Reanalysis was performed by an interdisciplinary team using a validated custom-built pipeline, "Variant Explorer Pipeline" (VExP). This reanalysis approach and results were compared with existing literature. Reanalysis of candidate variants from CES in 28 cases revealed 1 interpretation that needed to be reclassified. A confirmed or potential genetic diagnosis was identified in 24 of 75 CES-negative/reclassified cases (32.0%), including variants in known disease-causing genes (n = 6) or candidate genes (n = 18). This yield was higher compared with similar studies demonstrating the utility of this approach. In summary, reanalysis of negative CES in a research setting enhances diagnostic yield by about a third. This study suggests the need for comprehensive, continued reanalysis of exome data when molecular diagnosis is elusive.
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Affiliation(s)
- Klaus Schmitz-Abe
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Qifei Li
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Samantha M Rosen
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Neeharika Nori
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Monica H Wojcik
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Sadhana Ponnaluri
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cynthia S Gubbels
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jonathan D Picker
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne H O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Timothy W Yu
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Abstract
The practice of genomic medicine stands to revolutionize our approach to medical care, and to realize this goal will require discovery of the relationship between rare variation at each of the ~ 20,000 protein-coding genes and their consequent impact on individual health and expression of Mendelian disease. The step-wise evolution of broad-based, genome-wide cytogenetic and molecular genomic testing approaches (karyotyping, chromosomal microarray [CMA], exome sequencing [ES]) has driven much of the rare disease discovery to this point, with genome sequencing representing the newest member of this team. Each step has brought increased sensitivity to interrogate individual genomic variation in an unbiased method that does not require clinical prediction of the locus or loci involved. Notably, each step has also brought unique limitations in variant detection, for example, the low sensitivity of ES for detection of triploidy, and of CMA for detection of copy neutral structural variants. The utility of genome sequencing (GS) as a clinical molecular diagnostic test, and the increased sensitivity afforded by addition of long-read sequencing or other -omics technologies such as RNAseq or metabolomics, are not yet fully explored, though recent work supports improved sensitivity of variant detection, at least in a subset of cases. The utility of GS will also rely upon further elucidation of the complexities of genetic and allelic heterogeneity, multilocus rare variation, and the impact of rare and common variation at a locus, as well as advances in functional annotation of identified variants. Much discovery remains to be done before the potential utility of GS is fully appreciated.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, T603, Houston, TX, 77030, USA.
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42
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Bombard Y, Brothers KB, Fitzgerald-Butt S, Garrison NA, Jamal L, James CA, Jarvik GP, McCormick JB, Nelson TN, Ormond KE, Rehm HL, Richer J, Souzeau E, Vassy JL, Wagner JK, Levy HP. The Responsibility to Recontact Research Participants after Reinterpretation of Genetic and Genomic Research Results. Am J Hum Genet 2019; 104:578-595. [PMID: 30951675 PMCID: PMC6451731 DOI: 10.1016/j.ajhg.2019.02.025] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 02/25/2019] [Indexed: 11/16/2022] Open
Abstract
The evidence base supporting genetic and genomic sequence-variant interpretations is continuously evolving. An inherent consequence is that a variant's clinical significance might be reinterpreted over time as new evidence emerges regarding its pathogenicity or lack thereof. This raises ethical, legal, and financial issues as to whether there is a responsibility to recontact research participants to provide updates on reinterpretations of variants after the initial analysis. There has been discussion concerning the extent of this obligation in the context of both research and clinical care. Although clinical recommendations have begun to emerge, guidance is lacking on the responsibilities of researchers to inform participants of reinterpreted results. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in November 2018. The workgroup included representatives from the National Society of Genetic Counselors, the Canadian College of Medical Genetics, and the Canadian Association of Genetic Counsellors. The final statement includes twelve position statements that were endorsed or supported by the following organizations: Genetic Alliance, European Society of Human Genetics, Canadian Association of Genetic Counsellors, American Association of Anthropological Genetics, Executive Committee of the American Association of Physical Anthropologists, Canadian College of Medical Genetics, Human Genetics Society of Australasia, and National Society of Genetic Counselors.
