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Ma D, Ye M, Hu W, Gao H, Wang L, Song Y, Nie R, Hu Z, Guo H. Large regions of homozygosity in prenatal diagnosis. Am J Med Genet A 2024:e63712. [PMID: 38757552 DOI: 10.1002/ajmg.a.63712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/26/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Chromosomal microarrays (CMA) incorporate single nucleotide polymorphisms to enable the detection of regions of homozygosity (ROH). Here, we retrospectively analyzed 6288 prenatal cases who performed CMA to explored the clinical implications of large ROH in prenatal diagnosis. We analyzed cases with ROH larger than 10 megabases and reviewed the ultrasound findings; karyotype results and pregnancy follow-up data. Cases with possible imprinting disorders were assessed by methylation-specific multiplex ligation-dependent probe amplification. In total, we identified 50 cases with large ROH and chromosomes 1 and 2 were the most affected. About 59.18% of the ROH cases had ultrasound abnormalities, with the most common findings being ultrasound soft-marker abnormalities. There were seven fetuses had ROH which covered almost the entire chromosome and four had terminal ROH that involved almost the entire long arm of the chromosomes, which indicated uniparental disomy (UPD), of which 70% showed abnormal ultrasound findings. Ten cases with multiple ROH on different chromosomes indicated the third to fifth degree of consanguinity. In this study, we highlighted the clinical relevance of large ROH related to UPD. The analysis of ROH allowed us to gain further understanding of complex cytogenetic and disease mechanisms in prenatal diagnosis.
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Affiliation(s)
- Di Ma
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Mei Ye
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Clinical Medical Research Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Wenlong Hu
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Clinical Medical Research Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Hui Gao
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Lijuan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Yaqin Song
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Rui Nie
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Zhiyang Hu
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Department of Obstetrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Hui Guo
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
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Ghasemi MR, Tehrani Fateh S, Moeinafshar A, Sadeghi H, Karimzadeh P, Mirfakhraie R, Rezaei M, Hashemi-Gorji F, Rezvani Kashani M, Fazeli Bavandpour F, Bagheri S, Moghimi P, Rostami M, Madannejad R, Roudgari H, Miryounesi M. Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review. BMC Med Genomics 2024; 17:51. [PMID: 38347586 PMCID: PMC10863249 DOI: 10.1186/s12920-024-01810-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Pontocerebellar hypoplasia is an umbrella term describing a heterogeneous group of prenatal neurodegenerative disorders mostly affecting the pons and cerebellum, with 17 types associated with 25 genes. However, some types of PCH lack sufficient information, which highlights the importance of investigating and introducing more cases to further elucidate the clinical, radiological, and biochemical features of these disorders. The aim of this study is to provide an in-depth review of PCH and to identify disease genes and their inheritance patterns in 12 distinct Iranian families with clinically confirmed PCH. METHODS Cases included in this study were selected based on their phenotypic and genetic information available at the Center for Comprehensive Genetic Services. Whole-exome sequencing (WES) was used to discover the underlying genetic etiology of participants' problems, and Sanger sequencing was utilized to confirm any suspected alterations. We also conducted a comprehensive molecular literature review to outline the genetic features of the various subtypes of PCH. RESULTS This study classified and described the underlying etiology of PCH into three categories based on the genes involved. Twelve patients also were included, eleven of whom were from consanguineous parents. Ten different variations in 8 genes were found, all of which related to different types of PCH. Six novel variations were reported, including SEPSECS, TSEN2, TSEN54, AMPD2, TOE1, and CLP1. Almost all patients presented with developmental delay, hypotonia, seizure, and microcephaly being common features. Strabismus and elevation in lactate levels in MR spectroscopy were novel phenotypes for the first time in PCH types 7 and 9. CONCLUSIONS This study merges previously documented phenotypes and genotypes with unique novel ones. Due to the diversity in PCH, we provided guidance for detecting and diagnosing these heterogeneous groups of disorders. Moreover, since certain critical conditions, such as spinal muscular atrophy, can be a differential diagnosis, providing cases with novel variations and clinical findings could further expand the genetic and clinical spectrum of these diseases and help in better diagnosis. Therefore, six novel genetic variants and novel clinical and paraclinical findings have been reported for the first time. Further studies are needed to elucidate the underlying mechanisms and potential therapeutic targets for PCH.
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Affiliation(s)
- Mohammad-Reza Ghasemi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Aysan Moeinafshar
- School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Hossein Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
| | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Mofid Children's Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran
| | - Mitra Rezaei
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Morteza Rezvani Kashani
- Pediatric Neurology Department, Mofid Children's Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Saman Bagheri
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
| | - Parinaz Moghimi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- School of Medicine, Islamic Azad University Tehran Medical Sciences, Tehran, Iran
| | - Masoumeh Rostami
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rasoul Madannejad
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hassan Roudgari
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Miryounesi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, , Tehran, Iran.
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Zhao R, Zhang L, Lu H. Analysis of the Clinical Features and Imaging Findings of Pontocerebellar Hypoplasia Type 2D Caused by Mutations in SEPSECS Gene. CEREBELLUM (LONDON, ENGLAND) 2023; 22:938-946. [PMID: 36085396 DOI: 10.1007/s12311-022-01470-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Pontocerebellar hypoplasia type 2D (PCH2D) caused by SEPSECS gene mutations is very rare and only described in a few case reports. In this study, we analyzed the clinical features and imaging findings of these individuals, so as to provide references for the clinic. We reported a case of PCH2D caused by a new complex heterozygote mutation in SEPSECS gene, and reviewed the literatures to summarize the clinical features and imaging findings and compare the differences between early-onset patients (EOPs) and late-onset patients (LOPs). Of 23 PCH2D patients, 19 cases were early-onset and 4 cases were late-onset, with average ages of 4.1 ± 4.0 years and 21.8 ± 9.4 years, females were more prevalent (14/19). EOPs mainly distributed in Arab countries (10/14) and Finland (4/14), while LOPs in East Asia (3/3). EOPs develop severe initial symptoms at the average age of 4.1 ± 7.8 months or shortly after birth, while LOPs experienced mild developmental delay in infancy. Microcephaly (10/11), intellectual disability (10/11), decreased motor function (10/11), and spastic or dystonic quadriplegia (8/10) were the common clinical features of EOPs and LOPs. EOPs also presented with visual impairment (5/7), seizures (4/7), neonatal irritability/opisthotonus (3/7), tremors/myoclonus (3/7), dysmorphic features (3/7), and other symptoms. EOPs were characterized by cerebellar symptoms (4/4). Magnetic resonance imaging (MRI) revealed progressive cerebellar atrophy followed by less pronounced cerebral atrophy, and there was no pons atrophy in LOPs. Most patients of PCH2D were severe early-onset, and a few were late-onset with milder symptoms. EOPs and LOPs shared some common clinical features and MRI findings, but also had their own characteristics.
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Affiliation(s)
- Ran Zhao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Limin Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hong Lu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Ma X, Liu X, Duan X, Fan D. Screening for PRX mutations in a large Chinese Charcot-Marie-Tooth disease cohort and literature review. Front Neurol 2023; 14:1148044. [PMID: 37470010 PMCID: PMC10352492 DOI: 10.3389/fneur.2023.1148044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/06/2023] [Indexed: 07/21/2023] Open
Abstract
Background Periaxins (encoded by PRX) play an important role in the stabilization of peripheral nerve myelin. Mutations in PRX can lead to Charcot-Marie-Tooth disease type 4F (CMT4F). Methods In this study, we screened for PRX mutations using next-generation sequencing and whole-exome sequencing in a large Chinese CMT cohort consisting of 465 unrelated index patients and 650 healthy controls. Sanger sequencing was used for the validation of all identified variants. We also reviewed all previously reported PRX-related CMT cases and summarized the clinical manifestations and genetic features of PRX-related CMTs. Results The hit rate for biallelic PRX variants in our cohort of Chinese CMT patients was 0.43% (2/465). One patient carried a previously unreported splice-site mutation (c.25_27 + 9del) compound heterozygous with a known nonsense variant. Compiling data on CMT4F cases and PRX variants from the medical literature confirmed that early-onset (95.2%), distal amyotrophy or weakness (94.0%), feet deformity (75.0%), sensory impairment or sensory ataxia (65.5%), delayed motor milestones (60.7%), and spinal deformity (59.5%) are typical features for CMT4F. Less frequent features were auditory impairments, respiratory symptoms, late onset, dysarthria or hoarseness, ophthalmic problems, and central nervous system involvement. The two cases with biallelic missense mutations have later onset age than those with nonsense or frameshift mutations. We did not note clear correlations between the type and site of mutations and clinical severity or distinct constellations of symptoms. Conclusion Consistent with observations in other countries and ethnic groups, PRX-related CMT is rare in China. The clinical spectrum is wider than previously anticipated.
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Affiliation(s)
- Xinran Ma
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Xiaoxuan Liu
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Xiaohui Duan
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
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Mao K, Borel C, Ansar M, Jolly A, Makrythanasis P, Froehlich C, Iwaszkiewicz J, Wang B, Xu X, Li Q, Blanc X, Zhu H, Chen Q, Jin F, Ankamreddy H, Singh S, Zhang H, Wang X, Chen P, Ranza E, Paracha SA, Shah SF, Guida V, Piceci-Sparascio F, Melis D, Dallapiccola B, Digilio MC, Novelli A, Magliozzi M, Fadda MT, Streff H, Machol K, Lewis RA, Zoete V, Squeo GM, Prontera P, Mancano G, Gori G, Mariani M, Selicorni A, Psoni S, Fryssira H, Douzgou S, Marlin S, Biskup S, De Luca A, Merla G, Zhao S, Cox TC, Groves AK, Lupski JR, Zhang Q, Zhang YB, Antonarakis SE. FOXI3 pathogenic variants cause one form of craniofacial microsomia. Nat Commun 2023; 14:2026. [PMID: 37041148 PMCID: PMC10090152 DOI: 10.1038/s41467-023-37703-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Craniofacial microsomia (CFM; also known as Goldenhar syndrome), is a craniofacial developmental disorder of variable expressivity and severity with a recognizable set of abnormalities. These birth defects are associated with structures derived from the first and second pharyngeal arches, can occur unilaterally and include ear dysplasia, microtia, preauricular tags and pits, facial asymmetry and other malformations. The inheritance pattern is controversial, and the molecular etiology of this syndrome is largely unknown. A total of 670 patients belonging to unrelated pedigrees with European and Chinese ancestry with CFM, are investigated. We identify 18 likely pathogenic variants in 21 probands (3.1%) in FOXI3. Biochemical experiments on transcriptional activity and subcellular localization of the likely pathogenic FOXI3 variants, and knock-in mouse studies strongly support the involvement of FOXI3 in CFM. Our findings indicate autosomal dominant inheritance with reduced penetrance, and/or autosomal recessive inheritance. The phenotypic expression of the FOXI3 variants is variable. The penetrance of the likely pathogenic variants in the seemingly dominant form is reduced, since a considerable number of such variants in affected individuals were inherited from non-affected parents. Here we provide suggestive evidence that common variation in the FOXI3 allele in trans with the pathogenic variant could modify the phenotypic severity and accounts for the incomplete penetrance.
