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Zhou B, Liang C, Li P, Xiao H. Revisiting X-linked congenital ichthyosis. Int J Dermatol 2024. [PMID: 39086014 DOI: 10.1111/ijd.17396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 07/01/2024] [Accepted: 07/06/2024] [Indexed: 08/02/2024]
Abstract
X-linked recessive ichthyosis (XLI) is a hereditary skin disease characterized by generalized dryness and scaling of the skin, with frequent extracutaneous manifestations. It is the second most common type of ichthyosis, with a prevalence of 1/6,000 to 1/2,000 in males and without any racial or geographical differences. The causative gene for XLI is the steroid sulfatase gene (STS), located on Xp22.3. STS deficiency causes an abnormal cholesterol sulfate (CS) accumulation in the stratum corneum (SC). Excess CS induces epidermal permeability barrier dysfunction and scaling abnormalities. This review summarizes XLI's genetic, clinical, and pathological features, pathogenesis, diagnosis and differential diagnoses, and therapeutic perspectives. Further understanding the role of the STS gene pathogenic variants in XLI may contribute to a more accurate and efficient clinical diagnosis of XLI and provide novel strategies for its treatment and prenatal diagnosis.
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Affiliation(s)
- Baishun Zhou
- Department of Pathology, School of Medicine, Hunan Normal University, Changsha, People's Republic of China
| | - Cancan Liang
- Department of Pathology, School of Medicine, Hunan Normal University, Changsha, People's Republic of China
| | - Peiyao Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, China NHC Key Laboratory of Carcinogenesis, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Heng Xiao
- Department of Pathology, School of Medicine, Hunan Normal University, Changsha, People's Republic of China
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2
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Oliver KL, Trivisano M, Mandelstam SA, De Dominicis A, Francis DI, Green TE, Muir AM, Chowdhary A, Hertzberg C, Goldhahn K, Metreau J, Prager C, Pinner J, Cardamone M, Myers KA, Leventer RJ, Lesca G, Bahlo M, Hildebrand MS, Mefford HC, Kaindl AM, Specchio N, Scheffer IE. WWOX developmental and epileptic encephalopathy: Understanding the epileptology and the mortality risk. Epilepsia 2023; 64:1351-1367. [PMID: 36779245 PMCID: PMC10952634 DOI: 10.1111/epi.17542] [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: 08/24/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
OBJECTIVE WWOX is an autosomal recessive cause of early infantile developmental and epileptic encephalopathy (WWOX-DEE), also known as WOREE (WWOX-related epileptic encephalopathy). We analyzed the epileptology and imaging features of WWOX-DEE, and investigated genotype-phenotype correlations, particularly with regard to survival. METHODS We studied 13 patients from 12 families with WWOX-DEE. Information regarding seizure semiology, comorbidities, facial dysmorphisms, and disease outcome were collected. Electroencephalographic (EEG) and brain magnetic resonance imaging (MRI) data were analyzed. Pathogenic WWOX variants from our cohort and the literature were coded as either null or missense, allowing individuals to be classified into one of three genotype classes: (1) null/null, (2) null/missense, (3) missense/missense. Differences in survival outcome were estimated using the Kaplan-Meier method. RESULTS All patients experienced multiple seizure types (median onset = 5 weeks, range = 1 day-10 months), the most frequent being focal (85%), epileptic spasms (77%), and tonic seizures (69%). Ictal EEG recordings in six of 13 patients showed tonic (n = 5), myoclonic (n = 2), epileptic spasms (n = 2), focal (n = 1), and migrating focal (n = 1) seizures. Interictal EEGs demonstrated slow background activity with multifocal discharges, predominantly over frontal or temporo-occipital regions. Eleven of 13 patients had a movement disorder, most frequently dystonia. Brain MRIs revealed severe frontotemporal, hippocampal, and optic atrophy, thin corpus callosum, and white matter signal abnormalities. Pathogenic variants were located throughout WWOX and comprised both missense and null changes including five copy number variants (four deletions, one duplication). Survival analyses showed that patients with two null variants are at higher mortality risk (p-value = .0085, log-rank test). SIGNIFICANCE Biallelic WWOX pathogenic variants cause an early infantile developmental and epileptic encephalopathy syndrome. The most common seizure types are focal seizures and epileptic spasms. Mortality risk is associated with mutation type; patients with biallelic null WWOX pathogenic variants have significantly lower survival probability compared to those carrying at least one presumed hypomorphic missense pathogenic variant.
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Affiliation(s)
- Karen L. Oliver
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
- Population Health and Immunity DivisionWalter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Marina Trivisano
- Rare and Complex Epilepsy Unit, Department of NeuroscienceBambino Gesù Children's Hospital IRCCS, full member of European Reference Network EpiCARERomeItaly
| | - Simone A. Mandelstam
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Florey Institute of Neuroscience and Mental HealthMelbourneVictoriaAustralia
- Department of Radiology, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Angela De Dominicis
- Rare and Complex Epilepsy Unit, Department of NeuroscienceBambino Gesù Children's Hospital IRCCS, full member of European Reference Network EpiCARERomeItaly
- Department of Biomedicine and PreventionUniversity of Rome “Tor Vergata”RomeItaly
| | - David I. Francis
- Victorian Clinical Genetics ServicesMurdoch Children's Research Institute, Royal Children's HospitalMelbourneVictoriaAustralia
| | - Timothy E. Green
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
| | - Alison M. Muir
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
| | - Apoorva Chowdhary
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
| | - Christoph Hertzberg
- Zentrum für Sozialpädiatrie und Neuropädiatrie (DBZ)Vivantes Hospital NeukoellnBerlinGermany
| | - Klaus Goldhahn
- Department of Pediatrics and Neuropediatrics, DRK Klinikum WestendBerlinGermany
| | - Julia Metreau
- Department of Pediatric NeurologyHôpital Bicêtre, Assistance Publique Hopitaux de ParisLe Kremlin‐BicêtreFrance
| | - Christine Prager
- Center for Chronically Sick Children (SPZ)Charité‐Universitätsmedizin BerlinBerlinGermany
- Department of Pediatric NeurologyCharité–Universitätsmedizin BerlinBerlinGermany
| | - Jason Pinner
- Sydney Children's HospitalRandwickNew South WalesAustralia
- School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Michael Cardamone
- Sydney Children's HospitalRandwickNew South WalesAustralia
- School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Kenneth A. Myers
- Division of Child Neurology, Department of PediatricsMcGill UniversityMontrealQuebecCanada
- Research Institute of the McGill University Health CentreMontrealQuebecCanada
- Department of Neurology and NeurosurgeryMontreal Children's Hospital, McGill UniversityMontrealQuebecCanada
| | - Richard J. Leventer
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of NeurologyRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University HospitalUniversité Claude Bernard Lyon 1, member of the European Reference Network EpiCARELyonFrance
| | - Melanie Bahlo
- Population Health and Immunity DivisionWalter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Michael S. Hildebrand
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Heather C. Mefford
- Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Center for Pediatric Neurological Disease ResearchSt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Angela M. Kaindl
- Center for Chronically Sick Children (SPZ)Charité‐Universitätsmedizin BerlinBerlinGermany
- Department of Pediatric NeurologyCharité–Universitätsmedizin BerlinBerlinGermany
- Institute of Cell Biology and NeurobiologyCharité–Universitätsmedizin BerlinBerlinGermany
| | - Nicola Specchio
- Rare and Complex Epilepsy Unit, Department of NeuroscienceBambino Gesù Children's Hospital IRCCS, full member of European Reference Network EpiCARERomeItaly
| | - Ingrid E. Scheffer
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Florey Institute of Neuroscience and Mental HealthMelbourneVictoriaAustralia
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3
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Roos D, van Leeuwen K, Madkaikar M, Kambli PM, Gupta M, Mathews V, Rawat A, Kuhns DB, Holland SM, de Boer M, Kanegane H, Parvaneh N, Lorenz M, Schwarz K, Klein C, Sherkat R, Jafari M, Wolach B, den Dunnen JT, Kuijpers TW, Köker MY. Hematologically important mutations: Leukocyte adhesion deficiency (second update). Blood Cells Mol Dis 2023; 99:102726. [PMID: 36696755 DOI: 10.1016/j.bcmd.2023.102726] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Leukocyte adhesion deficiency (LAD) is an immunodeficiency caused by defects in the adhesion of leukocytes (especially neutrophils) to the blood vessel wall. As a result, patients with LAD suffer from severe bacterial infections and impaired wound healing, accompanied by neutrophilia. In LAD-I, characterized directly after birth by delayed separation of the umbilical cord, mutations are found in ITGB2, the gene that encodes the β subunit (CD18) of the β2 integrins. In the rare LAD-II disease, the fucosylation of selectin ligands is disturbed, caused by mutations in SLC35C1, the gene that encodes a GDP-fucose transporter of the Golgi system. LAD-II patients lack the H and Lewis Lea and Leb blood group antigens. Finally, in LAD-III, the conformational activation of the hematopoietically expressed β integrins is disturbed, leading to leukocyte and platelet dysfunction. This last syndrome is caused by mutations in FERMT3, encoding the kindlin-3 protein in all blood cells, involved in the regulation of β integrin conformation. This article contains an update of the mutations that we consider to be relevant for the various forms of LAD.
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Affiliation(s)
- Dirk Roos
- Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Karin van Leeuwen
- Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Manisha Madkaikar
- Pediatric Immunology and Leukocyte Biology Lab CMR, National Institute of Immunohaematology, K E M Hospital, Parel, Mumbai, India
| | - Priyanka M Kambli
- Pediatric Immunology and Leukocyte Biology Lab CMR, National Institute of Immunohaematology, K E M Hospital, Parel, Mumbai, India
| | - Maya Gupta
- Pediatric Immunology and Leukocyte Biology Lab CMR, National Institute of Immunohaematology, K E M Hospital, Parel, Mumbai, India
| | - Vikram Mathews
- Dept of Hematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Amit Rawat
- Paediatric Allergy Immunology Unit, Department of Paediatrics, Advanced Paediatrics Centre, Chandigarh, India
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Martin de Boer
- Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Nima Parvaneh
- Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Myriam Lorenz
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany; Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg - Hessen, Ulm, Germany
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Roya Sherkat
- Immunodeficiency Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahbube Jafari
- Immunodeficiency Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Baruch Wolach
- Pediatric Immunology Service, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Johan T den Dunnen
- Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Taco W Kuijpers
- Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands; Emma Children's Hospital, Amsterdam University Medical Centre, location AMC, Amsterdam, the Netherlands
| | - M Yavuz Köker
- Department of Immunology, Erciyes Medical School, University of Erciyes, Kayseri, Türkiye
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Ozyavuz Cubuk P. Goldberg-Shprintzen Syndrome Associated with a Novel Variant in the KIFBP Gene. Mol Syndromol 2021; 12:240-243. [PMID: 34421502 DOI: 10.1159/000514531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 11/19/2022] Open
Abstract
Goldberg-Shprintzen syndrome (GOSHS) is characterized by microcephaly, developmental delay, dysmorphic features, Hirschsprung disease (HSCR), and brain anomalies. The kinesin family binding protein (KIFBP; MIM 60937) gene has been identified as the responsible gene of the syndrome. To date, 16 different biallelic KIFBP mutations have been identified in 34 patients with GOSHS. Even though most of these mutations are nonsense and frameshift, 3 missense mutations have also been described. Here, we report an 18-month-old patient with microcephaly, developmental delay, dysmorphic features and HSCR. Exome analysis was performed to clarify the etiology of the clinical features. A previously unreported homozygous c.1723delC (p.H575Ifs*19) variant was detected in the last exon 7 of KIFBP which led to GOSHS. According to our findings, we suggest that this mutation expands mutational databases and contributes to the understanding of the phenotypic features of the syndrome.
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Affiliation(s)
- Pelin Ozyavuz Cubuk
- Department of Medical Genetics, Haseki Training and Research Hospital, Health Sciences University, Istanbul, Turkey
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5
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MacKenzie KC, de Graaf BM, Syrimis A, Zhao Y, Brosens E, Mancini GMS, Schot R, Halley D, Wilke M, Vøllo A, Flinter F, Green A, Mansour S, Pilch J, Stark Z, Zamba-Papanicolaou E, Christophidou-Anastasiadou V, Hofstra RMW, Jongbloed JDH, Nicolaou N, Tanteles GA, Brooks AS, Alves MM. Goldberg-Shprintzen syndrome is determined by the absence, or reduced expression levels, of KIFBP. Hum Mutat 2020; 41:1906-1917. [PMID: 32939943 PMCID: PMC7693350 DOI: 10.1002/humu.24097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 03/12/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022]
Abstract
Goldberg-Shprintzen syndrome (GOSHS) is caused by loss of function variants in the kinesin binding protein gene (KIFBP). However, the phenotypic range of this syndrome is wide, indicating that other factors may play a role. To date, 37 patients with GOSHS have been reported. Here, we document nine new patients with variants in KIFBP: seven with nonsense variants and two with missense variants. To our knowledge, this is the first time that missense variants have been reported in GOSHS. We functionally investigated the effect of the variants identified, in an attempt to find a genotype-phenotype correlation. We also determined whether common Hirschsprung disease (HSCR)-associated single nucleotide polymorphisms (SNPs), could explain the presence of HSCR in GOSHS. Our results showed that the missense variants led to reduced expression of KIFBP, while the truncating variants resulted in lack of protein. However, no correlation was found between the severity of GOSHS and the location of the variants. We were also unable to find a correlation between common HSCR-associated SNPs, and HSCR development in GOSHS. In conclusion, we show that reduced, as well as lack of KIFBP expression can lead to GOSHS, and our results suggest that a threshold expression of KIFBP may modulate phenotypic variability of the disease.