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Affiliation(s)
- Yvonne Bombard
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada.
| | - Kyle B Brothers
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Sara Fitzgerald-Butt
- National Society of Genetic Counselors, Chicago, IL 60611, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Nanibaa' A Garrison
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Leila Jamal
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; National Society of Genetic Counselors, Chicago, IL 60611, USA; National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cynthia A James
- National Society of Genetic Counselors, Chicago, IL 60611, USA; Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Gail P Jarvik
- Executive Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jennifer B McCormick
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Department of Humanities, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Tanya N Nelson
- Canadian College of Medical Geneticists, Kingston, ON K7K 1Z7, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, BC V6H 3N1, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Kelly E Ormond
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Department of Genetics and Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Heidi L Rehm
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Medical and Populations Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Julie Richer
- Canadian College of Medical Geneticists, Kingston, ON K7K 1Z7, Canada; Department of Pediatrics, Children's Hospital of Eastern Ontario (CHEO), Ottawa, ON K1H 8L1, Canada; University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Emmanuelle Souzeau
- Canadian Association of Genetic Counsellors, Oakville, ON L6J 7N5, Canada; Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - Jason L Vassy
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; VA Boston Healthcare System, Boston, MA 02130, USA
| | - Jennifer K Wagner
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA 17822, USA
| | - Howard P Levy
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Division of General Internal Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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43
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Al-Dewik N, Mohd H, Al-Mureikhi M, Ali R, Al-Mesaifri F, Mahmoud L, Shahbeck N, El-Akouri K, Almulla M, Al Sulaiman R, Musa S, Al-Marri AAN, Richard G, Juusola J, Solomon BD, Alkuraya FS, Ben-Omran T. Clinical exome sequencing in 509 Middle Eastern families with suspected Mendelian diseases: The Qatari experience. Am J Med Genet A 2019; 179:927-935. [PMID: 30919572 PMCID: PMC6916397 DOI: 10.1002/ajmg.a.61126] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/22/2019] [Accepted: 02/25/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Clinical exome sequencing (CES) is rapidly becoming the diagnostic test of choice in patients with suspected Mendelian diseases especially those that are heterogeneous in etiology and clinical presentation. Reporting large CES series can inform guidelines on best practices for test utilization, and improves accuracy of variant interpretation through clinically-oriented data sharing. METHODS This is a retrospective series of 509 probands from Qatar who underwent singleton or trio CES either as a reflex or naïve (first-tier) test from April 2014 to December 2016 for various clinical indications. RESULTS The CES diagnostic yield for the overall cohort was 48.3% (n = 246). Dual molecular diagnoses were observed in 2.1% of cases; nearly all of whom (91%) were consanguineous. We report compelling variants in 11 genes with no established Mendelian phenotypes. Unlike reflex-WES, naïve WES was associated with a significantly shorter diagnostic time (3 months vs. 18 months, p < 0.0001). CONCLUSION Middle Eastern patients tend to have a higher yield from CES than outbred populations, which has important implications in test choice especially early in the diagnostic process. The relatively high diagnostic rate is likely related to the predominance of recessive diagnoses (60%) since consanguinity and positive family history were strong predictors of a positive CES.