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Affiliation(s)
- Ke Mao
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
- Jules-Gonin Eye Hospital, Department of Ophthalmology, University of Lausanne, 1004, Lausanne, Switzerland
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Bingqing Wang
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China
| | - Xiaopeng Xu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Qiang Li
- Department of Plastic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland
| | - Hao Zhu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Qi Chen
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China
| | - Fujun Jin
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Harinarayana Ankamreddy
- Department of Biotechnology, School of Bioengineering, SRMIST, Kattankulathur, Tamilnadu, 603203, India
| | - Sunita Singh
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongyuan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaogang Wang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Peiwei Chen
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland
| | - Sohail Aziz Paracha
- Anatomy Department, Khyber Medical University Institute of Medical Sciences (KIMS), Kohat, Pakistan
| | - Syed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences (KIMS), DHQ Hospital KDA, Kohat, Pakistan
| | - Valentina Guida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Daniela Melis
- Department of Medicine, Surgery, and Dentistry, Università University degli of Studi di Salerno, Salerno, Italy
| | - Bruno Dallapiccola
- Medical Genetics and Rare Disease Research Division, Pediatric Cardiology, Medical Genetics Laboratory, Neuropsychiatry, Scientific Rectorate, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | | | - Antonio Novelli
- Sezione di Genetica Medica, Ospedale 'Bambino Gesù', Rome, Italy
| | - Monia Magliozzi
- Sezione di Genetica Medica, Ospedale 'Bambino Gesù', Rome, Italy
| | - Maria Teresa Fadda
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Keren Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
- Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges, 1066, Switzerland
| | - Gabriella Maria Squeo
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Giorgia Mancano
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Giulia Gori
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Milena Mariani
- Pediatric Department, ASST Lariana, Santa Anna General Hospital, Como, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Santa Anna General Hospital, Como, Italy
| | - Stavroula Psoni
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Helen Fryssira
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Sofia Douzgou
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Sandrine Marlin
- Centre de Référence Surdités Génétiques, Hôpital Necker, Institut Imagine, Paris, France
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, 72076, Germany
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Shouqin Zhao
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Timothy C Cox
- Departments of Oral & Craniofacial Sciences and Pediatrics, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Andrew K Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Qingguo Zhang
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China.
| | - Yong-Biao Zhang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland.
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland.
- iGE3 Institute of Genetics and Genomes in Geneva, Geneva, Switzerland.
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Jia A, Lei Y, Liu DP, Pan L, Guan HZ, Yang B. A Retrospective Analysis of Clinically Focused Exome Sequencing Results of 372 Infants with Suspected Monogenic Disorders in China. Pharmgenomics Pers Med 2023; 16:81-97. [PMID: 36755623 PMCID: PMC9901461 DOI: 10.2147/pgpm.s387767] [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: 09/05/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Objective The context was designed to optimize the diagnostic utility of clinically focused exome sequencing (CFES) and shorten the diagnostic odyssey among pediatric patients suspected of monogenic disorders (MDs). Methods Here, we retrospectively analyzed the clinical notes of 372 patients from different areas in the Jiangxi province that were referred for a diagnostic CFES and analysis from June 2018 to March 2022 with symptoms suggestive of MDs. In our study, preliminary tests using the proband-only clinical exome sequencing as a cost-effective first-tier diagnostic test for pediatric patients with unidentified MDs, supplemented by family segregation studies for targeted variants when indicated. Results Probands with confirmed diagnostic (CD) or likely diagnostic (LD) genetic influences accounted for 12% of all cases, whereas those with an uncertain diagnosis accounted for 48%. We also found that systemic primary carnitine deficiency (CDSP) (SLC22A5 gene) and phenylketonuria (PAH gene) were relatively more prevalent, and these patients with CDSP had the most frequent c.1400C > G variant (p.S467C) and c.51C > G variant (p. F17L) in this study. In addition, statistical analysis revealed that the estimates of diagnostic yields varied across certain phenotypic features of patients, and patients with specific phenotypic traits tended to benefit more from CFES. Conclusion The CFES may be a first-line genetic test for diagnosing young children with suspected genetic conditions, as it validates the identification of molecular genetics alterations and facilitates comprehensive medical management. Moreover, we found that infants exhibiting metabolism/homeostasis abnormalities, craniofacial /otolaryngology/ ophthalmologic abnormalities, and/or the integument were significantly more likely to receive a genetic diagnosis via CFES than infants without such features. However, due to the current study's low diagnostic yield and inherent limitations, high-quality clinical studies with larger sample sizes are still needed to provide more likely results and confirm our findings.
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Affiliation(s)
- An Jia
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China
| | - Yi Lei
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Dan-Ping Liu
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Lu Pan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Hui-Zhen Guan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Bicheng Yang
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China,Correspondence: Bicheng Yang, Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, People’s Republic of China, Tel +86 15350402147, Email
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7
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Sekulovski S, Trowitzsch S. What connects splicing of transfer RNA precursor molecules with pontocerebellar hypoplasia? Bioessays 2023; 45:e2200130. [PMID: 36517085 DOI: 10.1002/bies.202200130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023]
Abstract
Transfer RNAs (tRNAs) represent the most abundant class of RNA molecules in the cell and are key players during protein synthesis and cellular homeostasis. Aberrations in the extensive tRNA biogenesis pathways lead to severe neurological disorders in humans. Mutations in the tRNA splicing endonuclease (TSEN) and its associated RNA kinase cleavage factor polyribonucleotide kinase subunit 1 (CLP1) cause pontocerebellar hypoplasia (PCH), a heterogeneous group of neurodegenerative disorders, that manifest as underdevelopment of specific brain regions typically accompanied by microcephaly, profound motor impairments, and child mortality. Recently, we demonstrated that mutations leading to specific PCH subtypes destabilize TSEN in vitro and cause imbalances of immature to mature tRNA ratios in patient-derived cells. However, how tRNA processing defects translate to disease on a systems level has not been understood. Recent findings suggested that other cellular processes may be affected by mutations in TSEN/CLP1 and obscure the molecular mechanisms of PCH emergence. Here, we review PCH disease models linked to the TSEN/CLP1 machinery and discuss future directions to study neuropathogenesis.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
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8
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Rush ET, Johnson B, Aradhya S, Beltran D, Bristow SL, Eisenbeis S, Guerra NE, Krolczyk S, Miller N, Morales A, Ramesan P, Sarafrazi S, Truty R, Dahir K. Molecular Diagnoses of X-Linked and Other Genetic Hypophosphatemias: Results From a Sponsored Genetic Testing Program. J Bone Miner Res 2022; 37:202-214. [PMID: 34633109 PMCID: PMC9298723 DOI: 10.1002/jbmr.4454] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/27/2021] [Accepted: 10/02/2021] [Indexed: 12/20/2022]
Abstract
X-linked hypophosphatemia (XLH), a dominant disorder caused by pathogenic variants in the PHEX gene, affects both sexes of all ages and results in elevated serum fibroblast growth factor 23 (FGF23) and below-normal serum phosphate. In XLH, rickets, osteomalacia, short stature, and lower limb deformity may be present with muscle pain and/or weakness/fatigue, bone pain, joint pain/stiffness, hearing difficulty, enthesopathy, osteoarthritis, and dental abscesses. Invitae and Ultragenyx collaborated to provide a no-charge sponsored testing program using a 13-gene next-generation sequencing panel to confirm clinical XLH or aid diagnosis of suspected XLH/other genetic hypophosphatemia. Individuals aged ≥6 months with clinical XLH or suspected genetic hypophosphatemia were eligible. Of 831 unrelated individuals tested between February 2019 and June 2020 in this cross-sectional study, 519 (62.5%) individuals had a pathogenic or likely pathogenic variant in PHEX (PHEX-positive). Among the 312 PHEX-negative individuals, 38 received molecular diagnoses in other genes, including ALPL, CYP27B1, ENPP1, and FGF23; the remaining 274 did not have a molecular diagnosis. Among 319 patients with a provider-reported clinical diagnosis of XLH, 88.7% (n = 283) had a reportable PHEX variant; 81.5% (n = 260) were PHEX-positive. The most common variant among PHEX-positive individuals was an allele with both the gain of exons 13-15 and c.*231A>G (3'UTR variant) (n = 66/519). Importantly, over 80% of copy number variants would have been missed by traditional microarray analysis. A positive molecular diagnosis in 41 probands (4.9%; 29 PHEX positive, 12 non-PHEX positive) resulted in at least one family member receiving family testing. Additional clinical or family member information resulted in variant(s) of uncertain significance (VUS) reclassification to pathogenic/likely pathogenic (P/LP) in 48 individuals, highlighting the importance of segregation and clinical data. In one of the largest XLH genetic studies to date, 65 novel PHEX variants were identified and a high XLH diagnostic yield demonstrated broad insight into the genetic basis of XLH. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Eric T Rush
- Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri - Kansas City School of Medicine, Kansas City, MO, USA.,Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | | | | | | | | | | | - Norma E Guerra
- Department of Pediatric Nephrology, Hospital General del Centro Médico Nacional «La Raza», Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | | | | | | | | | | | | | - Kathryn Dahir
- Program for Metabolic Bone Disorders, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
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9
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Schoenmakers E, Chatterjee K. Human Genetic Disorders Resulting in Systemic Selenoprotein Deficiency. Int J Mol Sci 2021; 22:12927. [PMID: 34884733 PMCID: PMC8658020 DOI: 10.3390/ijms222312927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 01/01/2023] Open
Abstract
Selenium, a trace element fundamental to human health, is incorporated as the amino acid selenocysteine (Sec) into more than 25 proteins, referred to as selenoproteins. Human mutations in SECISBP2, SEPSECS and TRU-TCA1-1, three genes essential in the selenocysteine incorporation pathway, affect the expression of most if not all selenoproteins. Systemic selenoprotein deficiency results in a complex, multifactorial disorder, reflecting loss of selenoprotein function in specific tissues and/or long-term impaired selenoenzyme-mediated defence against oxidative and endoplasmic reticulum stress. SEPSECS mutations are associated with a predominantly neurological phenotype with progressive cerebello-cerebral atrophy. Selenoprotein deficiency due to SECISBP2 and TRU-TCA1-1 defects are characterized by abnormal circulating thyroid hormones due to lack of Sec-containing deiodinases, low serum selenium levels (low SELENOP, GPX3), with additional features (myopathy due to low SELENON; photosensitivity, hearing loss, increased adipose mass and function due to reduced antioxidant and endoplasmic reticulum stress defence) in SECISBP2 cases. Antioxidant therapy ameliorates oxidative damage in cells and tissues of patients, but its longer term benefits remain undefined. Ongoing surveillance of patients enables ascertainment of additional phenotypes which may provide further insights into the role of selenoproteins in human biological processes.