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Affiliation(s)
- Katherine C MacKenzie
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Bianca M de Graaf
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Andreas Syrimis
- Department of Clinical Genetics, The Cyprus Institute of Neurology & Genetics and Archbishop Makarios III Medical Centre, Nicosia, Cyprus
| | - Yuying Zhao
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Dicky Halley
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Arve Vøllo
- Department of Paediatrics, Sykehuset Østfold HF, Fredrikstad, Norway
| | - Frances Flinter
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andrew Green
- Department of Clinical Genetics, Children's Hospital Ireland at Crumlin, Dublin, Ireland
| | - Sahar Mansour
- South West Thames Regional Genetic Service, St George's Hospital Medical School, London, UK
| | - Jacek Pilch
- Department of Child Neurology, Medical University of Silesia, Katowice, Poland
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | | | | | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Jan D H Jongbloed
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Nayia Nicolaou
- Department of Clinical Genetics, The Cyprus Institute of Neurology & Genetics and Archbishop Makarios III Medical Centre, Nicosia, Cyprus
| | - George A Tanteles
- Department of Clinical Genetics, The Cyprus Institute of Neurology & Genetics and Archbishop Makarios III Medical Centre, Nicosia, Cyprus
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Maria M Alves
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
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6
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Mirzaei Gisomi N, Javadi G, Zare Karizi S, Miryounesi M, Keshavarz P. Evaluation of beta-thalassemia in the fetus through cffDNA with multiple polymorphisms as a haplotype in the beta-globin gene. Transfus Clin Biol 2020; 27:243-252. [PMID: 32798758 DOI: 10.1016/j.tracli.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Invasive biopsy during the pregnancy is associated with an abortion risk of approximately 1% for the fetus. Free fetal DNA in maternal plasma is an excellent source of genetic material for prenatal molecular diagnoses. This study was conducted to investigate beta-thalassemia mutation in the fetus through maternal blood with multiple polymorphisms as haplotypes in the beta-globin gene. METHODS In this study, a total of 33 beta-thalassemia carrier (minor) couples were genotyped by ARMS-PCR for IVSII-IG>A mutation. During pregnancy, 10mL of blood was collected from pregnant women, and DNA was extracted by the magnetic bead-based extraction, and fetal DNA was enriched with AMPure XP kit. Five polymorphisms in 4 haplotype groups were evaluated by the Sanger Sequencing method. Finally, results were compared with those of the invasion method. RESULTS Participants in study were 33 couples, mean age of the men was 26±5 years, and mean age of women was 23±4 years, and mean MCV, MCH, HbA2 blood parameters were 62.4±5.3, 19.6±3.1, 4.2±2.1 respectively. A total of 33 fetuses were genotyped for IVSII-IG>A mutation. Nine fetuses were affected, 10 fetuses were normal and 14 fetuses were carrier of beta-thalassemia. Sensitivity and specificity of Sanger Sequencing were equal to 88.8% and 91.6% respectively. Positive and negative predictive values were obtained as 80% and 95.6%, respectively. CONCLUSION Mutational status of the fetus can be assessed by determining inheritance of paternally-derived alleles based on detection of haplotype-associated SNP in maternal plasma. Magnetic-based DNA extraction and fetal DNA enrichment are very simple and easy to perform and have satisfactory accuracy.
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Affiliation(s)
- Nadia Mirzaei Gisomi
- Department of biology, science and research branch, Islamic Azad university, Tehran, Iran
| | - Gholamreza Javadi
- Department of biology, science and research branch, Islamic Azad university, Tehran, Iran
| | - Shohre Zare Karizi
- Department of biology, faculty of biological sciences, Islamic Azad university, Varamin-Pishva Branch, Varamin, Iran
| | - Mohammad Miryounesi
- Department of medical genetics, Shahid Beheshti university of medical sciences, Tehran, Iran
| | - Parvaneh Keshavarz
- Cellular and molecular research center, faculty of medicine, Guilan university of medical sciences, Rasht, Iran; Medical genetics laboratory, Rasht, Iran.