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Affiliation(s)
- Nader Al-Dewik
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Howaida Mohd
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Mariam Al-Mureikhi
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Rehab Ali
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Fatma Al-Mesaifri
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Laila Mahmoud
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Noora Shahbeck
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Karen El-Akouri
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Mariam Almulla
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Reem Al Sulaiman
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Sara Musa
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | | | - Gabriele Richard
- Clinical Genomics Program, GeneDx, Inc., Gaithersburg, Maryland, USA
| | - Jane Juusola
- Clinical Genomics Program, GeneDx, Inc., Gaithersburg, Maryland, USA
| | | | - Fowzan S Alkuraya
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar.,Department of pediatric, Weill Cornell Medical College, Doha, Qatar.,Division of Genetic & Genomics Medicine, Sidra Medicine, Doha, Qatar
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44
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Shamseldin HE, Makhseed N, Ibrahim N, Al-Sheddi T, Alobeid E, Abdulwahab F, Alkuraya FS. NUP214 deficiency causes severe encephalopathy and microcephaly in humans. Hum Genet 2019; 138:221-229. [PMID: 30758658 DOI: 10.1007/s00439-019-01979-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/07/2019] [Indexed: 10/27/2022]
Abstract
Nuclear pore complex (NPC) is a fundamental component of the nuclear envelope and is key to the nucleocytoplasmic transport. Mutations in several NUP genes that encode individual components of NPC known as nucleoporins have been identified in recent years among patients with static encephalopathies characterized by developmental delay and microcephaly. We describe a multiplex consanguineous family in which four affected members presented with severe neonatal hypotonia, profound global developmental delay, progressive microcephaly and early death. Autozygome and linkage analysis revealed that this phenotype is linked to a founder disease haplotype (chr9:127,113,732-135,288,807) in which whole exome sequencing revealed the presence of a novel homozygous missense variant in NUP214. Functional analysis of patient-derived fibroblasts recapitulated the dysmorphic phenotype of nuclei that was previously described in NUP214 knockdown cells. In addition, the typical rim staining of NUP214 is largely displaced, further supporting the deleterious effect of the variant. Our data expand the list of NUP genes that are mutated in encephalopathy disorders in humans.
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Affiliation(s)
- Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nawal Makhseed
- Department of Pediatrics, Al-Jahra Hospital, Kuwait City, Kuwait
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Al-Sheddi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - 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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45
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Maddirevula S, Alzahrani F, Al-Owain M, Al Muhaizea MA, Kayyali HR, AlHashem A, Rahbeeni Z, Al-Otaibi M, Alzaidan HI, Balobaid A, El Khashab HY, Bubshait DK, Faden M, Yamani SA, Dabbagh O, Al-Mureikhi M, Jasser AA, Alsaif HS, Alluhaydan I, Seidahmed MZ, Alabbasi BH, Almogarri I, Kurdi W, Akleh H, Qari A, Al Tala SM, Alhomaidi S, Kentab AY, Salih MA, Chedrawi A, Alameer S, Tabarki B, Shamseldin HE, Patel N, Ibrahim N, Abdulwahab F, Samira M, Goljan E, Abouelhoda M, Meyer BF, Hashem M, Shaheen R, AlShahwan S, Alfadhel M, Ben-Omran T, Al-Qattan MM, Monies D, Alkuraya FS. Autozygome and high throughput confirmation of disease genes candidacy. Genet Med 2018; 21:736-742. [PMID: 30237576 PMCID: PMC6752307 DOI: 10.1038/s41436-018-0138-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/05/2018] [Indexed: 02/06/2023] Open
Abstract
Purpose Establishing links between Mendelian phenotypes and genes enables the proper interpretation of variants therein. Autozygome, a rich source of homozygous variants, has been successfully utilized for the high throughput identification of novel autosomal recessive disease genes. Here, we highlight the utility of the autozygome for the high throughput confirmation of previously published tentative links to diseases. Methods Autozygome and exome analysis of patients with suspected Mendelian phenotypes. All variants were classified according to the American College of Medical Genetics and Genomics guidelines. Results We highlight 30 published candidate genes (ACTL6B, ADAM22, AGTPBP1, APC, C12orf4, C3orf17 (NEPRO), CENPF, CNPY3, COL27A1, DMBX1, FUT8, GOLGA2, KIAA0556, LENG8, MCIDAS, MTMR9, MYH11, QRSL1, RUBCN, SLC25A42, SLC9A1, TBXT, TFG, THUMPD1, TRAF3IP2, UFC1, UFM1, WDR81, XRCC2, ZAK) in which we identified homozygous likely deleterious variants in patients with compatible phenotypes. We also identified homozygous likely deleterious variants in 18 published candidate genes (ABCA2, ARL6IP1, ATP8A2, CDK9, CNKSR1, DGAT1, DMXL2, GEMIN4, HCN2, HCRT, MYO9A, PARS2, PLOD3, PREPL, SCLT1, STX3, TXNRD2, WIPI2) although the associated phenotypes are sufficiently different from the original reports that they represent phenotypic expansion or potentially distinct allelic disorders. Conclusions Our results should facilitate the timely relabeling of these candidate disease genes in relevant databases to improve the yield of clinical genomic sequencing.