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Affiliation(s)
| | - Krishna Chatterjee
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge, Cambridge CB2 0QQ, UK;
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10
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Dos Santos CMDA, Heller AH, Pena HB, Pena SDJ. A Protocol for Preconceptional Screening of Consanguineous Couples Using Whole Exome Sequencing. Front Genet 2021; 12:685123. [PMID: 34759951 PMCID: PMC8573158 DOI: 10.3389/fgene.2021.685123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic studies performed in consanguineous couples suggest that the reproductive risk that distinguish them from other couples in the general population is related to autosomal recessive (AR) diseases. This risk is scattered among the thousands of known and potential AR diseases. Thus, for effective preconceptional screening of consanguineous couples it is necessary a test that encompasses the largest number of genes possible. For that reason, we decided to create a protocol based on whole exome sequencing (WES). We sequenced completely the exomes of 39 consanguineous couples at high coverage (∼100×). Applying bioinformatics filters, we could detect genetic variants that were simultaneously present in both members of the couple in all genes listed in the Clinical Genomics Database as causally related to AR diseases. Shared variants were then assessed for pathogenicity. For non-truncating variants (missense and in-frame indels) we considered as pathogenic or likely pathogenic only the variants included as such in the ClinVar database. Shared truncating variants (frameshift, non-sense, and canonical splice variants) were considered likely pathogenic when loss-of-function was a known mechanism of disease. The 39 consanguineous cases included two couples with a coefficient of genetic relationship (CGR) of 0.25, 26 couples with a CGR of 0.125, three couples with a CGR of 0.0625 and eight couples with a CGR of 0.03125. In 21 of the 39 couples (53.8%) we ascertained sharing of heterozygosity for at least one variant considered pathogenic or likely pathogenic for an AR disease. In eight couples we found sharing of heterozygosity for at least two pathogenic variants. Once the specific pathogenic variant was identified, it became possible for the couple to undergo prenatal diagnosis or, if desired, preimplantation genetic diagnosis (PGD) involving in vitro fertilization and embryo screening. In conclusion, our results demonstrate that preconceptional screening by WES is a useful new procedure that should be incorporated in the genetic counseling of all consanguineous couples.
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Affiliation(s)
| | | | | | - Sérgio Danilo Junho Pena
- GENE - Núcleo de Genética Médica, Belo Horizonte, Brazil.,Laboratório de Genômica Clínica, Faculdade de Medicina da Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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11
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Ansar M, Ebstein F, Özkoç H, Paracha SA, Iwaszkiewicz J, Gesemann M, Zoete V, Ranza E, Santoni FA, Sarwar MT, Ahmed J, Krüger E, Bachmann-Gagescu R, Antonarakis SE. Biallelic variants in PSMB1 encoding the proteasome subunit β6 cause impairment of proteasome function, microcephaly, intellectual disability, developmental delay and short stature. Hum Mol Genet 2021; 29:1132-1143. [PMID: 32129449 DOI: 10.1093/hmg/ddaa032] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022] Open
Abstract
The molecular cause of the majority of rare autosomal recessive disorders remains unknown. Consanguinity due to extensive homozygosity unravels many recessive phenotypes and facilitates the detection of novel gene-disease links. Here, we report two siblings with phenotypic signs, including intellectual disability (ID), developmental delay and microcephaly from a Pakistani consanguineous family in which we have identified homozygosity for p(Tyr103His) in the PSMB1 gene (Genbank NM_002793) that segregated with the disease phenotype. PSMB1 encodes a β-type proteasome subunit (i.e. β6). Modeling of the p(Tyr103His) variant indicates that this variant weakens the interactions between PSMB1/β6 and PSMA5/α5 proteasome subunits and thus destabilizes the 20S proteasome complex. Biochemical experiments in human SHSY5Y cells revealed that the p(Tyr103His) variant affects both the processing of PSMB1/β6 and its incorporation into proteasome, thus impairing proteasome activity. CRISPR/Cas9 mutagenesis or morpholino knock-down of the single psmb1 zebrafish orthologue resulted in microcephaly, microphthalmia and reduced brain size. Genetic evidence in the family and functional experiments in human cells and zebrafish indicates that PSMB1/β6 pathogenic variants are the cause of a recessive disease with ID, microcephaly and developmental delay due to abnormal proteasome assembly.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland
| | - Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie, Universitätsmedizin Greifswald, Greifswald 17475, Germany
| | - Hayriye Özkoç
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Matthias Gesemann
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges 1066, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva 1205, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland.,Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Elke Krüger
- Institut für Medizinische Biochemie und Molekularbiologie, Universitätsmedizin Greifswald, Greifswald 17475, Germany
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland.,Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva 1205, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva 1211, Switzerland
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12
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Ansar M, Ranza E, Shetty M, Paracha SA, Azam M, Kern I, Iwaszkiewicz J, Farooq O, Pournaras CJ, Malcles A, Kecik M, Rivolta C, Muzaffar W, Qurban A, Ali L, Aggoun Y, Santoni FA, Makrythanasis P, Ahmed J, Qamar R, Sarwar MT, Henry LK, Antonarakis SE. Taurine treatment of retinal degeneration and cardiomyopathy in a consanguineous family with SLC6A6 taurine transporter deficiency. Hum Mol Genet 2021; 29:618-623. [PMID: 31903486 DOI: 10.1093/hmg/ddz303] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 01/05/2023] Open
Abstract
In a consanguineous Pakistani family with two affected individuals, a homozygous variant Gly399Val in the eighth transmembrane domain of the taurine transporter SLC6A6 was identified resulting in a hypomorph transporting capacity of ~15% compared with normal. Three-dimensional modeling of this variant has indicated that it likely causes displacement of the Tyr138 (TM3) side chain, important for transport of taurine. The affected individuals presented with rapidly progressive childhood retinal degeneration, cardiomyopathy and almost undetectable plasma taurine levels. Oral taurine supplementation of 100 mg/kg/day resulted in maintenance of normal blood taurine levels. Following approval by the ethics committee, a long-term supplementation treatment was introduced. Remarkably, after 24-months, the cardiomyopathy was corrected in both affected siblings, and in the 6-years-old, the retinal degeneration was arrested, and the vision was clinically improved. Similar therapeutic approaches could be employed in Mendelian phenotypes caused by the dysfunction of the hundreds of other molecular transporters.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Madhur Shetty
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Ilse Kern
- Pediatric Nephrology and Metabolism Unit, Pediatric Subspecialties Service, Children's Hospital, Geneva University Hospitals, Geneva, Switzerland
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, University of Lausanne, Lausanne, Switzerland
| | - Omer Farooq
- Bahria University Medical and Dental College, Karachi, Pakistan
| | | | - Ariane Malcles
- Department of Ophthalmology, University Hospitals of Geneva, Geneva, Switzerland
| | - Mateusz Kecik
- Department of Ophthalmology, University Hospitals of Geneva, Geneva, Switzerland
| | - Carlo Rivolta
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University Hospital Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Waqar Muzaffar
- Armed Forces Institute of Ophthalmology, Rawalpindi, Pakistan
| | - Aziz Qurban
- Armed Forces Institute of Ophthalmology, Rawalpindi, Pakistan
| | - Liaqat Ali
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Yacine Aggoun
- Pediatric Cardiology, Geneva University Hospitals, Geneva, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - L Keith Henry
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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13
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Webb BD, Evans A, Naidich TP, M Bird L, Parikh S, Fernandez Garcia M, Henderson LB, Millan F, Si Y, Brennand KJ, Hung P, Rucker JC, Wheeler PG, Schadt EE. Haploinsufficiency of POU4F1 causes an ataxia syndrome with hypotonia and intention tremor. Hum Mutat 2021; 42:685-693. [PMID: 33783914 DOI: 10.1002/humu.24201] [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: 12/05/2020] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 11/06/2022]
Abstract
De novo, heterozygous, loss-of-function variants were identified in Pou domain, class 4, transcription factor 1 (POU4F1) via whole-exome sequencing in four independent probands presenting with ataxia, intention tremor, and hypotonia. POU4F1 is expressed in the developing nervous system, and mice homozygous for null alleles of Pou4f1 exhibit uncoordinated movements with newborns being unable to successfully right themselves to feed. Head magnetic resonance imaging of the four probands was reviewed and multiple abnormalities were noted, including significant cerebellar vermian atrophy and hypertrophic olivary degeneration in one proband. Transcriptional activation of the POU4F1 p.Gln306Arg protein was noted to be decreased when compared with wild type. These findings suggest that heterozygous, loss-of-function variants in POU4F1 are causative of a novel ataxia syndrome.
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Affiliation(s)
- Bryn D Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anthony Evans
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas P Naidich
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, Rady Children's Hospital, San Diego, California, USA
| | - Sumit Parikh
- Neurometabolism & Neurogenetics, Cleveland Clinic, Cleveland, Ohio, USA
| | - Meilin Fernandez Garcia
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Yue Si
- GeneDx, Gaithersburg, Maryland, USA
| | - Kristen J Brennand
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Peter Hung
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Janet C Rucker
- Department of Neurology, New York University Grossman School of Medicine, New York, New York, USA.,Department of Ophthalmology, New York University Grossman School of Medicine, New York, New York, USA
| | | | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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14
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The Utility of Whole Exome Sequencing in Diagnosing Pediatric Neurological Disorders. Balkan J Med Genet 2021; 23:17-24. [PMID: 33816068 PMCID: PMC8009565 DOI: 10.2478/bjmg-2020-0028] [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] [Indexed: 12/03/2022] Open
Abstract
Pediatric neurological disorders have a wide spectrum of clinical presentations and can be challenging to diagnose. Whole exome sequencing (WES) is increasingly becoming an integral diagnostic tool in medicine. It is cost-effective and has high diagnostic yield, especially in consanguineous populations. This study aims to review WES results and its value in diagnosing neurological disorders. A retrospective chart review was performed for WES results between the period of January 2018 to November 2019. Whole exome sequencing was requested for children with unexplained neurological signs and symptoms such as epilepsy, developmental delay, visual impairment, spasticity, hypotonia and magnetic resonance imaging (MRI) brain changes. It was conducted for children in a pediatric neurology clinic of a tertiary center at Jeddah, Saudi Arabia. Twenty-six children with undiagnosed neurological conditions were identified and underwent WES diagnosis. Nineteen patients (73.0%) of the cohort were diagnosed with pathogenic variants, likely pathogenic variants or variants of unknown significance (VUS). Consanguinity was positive in 18 families of the cohort (69.0%). Seven patients showed homozygous mutations. Five patients had heterozygous mutations. There were six patients with VUS and six patients had negative WES results. Whole exome sequencing showed a high diagnostic rate in this group of children with variable neurological disorders.