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7
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Abdel-Hamid MS, Issa MY, Elbendary HM, Abdel-Ghafar SF, Rafaat K, Hosny H, Girgis M, Abdel-Salam GMH, Zaki MS. Phenotypic and mutational spectrum of thirty-five patients with Sjögren–Larsson syndrome: identification of eleven novel ALDH3A2 mutations and founder effects. J Hum Genet 2019; 64:859-865. [DOI: 10.1038/s10038-019-0637-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 04/21/2019] [Accepted: 06/17/2019] [Indexed: 01/06/2023]
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8
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La Cognata V, Morello G, Gentile G, Cavalcanti F, Cittadella R, Conforti FL, De Marco EV, Magariello A, Muglia M, Patitucci A, Spadafora P, D’Agata V, Ruggieri M, Cavallaro S. NeuroArray: A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders. Curr Genomics 2018; 19:431-443. [PMID: 30258275 PMCID: PMC6128384 DOI: 10.2174/1389202919666180404105451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases. METHODS In this report, we comprehensively describe the design method, the procedures, validation, and implementation of an exon-centric customized aCGH (NeuroArray 1.0), tailored to detect both single and multi-exon deletions or duplications in a large set of multi- and monogenic neurological diseases. This focused platform enables a targeted measurement of structural imbalances across the human genome, targeting the clinically relevant genes at exon-level resolution. CONCLUSION An increasing use of the NeuroArray platform may offer new insights in investigating potential overlapping gene signatures among neurological conditions and defining genotype-phenotype relationships.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sebastiano Cavallaro
- Address correspondence to this author at the Institute of Neurological Sciences, National Research Council, Via Paolo Gaifami 18, 95125, Catania, Italy; Tel: +39-095-7338111; E-mail:
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9
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Salpietro V, Manole A, Efthymiou S, Houlden H. A Review of Copy Number Variants in Inherited Neuropathies. Curr Genomics 2018; 19:412-419. [PMID: 30258273 PMCID: PMC6128387 DOI: 10.2174/1389202919666180330153316] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/23/2016] [Accepted: 03/13/2018] [Indexed: 11/22/2022] Open
Abstract
The rapid development in the last 10-15 years of microarray technologies, such as oligonucleotide array Comparative Genomic Hybridization (CGH) and Single Nucleotide Polymorphisms (SNP) genotyping array, has improved the identification of fine chromosomal structural variants, ranging in length from kilobases (kb) to megabases (Mb), as an important cause of genetic differences among healthy individuals and also as disease-susceptibility and/or disease-causing factors. Structural genomic variations due to unbalanced chromosomal rearrangements are known as Copy-Number Variants (CNVs) and these include variably sized deletions, duplications, triplications and translocations. CNVs can significantly contribute to human diseases and rearrangements in several dosage-sensitive genes have been identified as an important causative mechanism in the molecular aetiology of Charcot-Marie-Tooth (CMT) disease and of several CMT-related disorders, a group of inherited neuropathies with a broad range of clinical phenotypes, inheritance patterns and causative genes. Duplications or deletions of the dosage-sensitive gene PMP22 mapped to chromosome 17p12 represent the most frequent causes of CMT type 1A and Hereditary Neuropathy with liability to Pressure Palsies (HNPP), respectively. Additionally, CNVs have been identified in patients with other CMT types (e.g., CMT1X, CMT1B, CMT4D) and different hereditary poly- (e.g., giant axonal neuropathy) and focal- (e.g., hereditary neuralgic amyotrophy) neuropathies, supporting the notion of hereditary peripheral nerve diseases as possible genomic disorders and making crucial the identification of fine chromosomal rearrangements in the molecular assessment of such patients. Notably, the application of advanced computational tools in the analysis of Next-Generation Sequencing (NGS) data has emerged in recent years as a powerful technique for identifying a genome-wide scale complex structural variants (e.g., as the ones resulted from balanced rearrangements) and also smaller pathogenic (intragenic) CNVs that often remain beyond the detection limit of most conventional genomic microarray analyses; in the context of inherited neuropathies where more than 70 disease-causing genes have been identified to date, NGS and particularly Whole-Genome Sequencing (WGS) hold the potential to reduce the number of genomic assays required per patient to reach a diagnosis, analyzing with a single test all the Single Nucleotide Variants (SNVs) and CNVs in the genes possibly implicated in this heterogeneous group of disorders.
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Affiliation(s)
- Vincenzo Salpietro
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Andreea Manole
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London WC1N 3BG, UK
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10
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Diociaiuti A, Angioni A, Pisaneschi E, Alesi V, Zambruno G, Novelli A, El Hachem M. X-linked ichthyosis: Clinical and molecular findings in 35 Italian patients. Exp Dermatol 2018; 28:1156-1163. [PMID: 29672931 DOI: 10.1111/exd.13667] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2018] [Indexed: 11/29/2022]
Abstract
Recessive X-linked ichthyosis (XLI), the second most common ichthyosis, is caused by mutations in the STS gene encoding the steroid sulfatase enzyme. A complete deletion of the STS gene is found in 85%-90% of cases. Rarely, larger deletions involving contiguous genes are detected in syndromic patients. We report the clinical and molecular genetic findings in a series of 35 consecutive Italian male patients. All patients underwent molecular testing by MLPA or aCGH, followed, in case of negative results, by next-generation sequencing analysis. Neuropsychiatric, ophthalmological and paediatric evaluations were also performed. Our survey showed a frequent presence of disease manifestations at birth (42.8%). Fold and palmoplantar surfaces were involved in 18 (51%) and 7 (20%) patients, respectively. Fourteen patients (42%) presented neuropsychiatric symptoms, including attention-deficit hyperactivity disorder and motor disabilities. In addition, two patients with mental retardation were shown to be affected by a contiguous gene syndrome. Twenty-seven patients had a complete STS deletion, one a partial deletion and 7 carried missense mutations, two of which previously unreported. In addition, a de novo STS deletion was identified in a sporadic case. The frequent presence of palmoplantar and fold involvement in XLI should be taken into account when considering the differential diagnosis with ichthyosis vulgaris. Our findings also underline the relevance of involving the neuropsychiatrist in the multidisciplinary management of XLI. Finally, we report for the first time a de novo mutation which shows that STS deletion can also occur in oogenesis.
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Affiliation(s)
- Andrea Diociaiuti
- Dermatology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Adriano Angioni
- Molecular Genetics Laboratory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elisa Pisaneschi
- Molecular Genetics Laboratory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Viola Alesi
- Molecular Genetics Laboratory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Antonio Novelli
- Molecular Genetics Laboratory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - May El Hachem
- Dermatology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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11
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Zhou Z, Ma Y, Li Q, Zhang Y, Huang Y, Tu Z, Ma N, Li M, Wang J, Li J, Lu W. Massively parallel sequencing on human cleavage-stage embryos to detect chromosomal abnormality. Eur J Med Genet 2018; 61:34-42. [DOI: 10.1016/j.ejmg.2017.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 09/21/2017] [Accepted: 10/11/2017] [Indexed: 01/06/2023]
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12
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Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao HT, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang SHL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SW, Lupski JR, Patel A, Shaw CA, Stankiewicz P. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 2017; 9:83. [PMID: 28934986 PMCID: PMC5607840 DOI: 10.1186/s13073-017-0472-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. RESULTS In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses. CONCLUSIONS Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Amber N Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sailaja Golla
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lauren Dengle
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Reuben Matalon
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Lisa Emrick
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica B Proud
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Treadwell-Deering
- Department of Psychiatry and Behavioral Sciences, Child and Adolescent Psychiatry Division, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hannele Koillinen
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Chester Brown
- Genetics Division, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38105, USA.,Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | - Nora Urraca
- Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | | | | | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Patricia I Bader
- Northeast Indiana Genetic Counseling Center, Wayne, IN, 46804, USA
| | - Gary Bellus
- Section of Clinical Genetics & Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael Cummings
- Department of Psychiatry Erie County Medical Center, Buffalo, NY, 14215, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Myla Ashfaq
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | | | - Robert Wildin
- St. Luke's Children's Hospital, Boise, ID, 83702, USA.,The National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Anita E Beck
- Seattle Children's Hospital, Seattle, WA, 98105, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | | | - Lindsay Elton
- Child Neurology Consultants of Austin, Austin, TX, 78731, USA
| | - Shaun Varghese
- THINK Neurology for Kids/Children's Memorial Hermann Hospital, The Woodlands, TX, 77380, USA
| | - Edward Buchanan
- Division of Plastic Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Mathilde Lefebvre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sung-Hae L Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, 77021, USA.