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Affiliation(s)
- Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mohammad A Al Muhaizea
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Husam R Kayyali
- Department of Pediatrics, King Faisal Specialist hospital and Research Center, Jeddah, Saudi Arabia
| | - Amal AlHashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha Al-Otaibi
- Genetic Unit, Children's Hospital, King Saud Medical City, Riyadh, Saudi Arabia
| | - Hamad I Alzaidan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ameera Balobaid
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Heba Y El Khashab
- Department of Pediatrics, Children's Hospital, Ain Shams University, Cairo, Egypt.,Department of Pediatrics, Dr. Suliman Al Habib Medical Group, Riyadh, Saudi Arabia
| | - Dalal K Bubshait
- Department of Pediatrics, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Maha Faden
- Genetic Unit, Children's Hospital, King Saud Medical City, Riyadh, Saudi Arabia
| | - Suad Al Yamani
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Dabbagh
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mariam Al-Mureikhi
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Doha, Qatar
| | - Abdulla Al Jasser
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Iram Alluhaydan
- Genetics Division, Department of Pediatrics, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | | | | | - Ibrahim Almogarri
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wesam Kurdi
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hana Akleh
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Alya Qari
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saeed M Al Tala
- Department of Pediatrics, Armed Forces Hospital SR, Khamis Mushayt, Saudi Arabia
| | - Suzan Alhomaidi
- Genetic Unit, Children's Hospital, King Saud Medical City, Riyadh, Saudi Arabia
| | - Amal Y Kentab
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Aziza Chedrawi
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Seham Alameer
- Department of pediatrics, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Brahim Tabarki
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Menasria Samira
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ewa Goljan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saad AlShahwan
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genetic Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Tawfeg Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Doha, Qatar
| | - Mohammad M Al-Qattan
- Department of Surgery, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia. .,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
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46
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Al-Nabhani M, Al-Rashdi S, Al-Murshedi F, Al-Kindi A, Al-Thihli K, Al-Saegh A, Al-Futaisi A, Al-Mamari W, Zadjali F, Al-Maawali A. Reanalysis of exome sequencing data of intellectual disability samples: Yields and benefits. Clin Genet 2018; 94:495-501. [PMID: 30125339 DOI: 10.1111/cge.13438] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/08/2018] [Accepted: 08/15/2018] [Indexed: 01/07/2023]
Abstract
Recently, with the advancement in next generation sequencing (NGS) along with the improvement of bioinformatics tools, whole exome sequencing (WES) has become the most efficient diagnostic test for patients with intellectual disability (ID). This study aims to estimate the yield of a reanalysis of ID negative exome cases after data reannotation. Total of 50 data files of exome sequencing, representing 50 samples were collected. The inclusion criteria include ID phenotype, and previous analysis indicated a negative result (no abnormality detected). These files were pre-processed and reannotated using ANNOVAR tool. Prioritized variants in the 50 cases studied were classified into three groups, (1) disease-causative variants (2) possible disease-causing variants and (3) variants in novel genes. Reanalysis resulted in the identification of pathogenic/likely pathogenic variants in six cases (12%). Thirteen cases (26%) were classified as having possible disease-causing variants. Candidate genes requiring future functional studies were detected in seven cases (14%). Improvement in bioinformatics tools, update in the genetic databases and literature, and patients' clinical phenotype update were the main reasons for identification of these variants in this study.