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15
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Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome. Biochem J 2021; 477:4085-4132. [PMID: 33151299 PMCID: PMC7657662 DOI: 10.1042/bcj20190767] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]
Abstract
Mitochondria produce the bulk of the energy used by almost all eukaryotic cells through oxidative phosphorylation (OXPHOS) which occurs on the four complexes of the respiratory chain and the F1–F0 ATPase. Mitochondrial diseases are a heterogenous group of conditions affecting OXPHOS, either directly through mutation of genes encoding subunits of OXPHOS complexes, or indirectly through mutations in genes encoding proteins supporting this process. These include proteins that promote assembly of the OXPHOS complexes, the post-translational modification of subunits, insertion of cofactors or indeed subunit synthesis. The latter is important for all 13 of the proteins encoded by human mitochondrial DNA, which are synthesised on mitochondrial ribosomes. Together the five OXPHOS complexes and the mitochondrial ribosome are comprised of more than 160 subunits and many more proteins support their biogenesis. Mutations in both nuclear and mitochondrial genes encoding these proteins have been reported to cause mitochondrial disease, many leading to defective complex assembly with the severity of the assembly defect reflecting the severity of the disease. This review aims to act as an interface between the clinical and basic research underpinning our knowledge of OXPHOS complex and ribosome assembly, and the dysfunction of this process in mitochondrial disease.
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16
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Masri A, Hamamy H. Cost Effectiveness of Whole Exome Sequencing for Children with Developmental Delay in a Developing Country: A Study from Jordan. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0040-1722265] [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]
Abstract
AbstractThis retrospective study aimed to determine the cost effectiveness of whole exome sequencing (WES) in the diagnosis of children with developmental delay in a developing country. In this study of 40 patients, the average cost of traditional investigations and indirect costs related to rehabilitation and medications per child were USD847 and 6,585 per year, respectively. With a current cost for WES of approximately USD1,200, we concluded that performing WES could be cost effective, even in countries with limited resources, as it provides the option for genetic counseling in affected families with an ultimate reduction of overall financial burden to both parents and health care system.
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Affiliation(s)
- Amira Masri
- Division of Child Neurology, Department of Pediatrics, Faculty of Medicine, The University of Jordan, Amman, Jordan
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
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17
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Rong T, Yao R, Deng Y, Lin Q, Wang G, Wang J, Jiang F, Jiang Y. Case Report: A Relatively Mild Phenotype Produced by Novel Mutations in the SEPSECS Gene. Front Pediatr 2021; 9:805575. [PMID: 35155316 PMCID: PMC8826681 DOI: 10.3389/fped.2021.805575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/20/2021] [Indexed: 12/05/2022] Open
Abstract
Mutations in the human O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase gene (SEPSECS) are associated with progressive cerebello-cerebral atrophy (PCCA), also known as pontocerebellar hypoplasia type 2D (PCH2D). Early-onset profound developmental delay, progressive microcephaly, and hypotonia that develops toward severe spasticity have been previously reported with SEPSECS mutations. Herein we report a case with severe global developmental delay, myogenic changes in the lower limbs, and insomnia, but without progressive microcephaly and brain atrophy during infancy and toddlerhood in a child harboring the SEPSECS missense variant c.194A>G (p. Asn65Ser) and a novel splicing mutation c.701+1G>A. With these findings we communicate the first Chinese SEPSECS mutant case, and our report indicates that SEPSECS mutations can give rise to a milder phenotype.
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Affiliation(s)
- Tingyu Rong
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China
| | - Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yujiao Deng
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China
| | - Qingmin Lin
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China
| | - Guanghai Wang
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Jiang
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China
| | - Yanrui Jiang
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China
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18
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Cytochrome c oxidase deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148335. [PMID: 33171185 DOI: 10.1016/j.bbabio.2020.148335] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022]
Abstract
Cytochrome c oxidase (COX) deficiency is characterized by a high degree of genetic and phenotypic heterogeneity, partly reflecting the extreme structural complexity, multiple post-translational modification, variable, tissue-specific composition, and the high number of and intricate connections among the assembly factors of this enzyme. In fact, decreased COX specific activity can manifest with different degrees of severity, affect the whole organism or specific tissues, and develop a wide spectrum of disease natural history, including disease onsets ranging from birth to late adulthood. More than 30 genes have been linked to COX deficiency, but the list is still incomplete and in fact constantly updated. We here discuss the current knowledge about COX in health and disease, focusing on genetic aetiology and link to clinical manifestations. In addition, information concerning either fundamental biological features of the enzymes or biochemical signatures of its defects have been provided by experimental in vivo models, including yeast, fly, mouse and fish, which expanded our knowledge on the functional features and the phenotypical consequences of different forms of COX deficiency.
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19
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Aref-Eshghi E, Kerkhof J, Carere DA, Volodarsky M, Bhai P, Colaiacovo S, Saleh M, Caudle M, Karp N, Prasad C, Balci T, Lin H, Campbell C, Siu VM, Sadikovic B. Clinical and technical assessment of MedExome vs. NGS panels in patients with suspected genetic disorders in Southwestern Ontario. J Hum Genet 2020; 66:451-464. [PMID: 33093641 DOI: 10.1038/s10038-020-00860-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/24/2020] [Accepted: 10/05/2020] [Indexed: 11/10/2022]
Abstract
The adaptation of a broad genomic sequencing approach in the clinical setting has been accompanied by considerations regarding the clinical utility, technical performance, and diagnostic yield compared to targeted genetic approaches. We have developed MedExome, an integrated framework for sequencing, variant calling (SNVs, Indels, and CNVs), and clinical assessment of ~4600 medically relevant genes. We compared the technical performance of MedExome with the whole-exome and targeted gene-panel sequencing, assessed the reasons for discordance, and evaluated the added clinical yield of MedExome in a cohort of unresolved subjects suspected of genetic disease. Our analysis showed that despite a higher average read depth in panels (3058 vs. 855), MedExome yielded full coverage of the enriched regions (>20X) and 99% variant concordance rate with panels. The discordance rate was associated with low-complexity regions, high-GC content, and low allele fractions, observed in both platforms. MedExome yielded full sensitivity in detecting clinically actionable variants, and the assessment of 138 patients with suspected genetic conditions resulted in 76 clinical reports (31 full [22.1%], 3 partial, and 42 uncertain/possible molecular diagnoses). MedExome sequencing has comparable performance in variant detection to gene panels. Added diagnostic yield justifies expanded implementation of broad genomic approaches in unresolved patients; however, cost-benefit and health systems impact warrants assessment.
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Affiliation(s)
- Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Deana Alexis Carere
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Michael Volodarsky
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Samantha Colaiacovo
- Medical Genetics Program of Southwestern Ontario, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Maha Saleh
- Medical Genetics Program of Southwestern Ontario, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Michelle Caudle
- Medical Genetics Program of Southwestern Ontario, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Natalya Karp
- Medical Genetics Program of Southwestern Ontario, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Chitra Prasad
- Medical Genetics Program of Southwestern Ontario, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Tugce Balci
- Medical Genetics Program of Southwestern Ontario, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Craig Campbell
- Department of Pediatric Neurology, Children's Hospital, London Health Science Centre, London, ON, Canada
| | - Victoria Mok Siu
- Medical Genetics Program of Southwestern Ontario, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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20
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The tip of the iceberg for diagnostic dilemmas: Performance of current diagnostics and future complementary screening approaches. Eur J Med Genet 2020; 63:104089. [PMID: 33069933 DOI: 10.1016/j.ejmg.2020.104089] [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: 08/08/2020] [Revised: 09/15/2020] [Accepted: 10/12/2020] [Indexed: 11/24/2022]
Abstract
Genetic testing is currently the leading edge of clinical care when it comes to diagnostics. However, many questions remain unanswered even when employing next-generation sequencing techniques due to our inability to decode genetic variations and our limited repertoire of available diagnoses. Accordingly, diagnostic yields for current genomic screenings are <50% and fail to provide the whole picture, leaving the remaining patients without a definitive diagnosis. Human phenotypic/disease expression is explained by alterations not only at the genome, but also at the transcriptome, proteome and metabolome levels. These "higher" complexity levels represent at wealth of information, and diagnostic screenings tests at these levels have been shown to significantly improve diagnostic yields in specific populations compared to conventional diagnostic workup or gold standards in use (7-30% increase in diagnostic yields, depending on the population, approach and gold standard being compared against). However, these are not yet routinely available to clinicians. Due to their dynamic and modifiable nature, tapping into data from different omics will improve our understanding of the pathophysiological bases underlying (many yet to characterize) human disorders. We herein review how alterations at these levels (e.g. post-transcriptional and post-translational) may be pathogenic, how such tests may be implemented and in which situations they are of significant utility.
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21
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Fan Y, Wang L, Sun Y, Xu T, Gong Z, Zhao Q, Qiu W, Liang L, Xiao B, Zhang H, Han L, Lin F, Xu R, Gu X, Yu Y. Diagnostic yield of additional exome sequencing after the detection of long continuous stretches of homozygosity (LCSH) in SNP arrays. J Hum Genet 2020; 66:409-417. [PMID: 33040084 DOI: 10.1038/s10038-020-00854-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 11/09/2022]
Abstract
Long continuous stretches of homozygosity (LCSH) are associated with risk of recessive disorders. Though LCSH can be detected by SNP microarrays, additional testing is necessary to clarify the clinical significance. This study is to assess the yield of additional exome sequencing (ES) after LCSH detection and inform the likelihood of eventual diagnosis. In 2226 patients referred to SNP microarrays, 35 patients met the criteria of indicative LCSH. These patients were recruited and went through additional ES. The diagnostic yield was analyzed, and the LCSH pattern was compared between eventually diagnosed cases and those undiagnosed. The results showed additional ES attained a diagnostic yield of 31.4% (11/35), but only one-third of the yield (11.4%, 4/35) was relevant to LCSH. In contrast, two-thirds of the diagnostic variants (20%, 7/35) were de novo or dominantly inherited, irrelevant to the original LCSH finding. No particular LCSH pattern, including the chromosomal coverage or LCSH size, was found to associate with the diagnostic outcome. We concluded that additional ES after LCSH detection could reveal diagnostic variants, but it is strongly recommended to consider all possible inheritance mode, as the diagnostic variants may be irrelevant to the original LCSH finding.
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Affiliation(s)
- Yanjie Fan
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China. .,Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China. .,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, 200092, China.
| | - Lili Wang
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yu Sun
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, 200092, China
| | - Ting Xu
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Zhuwen Gong
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Qianfeng Zhao
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Lili Liang
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Bing Xiao
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.,Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Fujun Lin
- Department of Nephrology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Rang Xu
- Scientific Research Center, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China. .,Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China. .,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, 200092, China.