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13
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Desai R, Frazier AE, Durigon R, Patel H, Jones AW, Dalla Rosa I, Lake NJ, Compton AG, Mountford HS, Tucker EJ, Mitchell ALR, Jackson D, Sesay A, Di Re M, van den Heuvel LP, Burke D, Francis D, Lunke S, McGillivray G, Mandelstam S, Mochel F, Keren B, Jardel C, Turner AM, Ian Andrews P, Smeitink J, Spelbrink JN, Heales SJ, Kohda M, Ohtake A, Murayama K, Okazaki Y, Lombès A, Holt IJ, Thorburn DR, Spinazzola A. ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism. Brain 2017; 140:1595-1610. [PMID: 28549128 PMCID: PMC5445257 DOI: 10.1093/brain/awx094] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/09/2017] [Indexed: 12/03/2022] Open
Abstract
Although mitochondrial disorders are clinically heterogeneous, they frequently involve the central nervous system and are among the most common neurogenetic disorders. Identifying the causal genes has benefited enormously from advances in high-throughput sequencing technologies; however, once the defect is known, researchers face the challenge of deciphering the underlying disease mechanism. Here we characterize large biallelic deletions in the region encoding the ATAD3C, ATAD3B and ATAD3A genes. Although high homology complicates genomic analysis of the ATAD3 defects, they can be identified by targeted analysis of standard single nucleotide polymorphism array and whole exome sequencing data. We report deletions that generate chimeric ATAD3B/ATAD3A fusion genes in individuals from four unrelated families with fatal congenital pontocerebellar hypoplasia, whereas a case with genomic rearrangements affecting the ATAD3C/ATAD3B genes on one allele and ATAD3B/ATAD3A genes on the other displays later-onset encephalopathy with cerebellar atrophy, ataxia and dystonia. Fibroblasts from affected individuals display mitochondrial DNA abnormalities, associated with multiple indicators of altered cholesterol metabolism. Moreover, drug-induced perturbations of cholesterol homeostasis cause mitochondrial DNA disorganization in control cells, while mitochondrial DNA aggregation in the genetic cholesterol trafficking disorder Niemann-Pick type C disease further corroborates the interdependence of mitochondrial DNA organization and cholesterol. These data demonstrate the integration of mitochondria in cellular cholesterol homeostasis, in which ATAD3 plays a critical role. The dual problem of perturbed cholesterol metabolism and mitochondrial dysfunction could be widespread in neurological and neurodegenerative diseases.
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Affiliation(s)
- Radha Desai
- MRC Laboratory, Mill Hill, London NW71AA, UK
| | - Ann E Frazier
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Romina Durigon
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aleck W Jones
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Ilaria Dalla Rosa
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Nicole J Lake
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Alison G Compton
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Hayley S Mountford
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Elena J Tucker
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Alice L R Mitchell
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Deborah Jackson
- Bioinformatics and Biostatistics, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Abdul Sesay
- Bioinformatics and Biostatistics, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Miriam Di Re
- Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 0XY, UK
| | - Lambert P van den Heuvel
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Derek Burke
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK and Laboratory Medicine, Great Ormond Street Hospital, London, UK
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia.,Department of Pathology, University of Melbourne, Melbourne 3052, Australia
| | - George McGillivray
- MRC Laboratory, Mill Hill, London NW71AA, UK.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia
| | - Simone Mandelstam
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia.,The Florey Institute of Neuroscience and Mental Health Melbourne, Australia.,Departments of Radiology and Paediatrics, University of Melbourne, Melbourne, Australia
| | - Fanny Mochel
- AP-HP, Department of Genetics, GHU Pitié-Salpêtrière, Paris, F-75651 France.,Inserm U975; CNRS UMR 7225, ICM; F-75013, Paris, France
| | - Boris Keren
- Inserm U975; CNRS UMR 7225, ICM; F-75013, Paris, France.,AP-HP, Service de Biochimie Métabolique et Centre de Génétique moléculaire et chromosomique, GHU Pitié-Salpêtrière, Paris, F-75651 France
| | - Claude Jardel
- AP-HP, Service de Biochimie Métabolique et Centre de Génétique moléculaire et chromosomique, GHU Pitié-Salpêtrière, Paris, F-75651 France.,Inserm U1016; CNRS UMR 8104; Université Paris-Descartes-Paris 5; Institut Cochin, 75014 Paris, France
| | - Anne M Turner
- Department of Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Kensington, NSW, Australia
| | - P Ian Andrews
- School of Women's and Children's Health, University of New South Wales, Kensington, NSW, Australia.,Department of Paediatric Neurology, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Jan Smeitink
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johannes N Spelbrink
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simon J Heales
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK and Laboratory Medicine, Great Ormond Street Hospital, London, UK.,Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, London, UK
| | - Masakazu Kohda
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Akira Ohtake
- Department of Pediatrics, Saitama Medical University, Moroyama-machi, Iruma-gun, Saitama, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Yasushi Okazaki
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan.,Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Anne Lombès
- MRC Laboratory, Mill Hill, London NW71AA, UK.,Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ian J Holt
- MRC Laboratory, Mill Hill, London NW71AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK.,Biodonostia Health Research Institute, 20014 San Sebastián, Spain. IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - David R Thorburn
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia
| | - Antonella Spinazzola
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
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14
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Walsh M, Bell KM, Chong B, Creed E, Brett GR, Pope K, Thorne NP, Sadedin S, Georgeson P, Phelan DG, Day T, Taylor JA, Sexton A, Lockhart PJ, Kiers L, Fahey M, Macciocca I, Gaff CL, Oshlack A, Yiu EM, James PA, Stark Z, Ryan MM. Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy. Ann Clin Transl Neurol 2017; 4:318-325. [PMID: 28491899 PMCID: PMC5420808 DOI: 10.1002/acn3.409] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/07/2017] [Accepted: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
Objective To explore the diagnostic utility and cost effectiveness of whole exome sequencing (WES) in a cohort of individuals with peripheral neuropathy. Methods Singleton WES was performed in individuals recruited though one pediatric and one adult tertiary center between February 2014 and December 2015. Initial analysis was restricted to a virtual panel of 55 genes associated with peripheral neuropathies. Patients with uninformative results underwent expanded analysis of the WES data. Data on the cost of prior investigations and assessments performed for diagnostic purposes in each patient was collected. Results Fifty patients with a peripheral neuropathy were recruited (median age 18 years; range 2–68 years). The median time from initial presentation to study enrollment was 6 years 9 months (range 2 months–62 years), and the average cost of prior investigations and assessments for diagnostic purposes AU$4013 per patient. Eleven individuals received a diagnosis from the virtual panel. Eight individuals received a diagnosis following expanded analysis of the WES data, increasing the overall diagnostic yield to 38%. Two additional individuals were diagnosed with pathogenic copy number variants through SNP microarray. Conclusions This study provides evidence that WES has a high diagnostic utility and is cost effective in patients with a peripheral neuropathy. Expanded analysis of WES data significantly improves the diagnostic yield in patients in whom a diagnosis is not found on the initial targeted analysis. This is primarily due to diagnosis of conditions caused by newly discovered genes and the resolution of complex and atypical phenotypes.