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Affiliation(s)
- Maryam Al-Nabhani
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Samiya Al-Rashdi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Fathiya Al-Murshedi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Adila Al-Kindi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalid Al-Thihli
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Abeer Al-Saegh
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Amna Al-Futaisi
- Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Watfa Al-Mamari
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman.,Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Fahad Zadjali
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
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47
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Suleiman J, Al Hashem AM, Tabarki B, Al-Thihli K, Bi W, El-Hattab AW. PPP1R21 homozygous null variants associated with developmental delay, muscle weakness, distinctive facial features, and brain abnormalities. Clin Genet 2018; 94:351-355. [PMID: 29808498 DOI: 10.1111/cge.13387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 01/19/2023]
Abstract
We present 3 children with homozygous null variants in the PPP1R21 gene. A 3-year-old girl had profound developmental delay, hypotonia and weakness, poor feeding, recurrent chest infections and respiratory failure, rotatory nystagmus, absent reflexes, and a homozygous nonsense variant c.2089C>T (p.Arg697*). A 2-year-old boy had profound developmental delay, weakness and hypotonia, recurrent chest infections and respiratory distress, undescended testes, rotatory nystagmus, hyporeflexia, and a homozygous nonsense variant c.427C>T (p.Arg143*). An 11-year-old girl with profound developmental delay, weakness and hypotonia, stereotypic movements, growth failure, hyporeflexia, and a homozygous frameshift variant c.87_88delAG (p.Gly30Cysfs*4). In addition, these children shared common facial features (thick eyebrows, hypertelorism, broad nasal bridge, short nose with upturned nasal tip and broad low-hanging columella, thick lips, low-set ears, and coarse facies with excessive facial hair), and brain abnormalities (cerebellar vermis hypoplasia, ventricular dilatation, and reduced white matter volume). Although PPP1R21 has not yet been linked to human disease, the consistency in the phenotype of individuals from unrelated families, the nature of the variants which result in truncated proteins, and the expected vital role for PPP1R21 in cellular function, all support that PPP1R21 is a novel disease-associated gene responsible for the phenotype observed in these individuals.
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Affiliation(s)
- J Suleiman
- Division of Neurology, Pediatrics Department, Tawam Hospital, Al Ain, United Arab Emirates.,Department of Pediatrics, College of Medicine and Health sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - A M Al Hashem
- Division of Genetics, Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - B Tabarki
- Division of Neurology, Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - K Al-Thihli
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - W Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics, Houston, Texas
| | - A W El-Hattab
- Division of Genetic and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al Ain, United Arab Emirates
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48
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Maddirevula S, Alsahli S, Alhabeeb L, Patel N, Alzahrani F, Shamseldin HE, Anazi S, Ewida N, Alsaif HS, Mohamed JY, Alazami AM, Ibrahim N, Abdulwahab F, Hashem M, Abouelhoda M, Monies D, Al Tassan N, Alshammari M, Alsagheir A, Seidahmed MZ, Sogati S, Aglan MS, Hamad MH, Salih MA, Hamed AA, Alhashmi N, Nabil A, Alfadli F, Abdel-Salam GMH, Alkuraya H, Peitee WO, Keng WT, Qasem A, Mushiba AM, Zaki MS, Fassad MR, Alfadhel M, Alexander S, Sabr Y, Temtamy S, Ekbote AV, Ismail S, Hosny GA, Otaify GA, Amr K, Al Tala S, Khan AO, Rizk T, Alaqeel A, Alsiddiky A, Singh A, Kapoor S, Alhashem A, Faqeih E, Shaheen R, Alkuraya FS. Expanding the phenome and variome of skeletal dysplasia. Genet Med 2018; 20:1609-1616. [PMID: 29620724 DOI: 10.1038/gim.2018.50] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/13/2018] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To describe our experience with a large cohort (411 patients from 288 families) of various forms of skeletal dysplasia who were molecularly characterized. METHODS Detailed phenotyping and next-generation sequencing (panel and exome). RESULTS Our analysis revealed 224 pathogenic/likely pathogenic variants (54 (24%) of which are novel) in 123 genes with established or tentative links to skeletal dysplasia. In addition, we propose 5 genes as candidate disease genes with suggestive biological links (WNT3A, SUCO, RIN1, DIP2C, and PAN2). Phenotypically, we note that our cohort spans 36 established phenotypic categories by the International Skeletal Dysplasia Nosology, as well as 18 novel skeletal dysplasia phenotypes that could not be classified under these categories, e.g., the novel C3orf17-related skeletal dysplasia. We also describe novel phenotypic aspects of well-known disease genes, e.g., PGAP3-related Toriello-Carey syndrome-like phenotype. We note a strong founder effect for many genes in our cohort, which allowed us to calculate a minimum disease burden for the autosomal recessive forms of skeletal dysplasia in our population (7.16E-04), which is much higher than the global average. CONCLUSION By expanding the phenotypic, allelic, and locus heterogeneity of skeletal dysplasia in humans, we hope our study will improve the diagnostic rate of patients with these conditions.