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22
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Schoenmakers E, Chatterjee K. Human Disorders Affecting the Selenocysteine Incorporation Pathway Cause Systemic Selenoprotein Deficiency. Antioxid Redox Signal 2020; 33:481-497. [PMID: 32295391 PMCID: PMC7409586 DOI: 10.1089/ars.2020.8097] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Significance: Generalized selenoprotein deficiency has been associated with mutations in SECISBP2, SEPSECS, and TRU-TCA1-1, 3 factors that are crucial for incorporation of the amino acid selenocysteine (Sec) into at least 25 human selenoproteins. SECISBP2 and TRU-TCA1-1 defects are characterized by a multisystem phenotype due to deficiencies of antioxidant and tissue-specific selenoproteins, together with abnormal thyroid hormone levels reflecting impaired hormone metabolism by deiodinase selenoenzymes. SEPSECS mutations are associated with a predominantly neurological phenotype with progressive cerebello-cerebral atrophy. Recent Advances: The recent identification of individuals with defects in genes encoding components of the selenocysteine insertion pathway has delineated complex and multisystem disorders, reflecting a lack of selenoproteins in specific tissues, oxidative damage due to lack of oxidoreductase-active selenoproteins and other pathways whose nature is unclear. Critical Issues: Abnormal thyroid hormone metabolism in patients can be corrected by triiodothyronine (T3) treatment. No specific therapies for other phenotypes (muscular dystrophy, male infertility, hearing loss, neurodegeneration) exist as yet, but their severity often requires supportive medical intervention. Future Directions: These disorders provide unique insights into the role of selenoproteins in humans. The long-term consequences of reduced cellular antioxidant capacity remain unknown, and future surveillance of patients may reveal time-dependent phenotypes (e.g., neoplasia, aging) or consequences of deficiency of selenoproteins whose function remains to be elucidated. The role of antioxidant therapies requires evaluation. Antioxid. Redox Signal. 33, 481-497.
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Affiliation(s)
- Erik Schoenmakers
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, United Kingdom
| | - Krishna Chatterjee
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, United Kingdom
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23
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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: 4.0] [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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24
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Al-Kharusi K, Bruwer Z, Wessels TM. The experience of Preimplantation Genetic Testing (PGT) among Muslim couples in Oman in the Middle East. J Genet Couns 2020; 30:121-131. [PMID: 32578356 DOI: 10.1002/jgc4.1300] [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: 03/22/2019] [Revised: 07/11/2019] [Accepted: 05/05/2020] [Indexed: 11/06/2022]
Abstract
Preimplantation genetic testing (PGT) is an alternative reproductive technology integrated with in vitro fertilization (IVF). It is a well-established technique offering a reproductive option for families at a high risk of transmitting a genetic disorder, allowing them to avoid making a decision about termination of an affected pregnancy (TOP). In Arab communities and particularly in Oman, where TOP is not favored under the majority of implemented Muslim law, termination of pregnancy for fetal indications is not always possible. As these communities are in favor of consanguineous marriage, they are at increased risk of serious and lethal autosomal recessive conditions, and as a result, PGT is a feasible option as a TOP decision can be avoided. However, undergoing PGT is relatively new in the Arab Muslim countries and Omani patients have only recently had access to the service. This qualitative study utilized a phenomenological approach to explore the experience of Omani families who had selected to undergo PGT as a means of reducing the risk of having a child affected with a genetic disorder. Fourteen participants from eight families who underwent PGT were interviewed. Data collected were analyzed using thematic analysis. The research identified four main themes: Anxiously waiting 'Taraqub'; Unforeseen; Secrecy; and Me and My Partner. The findings of the research have provided insight into the PGT experiences of Omani families. Unique cultural and religious perspectives should be considered when counseling Omani Muslim couples.
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Affiliation(s)
- Khalsa Al-Kharusi
- Genetics and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Zandre Bruwer
- Genetics and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Tina-Marié Wessels
- Division of Human Genetics, Department of Pathology Faculty of Medicine, University of Cape Town, Cape Town, South Africa
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25
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Rexach J, Lee H, Martinez-Agosto JA, Németh AH, Fogel BL. Clinical application of next-generation sequencing to the practice of neurology. Lancet Neurol 2020; 18:492-503. [PMID: 30981321 DOI: 10.1016/s1474-4422(19)30033-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 01/05/2023]
Abstract
Next-generation sequencing technologies allow for rapid and inexpensive large-scale genomic analysis, creating unprecedented opportunities to integrate genomic data into the clinical diagnosis and management of neurological disorders. However, the scale and complexity of these data make them difficult to interpret and require the use of sophisticated bioinformatics applied to extensive datasets, including whole exome and genome sequences. Detailed analysis of genetic data has shown that accurate phenotype information is essential for correct interpretation of genetic variants and might necessitate re-evaluation of the patient in some cases. A multidisciplinary approach that incorporates bioinformatics, clinical evaluation, and human genetics can help to address these challenges. However, despite numerous studies that show the efficacy of next-generation sequencing in establishing molecular diagnoses, pathogenic mutations are generally identified in fewer than half of all patients with genetic neurological disorders, exposing considerable gaps in the understanding of the human genome and providing opportunities to focus research on improving the usefulness of genomics in clinical practice. Looking forward, the emergence of precision health in neurological care will increasingly apply genomic data analysis to pharmacogenetics, preventive medicine, and patient-targeted therapies.
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Affiliation(s)
- Jessica Rexach
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Clinical Neurogenomics Research Center, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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26
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Palombo F, Graziano C, Al Wardy N, Nouri N, Marconi C, Magini P, Severi G, La Morgia C, Cantalupo G, Cordelli DM, Gangarossa S, Al Kindi MN, Al Khabouri M, Salehi M, Giorgio E, Brusco A, Pisani F, Romeo G, Carelli V, Pippucci T, Seri M. Autozygosity-driven genetic diagnosis in consanguineous families from Italy and the Greater Middle East. Hum Genet 2020; 139:1429-1441. [PMID: 32488467 DOI: 10.1007/s00439-020-02187-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Autozygosity-driven exome analysis has been shown effective for identification of genes underlying recessive diseases especially in countries of the so-called Greater Middle East (GME), where high consanguinity unravels the phenotypic effects of recessive alleles and large family sizes facilitate homozygosity mapping. In Italy, as in most European countries, consanguinity is estimated low. Nonetheless, consanguineous Italian families are not uncommon in publications of genetic findings and are often key to new associations of genes with rare diseases. We collected 52 patients from 47 consanguineous families with suspected recessive diseases, 29 originated in GME countries and 18 of Italian descent. We performed autozygosity-driven exome analysis by detecting long runs of homozygosity (ROHs > 1.5 Mb) and by prioritizing candidate clinical variants within. We identified a pathogenic synonymous variant that had been previously missed in NARS2 and we increased an initial high diagnostic rate (47%) to 55% by matchmaking our candidate genes and including in the analysis shorter ROHs that may also happen to be autozygous. GME and Italian families contributed to diagnostic yield comparably. We found no significant difference either in the extension of the autozygous genome, or in the distribution of candidate clinical variants between GME and Italian families, while we showed that the average autozygous genome was larger and the mean number of candidate clinical variants was significantly higher (p = 0.003) in mutation-positive than in mutation-negative individuals, suggesting that these features influence the likelihood that the disease is autozygosity-related. We highlight the utility of autozygosity-driven genomic analysis also in countries and/or communities, where consanguinity is not widespread cultural tradition.
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Affiliation(s)
- Flavia Palombo
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy.,IRCCS Istituto Delle Scienze Neurologiche Di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Claudio Graziano
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Nadia Al Wardy
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Nayereh Nouri
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.,Craniofacial and Cleft Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Caterina Marconi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Giulia Severi
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Chiara La Morgia
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, UOC Clinica Neurologica, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Gaetano Cantalupo
- Child Neuropsychiatry, Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, University of Verona, Verona, Italy.,UOC Neuropsichiatria Infantile, DAI Materno-Infantile, AOUI Verona, Verona, Italy
| | - Duccio Maria Cordelli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.,Neuropsychiatry Sant'Orsola-Malpighi University Hospital of Bologna, Bologna, Italy
| | | | - Mohammed Nasser Al Kindi
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Mazin Al Khabouri
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Department of ENT, Al Nahdha Hospital, Ministry of Health, Muscat, Oman
| | - Mansoor Salehi
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Francesco Pisani
- Child Neuropsychiatry Unit, Department of Medicine & Surgery, University of Parma, Parma, Italy
| | - Giovanni Romeo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, UOC Clinica Neurologica, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Tommaso Pippucci
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy.