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Affiliation(s)
- Maie Walsh
- Murdoch Childrens Research Institute Melbourne Australia.,Royal Melbourne Hospital Melbourne Australia
| | - Katrina M Bell
- Murdoch Childrens Research Institute Melbourne Australia
| | - Belinda Chong
- Murdoch Childrens Research Institute Melbourne Australia
| | - Emma Creed
- Royal Melbourne Hospital Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Gemma R Brett
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Kate Pope
- Murdoch Childrens Research Institute Melbourne Australia
| | - Natalie P Thorne
- Melbourne Genomics Health Alliance Melbourne Australia.,Murdoch Childrens Research Institute Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Simon Sadedin
- Murdoch Childrens Research Institute Melbourne Australia
| | | | - Dean G Phelan
- Murdoch Childrens Research Institute Melbourne Australia
| | - Timothy Day
- Royal Melbourne Hospital Melbourne Australia
| | | | | | - Paul J Lockhart
- Murdoch Childrens Research Institute Melbourne Australia.,Bruce Lefroy Centre Murdoch Childrens Research Institute Parkville Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia
| | | | | | - Ivan Macciocca
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Clara L Gaff
- Melbourne Genomics Health Alliance Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Eppie M Yiu
- Bruce Lefroy Centre Murdoch Childrens Research Institute Parkville Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia.,Royal Children's Hospital Melbourne Australia
| | - Paul A James
- Royal Melbourne Hospital Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Zornitza Stark
- Murdoch Childrens Research Institute Melbourne Australia
| | - Monique M Ryan
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia.,Royal Children's Hospital Melbourne Australia
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15
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Wang B, Ji T, Zhou X, Wang J, Wang X, Wang J, Zhu D, Zhang X, Sham PC, Zhang X, Ma X, Jiang Y. CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens. Sci Rep 2016; 6:25954. [PMID: 27257017 PMCID: PMC4891738 DOI: 10.1038/srep25954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/06/2016] [Indexed: 12/28/2022] Open
Abstract
Rare copy number variations (CNVs) are a known genetic etiology in neurodevelopmental disorders (NDD). Comprehensive CNV analysis was performed in 287 Chinese children with mental retardation and/or development delay (MR/DD) and their unaffected parents. When compared with 5,866 ancestry-matched controls, 11~12% more MR/DD children carried rare and large CNVs. The increased CNV burden in MR/DD was predominantly due to de novo CNVs, the majority of which (62%) arose in the paternal germline. We observed a 2~3 fold increase of large CNV burden in the mothers of affected children. By implementing an evidence-based review approach, pathogenic structural variants were identified in 14.3% patients and 2.4% parents, respectively. Pathogenic CNVs in parents were all carried by mothers. The maternal transmission bias of deleterious CNVs was further replicated in a published dataset. Our study confirms the pathogenic role of rare CNVs in MR/DD, and provides additional evidence to evaluate the dosage sensitivity of some candidate genes. It also supports a population model of MR/DD that spontaneous mutations in males' germline are major contributor to the de novo mutational burden in offspring, with higher penetrance in male than female; unaffected carriers of causative mutations, mostly females, then contribute to the inherited mutational burden.
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Affiliation(s)
- Binbin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,National Research Institute of Family Planning, Beijing, China
| | - Taoyun Ji
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xueya Zhou
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China.,Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jing Wang
- Department of Medical Genetics, The Capital Medical University, Beijing, China
| | - Xi Wang
- National Research Institute of Family Planning, Beijing, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | | | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology at No.1 Hospital, Anhui Medical University, Heifei, Anhui, China
| | - Pak Chung Sham
- Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Xu Ma
- National Research Institute of Family Planning, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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16
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Rosenfeld JA, Patel A. Chromosomal Microarrays: Understanding Genetics of Neurodevelopmental Disorders and Congenital Anomalies. J Pediatr Genet 2016; 6:42-50. [PMID: 28180026 DOI: 10.1055/s-0036-1584306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/23/2016] [Indexed: 01/09/2023]
Abstract
Chromosomal microarray (CMA) testing, used to identify DNA copy number variations (CNVs), has helped advance knowledge about genetics of human neurodevelopmental disease and congenital anomalies. It has aided in discovering new CNV syndromes and uncovering disease genes. It has discovered CNVs that are not fully penetrant and/or cause a spectrum of phenotypes, including intellectual disability, autism, schizophrenia, and dysmorphisms. Such CNVs can pose challenges to genetic counseling. They also have helped increase knowledge of genetic risk factors for neurodevelopmental disease and raised awareness of possible shared etiologies among these variable phenotypes. Advances in CMA technology allow CNV identification at increasingly finer scales, improving detection of pathogenic changes, although these sometimes are difficult to distinguish from normal population variation. This paper confronts some of the challenges uncovered by CMA testing while reviewing advances in genetics and the clinical use of this test that has replaced standard karyotyping in most genetic evaluations.
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Affiliation(s)
- Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
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17
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Kondrashova O, Love CJ, Lunke S, Hsu AL, Waring PM, Taylor GR. High-Throughput Amplicon-Based Copy Number Detection of 11 Genes in Formalin-Fixed Paraffin-Embedded Ovarian Tumour Samples by MLPA-Seq. PLoS One 2015; 10:e0143006. [PMID: 26569395 PMCID: PMC4646639 DOI: 10.1371/journal.pone.0143006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
Whilst next generation sequencing can report point mutations in fixed tissue tumour samples reliably, the accurate determination of copy number is more challenging. The conventional Multiplex Ligation-dependent Probe Amplification (MLPA) assay is an effective tool for measurement of gene dosage, but is restricted to around 50 targets due to size resolution of the MLPA probes. By switching from a size-resolved format, to a sequence-resolved format we developed a scalable, high-throughput, quantitative assay. MLPA-seq is capable of detecting deletions, duplications, and amplifications in as little as 5ng of genomic DNA, including from formalin-fixed paraffin-embedded (FFPE) tumour samples. We show that this method can detect BRCA1, BRCA2, ERBB2 and CCNE1 copy number changes in DNA extracted from snap-frozen and FFPE tumour tissue, with 100% sensitivity and >99.5% specificity.