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Affiliation(s)
- Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lamees Alhabeeb
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shams Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jawahir Y Mohamed
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - 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
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Muneera Alshammari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Afaf Alsagheir
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Samira Sogati
- Department of Medical Genetics, King Fahad General Hospital, Jeddah, Saudi Arabia
| | - Mona S Aglan
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Muddathir H Hamad
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ahlam A Hamed
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | | | - Amira Nabil
- Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Fatima Alfadli
- Department of Pediatrics, Maternity and Children's Hospital, Medina, Saudi Arabia
| | - Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Hisham Alkuraya
- Global Eye Care, Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | | | - W T Keng
- Clinical Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Abdullah Qasem
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Aziza M Mushiba
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Mahmoud R Fassad
- The Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Genetics Division, Department of Pediatrics, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Saji Alexander
- Department of Paediatric Endocrinology and Diabetes, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Yasser Sabr
- Department of Obstetrics and Gynecology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Samia Temtamy
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Alka V Ekbote
- Clinical Genetics Unit, Christian Medical College, Vellore, India
| | - Samira Ismail
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | | | - Ghada A Otaify
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Khalda Amr
- Clinical Genetics Department, Human Genetics & Genome Research Division, Center of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Saeed Al Tala
- Department of Pediatrics, Armed Forces Hospital Program Southwest Region, Khamis Mushait, Saudi Arabia
| | - Arif O Khan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Tamer Rizk
- Department of Pediatric Neurology, Dr. Sulaiman Al Habib Hospital, Riyadh, Saudi Arabia
| | - Aida Alaqeel
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Abdulmonem Alsiddiky
- Department of Orthopedics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ankur Singh
- Department of Pediatrics, Genetic Clinic, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Seema Kapoor
- Department of Pediatrics, Maulana Azad Medical College, New Delhi, India
| | - Amal Alhashem
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Department of Pediatric, Prince Sultan Medical Military City, 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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Hartley T, Wagner JD, Warman-Chardon J, Tétreault M, Brady L, Baker S, Tarnopolsky M, Bourque PR, Parboosingh JS, Smith C, McInnes B, Innes AM, Bernier F, Curry CJ, Yoon G, Horvath GA, Bareke E, Gillespie M, Majewski J, Bulman DE, Dyment DA, Boycott KM. Whole-exome sequencing is a valuable diagnostic tool for inherited peripheral neuropathies: Outcomes from a cohort of 50 families. Clin Genet 2017; 93:301-309. [PMID: 28708278 DOI: 10.1111/cge.13101] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 01/02/2023]
Abstract
The inherited peripheral neuropathies (IPNs) are characterized by marked clinical and genetic heterogeneity and include relatively frequent presentations such as Charcot-Marie-Tooth disease and hereditary motor neuropathy, as well as more rare conditions where peripheral neuropathy is associated with additional features. There are over 250 genes known to cause IPN-related disorders but it is estimated that in approximately 50% of affected individuals a molecular diagnosis is not achieved. In this study, we examine the diagnostic utility of whole-exome sequencing (WES) in a cohort of 50 families with 1 or more affected individuals with a molecularly undiagnosed IPN with or without additional features. Pathogenic or likely pathogenic variants in genes known to cause IPN were identified in 24% (12/50) of the families. A further 22% (11/50) of families carried sequence variants in IPN genes in which the significance remains unclear. An additional 12% (6/50) of families had variants in novel IPN candidate genes, 3 of which have been published thus far as novel discoveries (KIF1A, TBCK, and MCM3AP). This study highlights the use of WES in the molecular diagnostic approach of highly heterogeneous disorders, such as IPNs, places it in context of other published neuropathy cohorts, while further highlighting associated benefits for discovery.