| | - Marco Seri
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy.,Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
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27
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Daneshjoo O, hosseini A, Garshasbi M, Pizzuti A. Evidence of involvement of a novel VUS variant in the CHKB gene to congenital muscular dystrophy affection. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Ansar M, Paracha SA, Serretti A, Sarwar MT, Khan J, Ranza E, Falconnet E, Iwaszkiewicz J, Shah SF, Qaisar AA, Santoni FA, Zoete V, Megarbane A, Ahmed J, Colombo R, Makrythanasis P, Antonarakis SE. Biallelic variants in FBXL3 cause intellectual disability, delayed motor development and short stature. Hum Mol Genet 2020; 28:972-979. [PMID: 30481285 DOI: 10.1093/hmg/ddy406] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 12/20/2022] Open
Abstract
FBXL3 (F-Box and Leucine Rich Repeat Protein 3) encodes a protein that contains an F-box and several tandem leucine-rich repeats (LRR) domains. FBXL3 is part of the SCF (Skp1-Cullin-F box protein) ubiquitin ligase complex that binds and leads to phosphorylation-dependent degradation of the central clock protein cryptochromes (CRY1 and CRY2) by the proteasome and its absence causes circadian phenotypes in mice and behavioral problems. No FBXL3-related phenotypes have been described in humans. By a combination of exome sequencing and homozygosity mapping, we analyzed two consanguineous families with intellectual disability and identified homozygous loss-of-function (LoF) variants in FBXL3. In the first family, from Pakistan, an FBXL3 frameshift variant [NM_012158.2:c.885delT:p.(Leu295Phefs*25)] was the onlysegregating variant in five affected individuals in two family loops (LOD score: 3.12). In the second family, from Lebanon, we identified a nonsense variant [NM_012158.2:c.445C>T:p.(Arg149*)]. In a third patient from Italy, a likely deleterious non-synonymous variant [NM_012158.2:c.1072T>C:p.(Cys358Arg)] was identified in homozygosity. Protein 3D modeling predicted that the Cys358Arg change influences the binding with CRY2 by destabilizing the structure of the FBXL3, suggesting that this variant is also likely to be LoF. The eight affected individuals from the three families presented with a similar phenotype that included intellectual disability, developmental delay, short stature and mild facial dysmorphism, mainly large nose with a bulbous tip. The phenotypic similarity and the segregation analysis suggest that FBXL3 biallelic, LoF variants link this gene with syndromic autosomal recessive developmental delay/intellectual disability.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Sohail Aziz Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Jamshed Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, Lausanne, Switzerland
| | - Sayyed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences, Kohat, Pakistan
| | | | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Department of Endocrinology Diabetes and Metabolism, University Hospital of Lausanne, Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, Lausanne, Switzerland.,Department of Fundamental Oncology, Lausanne University, Ludwig Institute for Cancer Research, Route de la Corniche 9A, Epalinges, Switzerland
| | | | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Roberto Colombo
- Institute of Clinical Biochemistry, Faculty of Medicine, Catholic University IRCCS Policlinico Gemelli, Rome, Italy.,Center for the Study of Rare Hereditary Diseases, Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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Paroxysmal tonic upgaze: A heterogeneous clinical condition responsive to carbonic anhydrase inhibition. Eur J Paediatr Neurol 2020; 25:181-186. [PMID: 31810576 DOI: 10.1016/j.ejpn.2019.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/15/2019] [Accepted: 11/09/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Paroxysmal tonic upgaze (PTU), defined as an involuntary upward movement of the eyes, has been considered as a benign phenomenon but may also be associated with ataxia and developmental delay. METHODS We report eight children with PTU; six of them also exhibiting symptoms of ataxia and/or developmental delay. Treatment with carbonic anhydrase inhibition was offered to children with persisting and/or severe forms. RESULTS Whole-exome sequencing and genome-wide array analysis (n = 7) did not reveal mutations in the three known genes associated with PTU (CACNA1A, GRID2, SEPSECS), whereas by MLPA a heterozygous deletion of exon 31 of the CACNA1A gene could be detected in one patient, her mother and two further family members. Further exome and array analysis showed no recurrent variants in potentially novel PTU-related genes in more than one patient. A de novo variant at a highly conserved position in the SIM1 gene was detected in one patient, for which a pathogenic effect could be speculated. Carbonic anhydrase inhibition was started in five children and proved at least partially effective in all of them. CONCLUSION Irrespective of the clinical background and the molecular basic mechanism of PTU, therapeutic carbonic anhydrase inhibition was effective in all five children (acetazolamide, n = 3; sultiame, n = 2) who received this treatment.
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Ansar M, Chung H, Waryah YM, Makrythanasis P, Falconnet E, Rao AR, Guipponi M, Narsani AK, Fingerhut R, Santoni FA, Ranza E, Waryah AM, Bellen HJ, Antonarakis SE. Visual impairment and progressive phthisis bulbi caused by recessive pathogenic variant in MARK3. Hum Mol Genet 2019; 27:2703-2711. [PMID: 29771303 DOI: 10.1093/hmg/ddy180] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/02/2018] [Accepted: 05/06/2018] [Indexed: 12/20/2022] Open
Abstract
Developmental eye defects often severely reduce vision. Despite extensive efforts, for a substantial fraction of these cases the molecular causes are unknown. Recessive eye disorders are frequent in consanguineous populations and such large families with multiple affected individuals provide an opportunity to identify recessive causative genes. We studied a Pakistani consanguineous family with three affected individuals with congenital vision loss and progressive eye degeneration. The family was analyzed by exome sequencing of one affected individual and genotyping of all family members. We have identified a non-synonymous homozygous variant (NM_001128918.2: c.1708C > G: p.Arg570Gly) in the MARK3 gene as the likely cause of the phenotype. Given that MARK3 is highly conserved in flies (I: 55%; S: 67%) we knocked down the MARK3 homologue, par-1, in the eye during development. This leads to a significant reduction in eye size, a severe loss of photoreceptors and loss of vision based on electroretinogram (ERG) recordings. Expression of the par-1 p.Arg792Gly mutation (equivalent to the MARK3 variant found in patients) in developing fly eyes also induces loss of eye tissue and reduces the ERG signals. The data in flies and human indicate that the MARK3 variant corresponds to a loss of function. We conclude that the identified mutation in MARK3 establishes a new gene-disease link, since it likely causes structural abnormalities during eye development and visual impairment in humans, and that the function of MARK3/par-1 is evolutionarily conserved in eye development.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Hyunglok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Yar M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ali Raza Rao
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Ashok K Narsani
- Institute of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ralph Fingerhut
- Swiss Newborn Screening Laboratory, University Children's Hospital, Zurich, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Ali M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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Ansar M, Chung HL, Al-Otaibi A, Elagabani MN, Ravenscroft TA, Paracha SA, Scholz R, Abdel Magid T, Sarwar MT, Shah SF, Qaisar AA, Makrythanasis P, Marcogliese PC, Kamsteeg EJ, Falconnet E, Ranza E, Santoni FA, Aldhalaan H, Al-Asmari A, Faqeih EA, Ahmed J, Kornau HC, Bellen HJ, Antonarakis SE. Bi-allelic Variants in IQSEC1 Cause Intellectual Disability, Developmental Delay, and Short Stature. Am J Hum Genet 2019; 105:907-920. [PMID: 31607425 DOI: 10.1016/j.ajhg.2019.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022] Open
Abstract
We report two consanguineous families with probands that exhibit intellectual disability, developmental delay, short stature, aphasia, and hypotonia in which homozygous non-synonymous variants were identified in IQSEC1 (GenBank: NM_001134382.3). In a Pakistani family, the IQSEC1 segregating variant is c.1028C>T (p.Thr343Met), while in a Saudi Arabian family the variant is c.962G>A (p.Arg321Gln). IQSEC1-3 encode guanine nucleotide exchange factors for the small GTPase ARF6 and their loss affects a variety of actin-dependent cellular processes, including AMPA receptor trafficking at synapses. The ortholog of IQSECs in the fly is schizo and its loss affects growth cone guidance at the midline in the CNS, also an actin-dependent process. Overexpression of the reference IQSEC1 cDNA in wild-type flies is lethal, but overexpression of the two variant IQSEC1 cDNAs did not affect viability. Loss of schizo caused embryonic lethality that could be rescued to 2nd instar larvae by moderate expression of the human reference cDNA. However, the p.Arg321Gln and p.Thr343Met variants failed to rescue embryonic lethality. These data indicate that the variants behave as loss-of-function mutations. We also show that schizo in photoreceptors is required for phototransduction. Finally, mice with a conditional Iqsec1 deletion in cortical neurons exhibited an increased density of dendritic spines with an immature morphology. The phenotypic similarity of the affecteds and the functional experiments in flies and mice indicate that IQSEC1 variants are the cause of a recessive disease with intellectual disability, developmental delay, and short stature, and that axonal guidance and dendritic projection defects as well as dendritic spine dysgenesis may underlie disease pathogenesis.
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Temtamy SA. The Development of Human Genetics at the National Research Centre, Cairo, Egypt: A Story of 50 Years. Annu Rev Genomics Hum Genet 2019; 20:1-19. [PMID: 30848958 DOI: 10.1146/annurev-genom-083118-015201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This article describes my experiences over more than 50 years in initiating and maintaining research on human genetics and genomics at the National Research Centre in Cairo, Egypt, from its beginnings in a small unit of human genetics to the creation of the Center of Excellence for Human Genetics. This was also the subject of a lecture I gave at the 10th Conference of the African Society of Human Genetics, held in Cairo in November 2017, after which Professor Michèle Ramsay, president of the society, suggested that I write an autobiographical article for the Annual Review of Genomics and Human Genetics. I hope that I succeeded in the difficult assignment of summarizing the efforts of a researcher from a developing country to initiate and maintain the rapidly advancing science of human genetics and genomics in my own country and make contributions to the worldwide scientific community.
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Affiliation(s)
- Samia A Temtamy
- Center of Excellence for Human Genetics, National Research Centre, Cairo 12622, Egypt;
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Nedelec B, Rozet JM, Fares Taie L. Genetic architecture of retinoic-acid signaling-associated ocular developmental defects. Hum Genet 2019; 138:937-955. [DOI: 10.1007/s00439-019-02052-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022]
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Ansar M, Ullah F, Paracha SA, Adams DJ, Lai A, Pais L, Iwaszkiewicz J, Millan F, Sarwar MT, Agha Z, Shah SF, Qaisar AA, Falconnet E, Zoete V, Ranza E, Makrythanasis P, Santoni FA, Ahmed J, Katsanis N, Walsh C, Davis EE, Antonarakis SE. Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features. Am J Hum Genet 2019; 104:1073-1087. [PMID: 31079899 PMCID: PMC6556908 DOI: 10.1016/j.ajhg.2019.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/01/2019] [Indexed: 12/30/2022] Open
Abstract
Cargo transport along the cytoplasmic microtubular network is essential for neuronal function, and cytoplasmic dynein-1 is an established molecular motor that is critical for neurogenesis and homeostasis. We performed whole-exome sequencing, homozygosity mapping, and chromosomal microarray studies in five individuals from three independent pedigrees and identified likely-pathogenic variants in DYNC1I2 (Dynein Cytoplasmic 1 Intermediate Chain 2), encoding a component of the cytoplasmic dynein 1 complex. In a consanguineous Pakistani family with three affected individuals presenting with microcephaly, severe intellectual disability, simplification of cerebral gyration, corpus callosum hypoplasia, and dysmorphic facial features, we identified a homozygous splice donor site variant (GenBank: NM_001378.2:c.607+1G>A). We report two additional individuals who have similar neurodevelopmental deficits and craniofacial features and harbor deleterious variants; one individual bears a c.740A>G (p.Tyr247Cys) change in trans with a 374 kb deletion encompassing DYNC1I2, and an unrelated individual harbors the compound-heterozygous variants c.868C>T (p.Gln290∗) and c.740A>G (p.Tyr247Cys). Zebrafish larvae subjected to CRISPR-Cas9 gene disruption or transient suppression of dync1i2a displayed significantly altered craniofacial patterning with concomitant reduction in head size. We monitored cell death and cell cycle progression in dync1i2a zebrafish models and observed significantly increased apoptosis, likely due to prolonged mitosis caused by abnormal spindle morphology, and this finding offers initial insights into the cellular basis of microcephaly. Additionally, complementation studies in zebrafish demonstrate that p.Tyr247Cys attenuates gene function, consistent with protein structural analysis. Our genetic and functional data indicate that DYNC1I2 dysfunction probably causes an autosomal-recessive microcephaly syndrome and highlight further the critical roles of the dynein-1 complex in neurodevelopment.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland
| | - Farid Ullah
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, 38000 Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, 45650 Islamabad, Pakistan
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Darius J Adams
- Atlantic Health System, Goryeb Children's Hospital, Morristown, NJ 07960, USA
| | - Abbe Lai
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Center for Life Sciences, Blackfan Circle, Boston, MA 02115, USA
| | - Lynn Pais
- Medical and Population Genetics Program, Broad Institute of MIT, Cambridge, MA 02142, USA; Center for Mendelian Genomics, Harvard University, Cambridge, MA 02142, USA
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, 1015 Lausanne, Switzerland
| | | | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Zehra Agha
- Department of Biosciences, COMSATS University, 45500 Islamabad, Pakistan
| | - Sayyed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences, 26000 Kohat, Pakistan
| | - Azhar Ali Qaisar
- Radiology Department, Lady Reading Hospital, 25000 Peshawar, Pakistan
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Batiment Genopode, Unil Sorge, 1015 Lausanne, Switzerland; Department of Fundamental Oncology, Lausanne University, Ludwig Institute for Cancer Research, Route de la Corniche 9A, 1066 Epalinges, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Department of Endocrinology Diabetes and Metabolism, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, 25100 Peshawar, Pakistan
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Christopher Walsh
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Center for Life Sciences, Blackfan Circle, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT, Cambridge, MA 02142, USA; Center for Mendelian Genomics, Harvard University, Cambridge, MA 02142, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland.