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Affiliation(s)
- Olga Kondrashova
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Clare J. Love
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Arthur L. Hsu
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Australian Ovarian Cancer Study (AOCS) Group
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Departments of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Paul M. Waring
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Graham R. Taylor
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
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18
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Abstract
Incidental findings are the subject of intense ethical debate in medical genomic research. Every human genome contains a number of potentially disease-causing alterations that may be detected during comprehensive genetic analyses to investigate a specific condition. Yet available evidence shows that the frequency of incidental findings in research is much lower than expected. In this Opinion, we argue that the reason for the low level of incidental findings is that the filtering techniques and methods that are applied during the routine handling of genomic data remove these alterations. As incidental findings are systematically filtered out, it is now time to evaluate whether the ethical debate is focused on the right issues. We conclude that the key question is whether to deliberately target and search for disease-causing variations outside the indication that has originally led to the genetic analysis, for instance by using positive lists and algorithms.
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19
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Chen JJ, Tan JAMA, Chua KH, Tan PC, George E. Non-invasive prenatal diagnosis using fetal DNA in maternal plasma: a preliminary study for identification of paternally-inherited alleles using single nucleotide polymorphisms. BMJ Open 2015; 5:e007648. [PMID: 26201722 PMCID: PMC4513519 DOI: 10.1136/bmjopen-2015-007648] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Single nucleotide polymorphism (SNP) with a mutation can be used to identify the presence of the paternally-inherited wild-type or mutant allele as result of the inheritance of either allele in the fetus and allows the prediction of the fetal genotype. This study aims to identify paternal SNPs located at the flanking regions upstream or downstream from the β-globin gene mutations at CD41/42 (HBB:c.127_130delCTTT), IVS1-5 (HBB:c.92+5G>C) and IVS2-654 (HBB:c.316-197C>T) using free-circulating fetal DNA. SETTING Haematology Lab, Department of Biomedical Science, University of Malaya. PARTICIPANTS Eight couples characterised as β-thalassaemia carriers where both partners posed the same β-globin gene mutations at CD41/42, IVS1-5 and IVS2-654, were recruited in this study. OUTCOME MEASURES Genotyping was performed by allele specific-PCR and the locations of SNPs were identified after sequencing alignment. RESULTS Genotype analysis revealed that at least one paternal SNP was present for each of the couples. Amplification on free-circulating DNA revealed that the paternal mutant allele of SNP was present in three fcDNA. Thus, the fetuses may be β-thalassaemia carriers or β-thalassaemia major. Paternal wild-type alleles of SNP were present in the remaining five fcDNA samples, thus indicating that the fetal genotypes would not be homozygous mutants. CONCLUSIONS This preliminary research demonstrates that paternal allele of SNP can be used as a non-invasive prenatal diagnosis approach for at-risk couples to determine the β-thalassaemia status of the fetus.
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Affiliation(s)
- J J Chen
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - J A M A Tan
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - K H Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - P C Tan
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - E George
- Assunta Hospital, Petaling Jaya, Selangor, Malaysia
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20
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Gaboon NEA, Jelani M, Almramhi MM, Mohamoud HSA, Al-Aama JY. Case of Sjögren-Larsson syndrome with a large deletion in the ALDH3A2 gene confirmed by single nucleotide polymorphism array analysis. J Dermatol 2015; 42:706-9. [PMID: 25855245 DOI: 10.1111/1346-8138.12861] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/16/2015] [Indexed: 11/27/2022]
Abstract
Sjögren-Larsson syndrome (SLS) is a neurocutaneous disorder inherited in an autosomal recessive fashion. SLS patients are characterized by lipid metabolism error, primarily leading to cardinal signs of ichthyosis, spasticity and mental retardation. Additional signs include short stature, epilepsy, retinal abnormalities and photophobia. More than 90 mutations of the ALDH3A2 gene have been reported for SLS, and such variants can be successfully detected at a rate of 94% by direct DNA sequencing. We performed direct sequencing of ALDH3A2 gene from the index patient, however, no mutation could be detected. HumanCytoSNPs12 array analysis and subsequent targeted single nucleotide polymorphism analysis revealed a novel deletion mutation at chromosome 17p11.2. This 67-Kb region includes the first five coding exons of ALDH3A2, and is flanked by rs2245639 and rs962801. To the best of our knowledge, this mutation is novel and our findings broaden the mutation spectrum of ALDH3A2 causing SLS phenotype.
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Affiliation(s)
- Nagwa E A Gaboon
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Genetic Center, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Musharraf Jelani
- Princess Al-Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Genetics and Molecular Biology Unit, Biochemistry Department, Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Mona M Almramhi
- Princess Al-Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hussein S A Mohamoud
- Princess Al-Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Human Genetics Research Centre, Division of Biomedical Sciences (BMS), St George's University of London, London, UK
| | - Jumana Y Al-Aama
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Princess Al-Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
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21
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Srebniak MI, Van Opstal D, Joosten M, Diderich KEM, de Vries FAT, Riedijk S, Knapen MFCM, Go ATJI, Govaerts LCP, Galjaard RJH. Whole-genome array as a first-line cytogenetic test in prenatal diagnosis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 45:363-372. [PMID: 25488734 DOI: 10.1002/uog.14745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Affiliation(s)
- M I Srebniak
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
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22
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Rothlin CV, Carrera-Silva EA, Bosurgi L, Ghosh S. TAM receptor signaling in immune homeostasis. Annu Rev Immunol 2015; 33:355-91. [PMID: 25594431 DOI: 10.1146/annurev-immunol-032414-112103] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The TAM receptor tyrosine kinases (RTKs)-TYRO3, AXL, and MERTK-together with their cognate agonists GAS6 and PROS1 play an essential role in the resolution of inflammation. Deficiencies in TAM signaling have been associated with chronic inflammatory and autoimmune diseases. Three processes regulated by TAM signaling may contribute, either independently or collectively, to immune homeostasis: the negative regulation of the innate immune response, the phagocytosis of apoptotic cells, and the restoration of vascular integrity. Recent studies have also revealed the function of TAMs in infectious diseases and cancer. Here, we review the important milestones in the discovery of these RTKs and their ligands and the studies that underscore the functional importance of this signaling pathway in physiological immune settings and disease.