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Affiliation(s)
- T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J D Wagner
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J Warman-Chardon
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - M Tétreault
- Department of Human Genetics, McGill University, Montréal, Canada
| | - L Brady
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - S Baker
- Department of Medicine, McMaster University Medical Centre, Hamilton, Canada
| | - M Tarnopolsky
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - P R Bourque
- Department of Medicine, University of Ottawa, Ottawa, Canada
| | - J S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - C Smith
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B McInnes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - A M Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - F Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - C J Curry
- Department of Pediatrics, University of California, San Francisco, California
| | - G Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G A Horvath
- Division of Biochemical Diseases, Department of Pediatrics, B.C. Children's Hospital, University of British Columbia, Vancouver, Canada
| | - E Bareke
- Department of Human Genetics, McGill University, Montréal, Canada
| | - M Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | | | - J Majewski
- Department of Human Genetics, McGill University, Montréal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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50
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Anazi S, Maddirevula S, Salpietro V, Asi YT, Alsahli S, Alhashem A, Shamseldin HE, AlZahrani F, Patel N, Ibrahim N, Abdulwahab FM, Hashem M, Alhashmi N, Al Murshedi F, Al Kindy A, Alshaer A, Rumayyan A, Al Tala S, Kurdi W, Alsaman A, Alasmari A, Banu S, Sultan T, Saleh MM, Alkuraya H, Salih MA, Aldhalaan H, Ben-Omran T, Al Musafri F, Ali R, Suleiman J, Tabarki B, El-Hattab AW, Bupp C, Alfadhel M, Al Tassan N, Monies D, Arold ST, Abouelhoda M, Lashley T, Houlden H, Faqeih E, Alkuraya FS. Expanding the genetic heterogeneity of intellectual disability. Hum Genet 2017; 136:1419-1429. [PMID: 28940097 DOI: 10.1007/s00439-017-1843-2] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/15/2017] [Indexed: 11/30/2022]
Abstract
Intellectual disability (ID) is a common morbid condition with a wide range of etiologies. The list of monogenic forms of ID has increased rapidly in recent years thanks to the implementation of genomic sequencing techniques. In this study, we describe the phenotypic and genetic findings of 68 families (105 patients) all with novel ID-related variants. In addition to established ID genes, including ones for which we describe unusual mutational mechanism, some of these variants represent the first confirmatory disease-gene links following previous reports (TRAK1, GTF3C3, SPTBN4 and NKX6-2), some of which were based on single families. Furthermore, we describe novel variants in 14 genes that we propose as novel candidates (ANKHD1, ASTN2, ATP13A1, FMO4, MADD, MFSD11, NCKAP1, NFASC, PCDHGA10, PPP1R21, SLC12A2, SLK, STK32C and ZFAT). We highlight MADD and PCDHGA10 as particularly compelling candidates in which we identified biallelic likely deleterious variants in two independent ID families each. We also highlight NCKAP1 as another compelling candidate in a large family with autosomal dominant mild intellectual disability that fully segregates with a heterozygous truncating variant. The candidacy of NCKAP1 is further supported by its biological function, and our demonstration of relevant expression in human brain. Our study expands the locus and allelic heterogeneity of ID and demonstrates the power of positional mapping to reveal unusual mutational mechanisms.
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Affiliation(s)
- Shams Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Yasmine T Asi
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema AlZahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous M 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
| | - Nadia Alhashmi
- Department of Genetics, College of Medicine, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Fathiya Al Murshedi
- Department of Genetics, College of Medicine, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Adila Al Kindy
- Department of Genetics, College of Medicine, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Ahmad Alshaer
- Pediatric Neurology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ahmed Rumayyan
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Neurology Division, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Department of Pediatrics and Genetic Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Wesam Kurdi
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital, Riyadh, Saudi Arabia
| | - Abdulaziz Alsaman
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Alasmari
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Selina Banu
- Department of Pediatric Neurology, ICH and SSF Hospital Mirpur, Dhaka, 1216, Bangladesh
| | - Tipu Sultan
- Department of Pediatric Neurology, Institute of Child Health and The Children's Hospital Lahore, 381-D/2, Lahore, Pakistan
| | - Mohammed M Saleh
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Department of Ophthalmology, Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Hesham Aldhalaan
- Pediatric Neurology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Fatima Al Musafri
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Rehab Ali
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Jehan Suleiman
- Division of Neurology, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Brahim Tabarki
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Caleb Bupp
- Spectrum Health Genetics, Grand Rapids, MI, USA
| | - Majid Alfadhel
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Stefan T Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Eissa Faqeih
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Spectrum Health Genetics, Grand Rapids, MI, USA. .,Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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