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Mu W, Schiess N, Orthmann-Murphy JL, El-Hattab AW. The utility of whole exome sequencing in diagnosing neurological disorders in adults from a highly consanguineous population. J Neurogenet 2019; 33:21-26. [PMID: 30724636 DOI: 10.1080/01677063.2018.1555249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is increasing evidence that whole exome sequencing (WES) has a high diagnostic yield and is cost-efficient for individuals with neurological phenotypes. However, there is limited data on the use of WES in non-Western populations, including populations with a high rate of consanguinity. Retrospective chart review was performed on 24 adults with undiagnosed neurological symptoms evaluated in genetics and neurology clinics in a tertiary care facility on the Arabian Peninsula, and had WES between 2014 and 2016. Definitive diagnoses were made in 13/24 (54%) of cases. Of these, 5/13 (38%) revealed novel pathogenic variants. Of the known 19/24 (79%) consanguineous cases, diagnostic rate was slightly higher, 11/19 (58%) as compared to 2/5 (40%) among non-consanguineous cases. Autosomal recessive disorders comprised 10/13 (77%) of molecular diagnoses, all found to be due to homozygous pathogenic variants among consanguineous cases. WES in this cohort of adults with neurological symptoms had a high diagnostic rate likely due to high consanguinity rates in this population, as evidenced by the high diagnostic rate of homozygous pathogenic variants.
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Affiliation(s)
- Weiyi Mu
- a Institute of Genetic Medicine , Johns Hopkins University , Baltimore , MD , USA
| | - Nicoline Schiess
- b Department of Neurology , Johns Hopkins University , Baltimore , MD , USA
| | - Jennifer L Orthmann-Murphy
- b Department of Neurology , Johns Hopkins University , Baltimore , MD , USA.,c Department of Neurology , Hospital of the University of Pennsylvania , Philadelphia , PA , USA
| | - Ayman W El-Hattab
- d Division of Clinical Genetics and Metabolic Disorder , Tawam Hospital , Al-Ain , United Arab Emirates
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Fradejas-Villar N. Consequences of mutations and inborn errors of selenoprotein biosynthesis and functions. Free Radic Biol Med 2018; 127:206-214. [PMID: 29709707 DOI: 10.1016/j.freeradbiomed.2018.04.572] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 12/23/2022]
Abstract
In its 200 years of history, selenium has been defined first as a toxic element and finally as a micronutrient. Selenium is incorporated into selenoproteins as selenocysteine (Sec), the 21st proteinogenic amino acid codified by a stop codon. Specific biosynthetic factors recode UGA stop codon as Sec. The significance of selenoproteins in human health is manifested through the identification of patients with inborn errors in selenoproteins or their biosynthetic factors. Selenoprotein N-related myopathy was the first disease identified due to mutations in a selenoprotein gene. Mutations in GPX4 were linked to Sedaghatian disease, characterized by bone and brain anomalies and cardiorespiratory failure. Mutations in TXNRD2 produced familial glucocorticoid deficiency (FGD) and dilated cardiomyopathy (DCM). Genetic generalized epilepsy was associated with mutations in TXNRD1 gene. Mutations in biosynthetic factors as SEPSECS, SECISBP2 and even tRNA[Ser]Sec, have been also related to diseases. Thus, SEPSECS mutations produce a neurodegenerative disease called now pontocerebellar hypoplasia type 2D (PCH2D). SECISBP2 syndrome, caused by SECISBP2 mutations, is a multifactorial disease affecting mainly thyroid metabolism, bone, inner ear and muscle. Similar symptoms were reproduced in a patient carrying a mutation in tRNA[Ser]Sec gene, TRU-TCA1-1. This review describes human genetic disorders caused by selenoprotein deficiency. Human phenotypes will be compared with mouse models to explain the pathologic mechanisms of lack of selenoproteins.
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Affiliation(s)
- Noelia Fradejas-Villar
- Institut für Biochemie und Molekularbiologie, Rheinischen Friedrich-Wilhelms-Universität, Nussallee 11, 53115 Bonn Germany.
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Kvarnung M, Taylan F, Nilsson D, Anderlid BM, Malmgren H, Lagerstedt-Robinson K, Holmberg E, Burstedt M, Nordenskjöld M, Nordgren A, Lundberg ES. Genomic screening in rare disorders: New mutations and phenotypes, highlighting ALG14 as a novel cause of severe intellectual disability. Clin Genet 2018; 94:528-537. [PMID: 30221345 DOI: 10.1111/cge.13448] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/04/2018] [Accepted: 09/11/2018] [Indexed: 01/20/2023]
Abstract
We have investigated 20 consanguineous families with multiple children affected by rare disorders. Detailed clinical examinations, exome sequencing of affected as well as unaffected family members and further validation of likely pathogenic variants were performed. In 16/20 families, we identified pathogenic variants in autosomal recessive disease genes (ALMS1, PIGT, FLVCR2, TFG, CYP7B1, ALG14, EXOSC3, MEGF10, ASAH1, WDR62, ASPM, PNPO, ERCC5, KIAA1109, RIPK4, MAN1B1). A number of these genes have only rarely been reported previously and our findings thus confirm them as disease genes, further delineate the associated phenotypes and expand the mutation spectrum with reports of novel variants. We highlight the findings in two affected siblings with splice altering variants in ALG14 and propose a new clinical entity, which includes severe intellectual disability, epilepsy, behavioral problems and mild dysmorphic features, caused by biallelic variants in ALG14.
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Affiliation(s)
- Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Holmberg
- Department of Medical Bioscience, Medical and Clinical Genetics, Umeå University, Umeå, Sweden
| | - Magnus Burstedt
- Department of Medical Bioscience, Medical and Clinical Genetics, Umeå University, Umeå, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabeth S Lundberg
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Bi-allelic Loss-of-Function Variants in DNMBP Cause Infantile Cataracts. Am J Hum Genet 2018; 103:568-578. [PMID: 30290152 DOI: 10.1016/j.ajhg.2018.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
Infantile and childhood-onset cataracts form a heterogeneous group of disorders; among the many genetic causes, numerous pathogenic variants in additional genes associated with autosomal-recessive infantile cataracts remain to be discovered. We identified three consanguineous families affected by bilateral infantile cataracts. Using exome sequencing, we found homozygous loss-of-function variants in DNMBP: nonsense variant c.811C>T (p.Arg271∗) in large family F385 (nine affected individuals; LOD score = 5.18 at θ = 0), frameshift deletion c.2947_2948del (p.Asp983∗) in family F372 (two affected individuals), and frameshift variant c.2852_2855del (p.Thr951Metfs∗41) in family F3 (one affected individual). The phenotypes of all affected individuals include infantile-onset cataracts. RNAi-mediated knockdown of the Drosophila ortholog still life (sif), enriched in lens-secreting cells, affects the development of these cells as well as the localization of E-cadherin, alters the distribution of septate junctions in adjacent cone cells, and leads to a ∼50% reduction in electroretinography amplitudes in young flies. DNMBP regulates the shape of tight junctions, which correspond to the septate junctions in invertebrates, as well as the assembly pattern of E-cadherin in human epithelial cells. E-cadherin has an important role in lens vesicle separation and lens epithelial cell survival in humans. We therefore conclude that DNMBP loss-of-function variants cause infantile-onset cataracts in humans.
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Fogel BL. Genetic and genomic testing for neurologic disease in clinical practice. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:11-22. [PMID: 29325607 DOI: 10.1016/b978-0-444-63233-3.00002-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The influence of genetics on neurologic disease is broad and it is becoming more common that clinicians are presented with a patient whose disease is likely of genetic origin. In the search for mutations causing Mendelian disorders, advances in genetic testing methodology have propelled modern neurologic practice beyond single-gene testing into the realm of genomic medicine, where routine evaluations encompass hundreds or thousands of genes, or even the entire exome, representing all protein-coding genes in the genome. The role of various single-gene, multigene, and genomic testing methods, including chromosomal microarray and next-generation sequencing, in the evaluation of neurologic disease is discussed here to provide a framework for their use in a modern neurologic practice. Understanding the inherent issues that arise during the interpretation of sequence variants as pathogenic or benign and the potential discovery of incidental medically relevant findings are important considerations for neurologists utilizing these tests clinically. Strategies for the evaluation of clinically heterogeneous disorders are presented to guide neurologists in the transition from single-gene to genomic considerations and toward the prospect of the widespread routine use of exome sequencing in the continuing goal to achieve more rapid and more precise diagnoses that will improve management and outcome in patients challenged by neurologic disease.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, United States.
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Mitochondrial DNA transcription and translation: clinical syndromes. Essays Biochem 2018; 62:321-340. [PMID: 29980628 PMCID: PMC6056718 DOI: 10.1042/ebc20170103] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/17/2018] [Accepted: 05/21/2018] [Indexed: 01/15/2023]
Abstract
Diagnosing primary mitochondrial diseases is challenging in clinical practice. Although, defective oxidative phosphorylation (OXPHOS) is the common final pathway, it is unknown why different mtDNA or nuclear mutations result in largely heterogeneous and often tissue -specific clinical presentations. Mitochondrial tRNA (mt-tRNA) mutations are frequent causes of mitochondrial diseases both in children and adults. However numerous nuclear mutations involved in mitochondrial protein synthesis affecting ubiquitously expressed genes have been reported in association with very tissue specific clinical manifestations suggesting that there are so far unknown factors determining the tissue specificity in mitochondrial translation. Most of these gene defects result in histological abnormalities and multiple respiratory chain defects in the affected organs. The clinical phenotypes are usually early-onset, severe, and often fatal, implying the importance of mitochondrial translation from birth. However, some rare, reversible infantile mitochondrial diseases are caused by very specific defects of mitochondrial translation. An unbiased genetic approach (whole exome sequencing, RNA sequencing) combined with proteomics and functional studies revealed novel factors involved in mitochondrial translation which contribute to the clinical manifestation and recovery in these rare reversible mitochondrial conditions.
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On elongation factor eEFSec, its role and mechanism during selenium incorporation into nascent selenoproteins. Biochim Biophys Acta Gen Subj 2018; 1862:2463-2472. [PMID: 29555379 DOI: 10.1016/j.bbagen.2018.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 02/02/2023]
Abstract
BACKGROUND Selenium, an essential dietary micronutrient, is incorporated into proteins as the amino acid selenocysteine (Sec) in response to in-frame UGA codons. Complex machinery ensures accurate recoding of Sec codons in higher organisms. A specialized elongation factor eEFSec is central to the process. SCOPE OF REVIEW Selenoprotein synthesis relies on selenocysteinyl-tRNASec (Sec-tRNASec), selenocysteine inserting sequence (SECIS) and other selenoprotein mRNA elements, an in-trans SECIS binding protein 2 (SBP2) protein factor, and eEFSec. The exact mechanisms of discrete steps of the Sec UGA recoding are not well understood. However, recent studies on mammalian model systems have revealed the first insights into these mechanisms. Herein, we summarize the current knowledge about the structure and role of mammalian eEFSec. MAJOR CONCLUSIONS eEFSec folds into a chalice-like structure resembling that of the archaeal and bacterial orthologues SelB and the initiation protein factor IF2/eIF5B. The three N-terminal domains harbor major functional sites and adopt an EF-Tu-like fold. The C-terminal domain 4 binds to Sec-tRNASec and SBP2, senses distinct binding domains, and modulates the GTPase activity. Remarkably, GTP hydrolysis does not induce a canonical conformational change in eEFSec, but instead promotes a slight ratchet of domains 1 and 2 and a lever-like movement of domain 4, which may be critical for the release of Sec-tRNASec on the ribosome. GENERAL SIGNIFICANCE Based on current findings, a non-canonical mechanism for elongation of selenoprotein synthesis at the Sec UGA codon is proposed. Although incomplete, our understanding of this fundamental biological process is significantly improved, and it is being harnessed for biomedical and synthetic biology initiatives. This article is part of a Special Issue entitled "Selenium research" in celebration of 200 years of selenium discovery, edited by Dr. Elias Arnér and Dr. Regina Brigelius-Flohe.
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Targeted next-generation sequencing analysis in couples at increased risk for autosomal recessive disorders. Orphanet J Rare Dis 2018; 13:23. [PMID: 29373990 PMCID: PMC5787287 DOI: 10.1186/s13023-018-0763-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Background Many of the genetic childhood disorders leading to death in the pre- or neonatal period or during early childhood follow autosomal recessive modes of inheritance and bear specific challenges for genetic counseling and prenatal diagnostics. Parents are carriers but clinically unaffected, and diseases are rare but have recurrence risks of 25% in the same family. Often, affected children (or fetuses) die before a genetic diagnosis can be established, post-mortem analysis and phenotypic descriptions are insufficient and DNA from affected fetuses or children is not available for later analysis. A genetic diagnosis showing biallelic causative mutations is, however, the requirement for targeted carrier testing in parents and prenatal and preimplantation genetic diagnosis in further pregnancies. Methods We undertook targeted next-generation sequencing (NGS) for carrier screening of autosomal recessive lethal disorders in 8 consanguineous and 5 non-consanguineous couples with one or more affected children. We searched for heterozygous variants (non-synonymous coding or splice variants) in parents’ DNA, using a set of 430 genes known to be causative for rare autosomal recessive diseases with poor prognosis, and then filtering for variants present in genes overlapping in both partners. Putative pathogenic variants were tested for cosegregation in affected fetuses or children where material was available. Results The diagnosis for the premature death in children was established in 5 of the 13 couples. Out of the 8 couples in which no causative diagnosis could be established 4 consented to undergo further analysis, in two of those a potentially causative variant in a novel candidate gene was identified. Conclusions For the families in whom causative variants could be identified, these may now be used for prenatal and preimplantation genetic diagnostics. Our data show that NGS based gene panel sequencing of selected genes involved in lethal autosomal recessive disorders is an effective tool for carrier screening in parents and for the identification of recessive gene defects and offers the possibility of prenatal and preimplantation genetic diagnosis in further pregnancies in families that have experienced deaths in early childhood and /or multiple abortions. Electronic supplementary material The online version of this article (10.1186/s13023-018-0763-0) contains supplementary material, which is available to authorized users.
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Biallelic variants in KIF14 cause intellectual disability with microcephaly. Eur J Hum Genet 2018; 26:330-339. [PMID: 29343805 PMCID: PMC5839044 DOI: 10.1038/s41431-017-0088-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/31/2017] [Accepted: 11/29/2017] [Indexed: 02/07/2023] Open
Abstract
Kinesin proteins are critical for various cellular functions such as intracellular transport and cell division, and many members of the family have been linked to monogenic disorders and cancer. We report eight individuals with intellectual disability and microcephaly from four unrelated families with parental consanguinity. In the affected individuals of each family, homozygosity for likely pathogenic variants in KIF14 were detected; two loss-of-function (p.Asn83Ilefs*3 and p.Ser1478fs), and two missense substitutions (p.Ser841Phe and p.Gly459Arg). KIF14 is a mitotic motor protein that is required for spindle localization of the mitotic citron rho-interacting kinase, CIT, also mutated in microcephaly. Our results demonstrate the involvement of KIF14 in development and reveal a wide phenotypic variability ranging from fetal lethality to moderate developmental delay and microcephaly.
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Abstract
The approach to identifying a genetic cause in patients with cerebellar disorders relies on history, examination, consultation, and testing, combined with specialized expertise because they are rare and genetically diverse. Cerebellar disorders can be caused by a variety of DNA alterations including single-nucleotide changes, small insertions or deletions, larger copy number variants, and nucleotide repeat expansions, exhibiting autosomal-recessive, autosomal-dominant (inherited and de novo), X-linked, and mitochondrial modes of inheritance. Imaging findings and a variety of neurologic and nonneurologic clinical features can help direct genetic testing and choose the most appropriate strategy. Clinical and genetic diagnoses are complementary, each providing distinct information for the care of the patient. In this chapter, we provide an overview of inheritance modes for different cerebellar disorders and the variety of genetic testing and tools that are currently available to reach a genetic diagnosis, including conventional and next-generation sequencing, classic, molecular and virtual cytogenetics, testing for repeat expansions, and other techniques. Practical examples are presented in both the text and accompanying vignettes.
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Affiliation(s)
- Enza Maria Valente
- Neurogenetics Unit, IRCCS Santa Lucia Foundation, Rome, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy.
| | - Sara Nuovo
- Neurogenetics Unit, IRCCS Santa Lucia Foundation, Rome, Italy; Department of Medicine and Surgery, University of Salerno, Salerno, Italy
| | - Dan Doherty
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, United States
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Ansar M, Riazuddin S, Sarwar MT, Makrythanasis P, Paracha SA, Iqbal Z, Khan J, Assir MZ, Hussain M, Razzaq A, Polla DL, Taj AS, Holmgren A, Batool N, Misceo D, Iwaszkiewicz J, de Brouwer APM, Guipponi M, Hanquinet S, Zoete V, Santoni FA, Frengen E, Ahmed J, Riazuddin S, van Bokhoven H, Antonarakis SE. Biallelic variants in LINGO1 are associated with autosomal recessive intellectual disability, microcephaly, speech and motor delay. Genet Med 2017; 20:778-784. [DOI: 10.1038/gim.2017.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/31/2017] [Indexed: 02/04/2023] Open
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Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017. [PMID: 28349240 DOI: 10.1007/s00439‐017‐1779‐6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD ( http://www.hgmd.org ) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.
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Affiliation(s)
- Peter D Stenson
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Hayden
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michelle Hussain
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 2017; 136:665-677. [PMID: 28349240 PMCID: PMC5429360 DOI: 10.1007/s00439-017-1779-6] [Citation(s) in RCA: 883] [Impact Index Per Article: 126.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.
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Affiliation(s)
- Peter D Stenson
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Hayden
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michelle Hussain
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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50
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Trujillano D, Bertoli-Avella AM, Kumar Kandaswamy K, Weiss ME, Köster J, Marais A, Paknia O, Schröder R, Garcia-Aznar JM, Werber M, Brandau O, Calvo Del Castillo M, Baldi C, Wessel K, Kishore S, Nahavandi N, Eyaid W, Al Rifai MT, Al-Rumayyan A, Al-Twaijri W, Alothaim A, Alhashem A, Al-Sannaa N, Al-Balwi M, Alfadhel M, Rolfs A, Abou Jamra R. Clinical exome sequencing: results from 2819 samples reflecting 1000 families. Eur J Hum Genet 2016; 25:176-182. [PMID: 27848944 PMCID: PMC5255946 DOI: 10.1038/ejhg.2016.146] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/07/2016] [Accepted: 09/23/2016] [Indexed: 02/01/2023] Open
Abstract
We report our results of 1000 diagnostic WES cases based on 2819 sequenced samples from 54 countries with a wide phenotypic spectrum. Clinical information given by the requesting physicians was translated to HPO terms. WES processes were performed according to standardized settings. We identified the underlying pathogenic or likely pathogenic variants in 307 families (30.7%). In further 253 families (25.3%) a variant of unknown significance, possibly explaining the clinical symptoms of the index patient was identified. WES enabled timely diagnosing of genetic diseases, validation of causality of specific genetic disorders of PTPN23, KCTD3, SCN3A, PPOX, FRMPD4, and SCN1B, and setting dual diagnoses by detecting two causative variants in distinct genes in the same patient. We observed a better diagnostic yield in consanguineous families, in severe and in syndromic phenotypes. Our results suggest that WES has a better yield in patients that present with several symptoms, rather than an isolated abnormality. We also validate the clinical benefit of WES as an effective diagnostic tool, particularly in nonspecific or heterogeneous phenotypes. We recommend WES as a first-line diagnostic in all cases without a clear differential diagnosis, to facilitate personal medical care.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wafaa Eyaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Muhammad Talal Al Rifai
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmed Al-Rumayyan
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Waleed Al-Twaijri
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ali Alothaim
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Department of pathology, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Division of Metabolic and Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Nouriya Al-Sannaa
- Division of Pediatrics, Johns Hopkins Aramco hospital, Dhahran Health Center, Saudi Aramco, Dhahran, Saudi Arabia
| | - Mohammed Al-Balwi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Arndt Rolfs
- Centogene AG, Rostock, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
| | - Rami Abou Jamra
- Centogene AG, Rostock, Germany.,Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
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