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23
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D'Amours G, Langlois M, Mathonnet G, Fetni R, Nizard S, Srour M, Tihy F, Phillips MS, Michaud JL, Lemyre E. SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay. BMC Med Genomics 2014; 7:70. [PMID: 25539807 PMCID: PMC4299176 DOI: 10.1186/s12920-014-0070-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 12/11/2014] [Indexed: 11/28/2022] Open
Abstract
Background Molecular karyotyping is now the first-tier genetic test for patients affected with unexplained intellectual disability (ID) and/or multiple congenital anomalies (MCA), since it identifies a pathogenic copy number variation (CNV) in 10-14% of them. High-resolution microarrays combining molecular karyotyping and single nucleotide polymorphism (SNP) genotyping were recently introduced to the market. In addition to identifying CNVs, these platforms detect loss of heterozygosity (LOH), which can indicate the presence of a homozygous mutation or uniparental disomy. Since these abnormalities can be associated with ID and/or MCA, their detection is of particular interest for patients whose phenotype remains unexplained. However, the diagnostic yield obtained with these platforms is not confirmed, and the real clinical value of LOH detection has not been established. Methods We selected 21 children affected with ID, with or without congenital malformations, for whom standard genetic analyses failed to provide a diagnosis. We performed high-resolution SNP array analysis with four platforms (Affymetrix Genome-Wide Human SNP Array 6.0, Affymetrix Cytogenetics Whole-Genome 2.7 M array, Illumina HumanOmni1-Quad BeadChip, and Illumina HumanCytoSNP-12 DNA Analysis BeadChip) on whole-blood samples obtained from children and their parents to detect pathogenic CNVs and LOHs, and compared the results with those obtained on a moderate resolution array-based comparative genomic hybridization platform (NimbleGen CGX-12 Cytogenetics Array), already used in the clinical setting. Results We identified a total of four pathogenic CNVs in three patients, and all arrays successfully detected them. With the SNP arrays, we also identified a LOH containing a gene associated with a recessive disorder consistent with the patient’s phenotype (i.e., an informative LOH) in four children (including two siblings). A homozygous mutation within the informative LOH was found in three of these patients. Therefore, we were able to increase the diagnostic yield from 14.3% to 28.6% as a result of the information provided by LOHs. Conclusions This study shows the clinical usefulness of SNP arrays in children with ID, since they successfully detect pathogenic CNVs, identify informative LOHs that can lead to the diagnosis of a recessive disorder. It also highlights some challenges associated with the use of SNP arrays in a clinical laboratory. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0070-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guylaine D'Amours
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
| | - Mathieu Langlois
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | | | - Raouf Fetni
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Département de pathologie, CHU Sainte-Justine, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Sonia Nizard
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Myriam Srour
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada.
| | - Frédérique Tihy
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Michael S Phillips
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | - Jacques L Michaud
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Emmanuelle Lemyre
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
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24
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Utine GE, Haliloğlu G, Volkan-Salancı B, Çetinkaya A, Kiper PÖ, Alanay Y, Aktaş D, Anlar B, Topçu M, Boduroğlu K, Alikaşifoğlu M. Etiological yield of SNP microarrays in idiopathic intellectual disability. Eur J Paediatr Neurol 2014; 18:327-37. [PMID: 24508361 DOI: 10.1016/j.ejpn.2014.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 12/23/2013] [Accepted: 01/10/2014] [Indexed: 01/30/2023]
Abstract
Intellectual disability (ID) has a prevalence of 3% and is classified according to its severity. An underlying etiology cannot be determined in 75-80% in mild ID, and in 20-50% of severe ID. After it has been shown that copy number variations involving short DNA segments may cause ID, genome-wide SNP microarrays are being used as a tool for detecting submicroscopic copy number changes and uniparental disomy. This study was performed to investigate the presence of copy number changes in patients with ID of unidentified etiology. Affymetrix(®) 6.0 SNP microarray platform was used for analysis of 100 patients and their healthy parents, and data were evaluated using various databases and literature. Etiological diagnoses were made in 12 patients (12%). Homozygous deletion in NRXN1 gene and duplication in IL1RAPL1 gene were detected for the first time. Two separate patients had deletions in FOXP2 and UBE2A genes, respectively, for which only few patients have recently been reported. Interstitial and subtelomeric copy number changes were described in 6 patients, in whom routine cytogenetic tools revealed normal results. In one patient uniparental disomy type of Angelman syndrome was diagnosed. SNP microarrays constitute a screening test able to detect very small genomic changes, with a high etiological yield even in patients already evaluated using traditional cytogenetic tools, offer analysis for uniparental disomy and homozygosity, and thereby are helpful in finding novel disease-causing genes: for these reasons they should be considered as a first-tier genetic screening test in the evaluation of patients with ID and autism.
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Affiliation(s)
- G Eda Utine
- Hacettepe University, Department of Pediatrics, Ankara, Turkey; Hacettepe University, Department of Pediatric Genetics, Ankara, Turkey.
| | - Göknur Haliloğlu
- Hacettepe University, Department of Pediatrics, Ankara, Turkey; Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Bilge Volkan-Salancı
- Hacettepe University, Department of Pediatrics, Ankara, Turkey; Hacettepe University, Department of Pediatric Genetics, Ankara, Turkey
| | - Arda Çetinkaya
- Hacettepe University, Department of Pediatric Genetics, Ankara, Turkey; Hacettepe University, Department of Medical Genetics, Ankara, Turkey
| | - Pelin Ö Kiper
- Hacettepe University, Department of Pediatrics, Ankara, Turkey; Hacettepe University, Department of Pediatric Genetics, Ankara, Turkey
| | - Yasemin Alanay
- Hacettepe University, Department of Pediatrics, Ankara, Turkey; Hacettepe University, Department of Pediatric Genetics, Ankara, Turkey
| | - Dilek Aktaş
- Hacettepe University, Department of Pediatric Genetics, Ankara, Turkey; Hacettepe University, Department of Medical Genetics, Ankara, Turkey
| | - Banu Anlar
- Hacettepe University, Department of Pediatrics, Ankara, Turkey; Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Meral Topçu
- Hacettepe University, Department of Pediatrics, Ankara, Turkey; Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Koray Boduroğlu
- Hacettepe University, Department of Pediatrics, Ankara, Turkey; Hacettepe University, Department of Pediatric Genetics, Ankara, Turkey
| | - Mehmet Alikaşifoğlu
- Hacettepe University, Department of Pediatric Genetics, Ankara, Turkey; Hacettepe University, Department of Medical Genetics, Ankara, Turkey
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25
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Tucker EJ, Wanschers BFJ, Szklarczyk R, Mountford HS, Wijeyeratne XW, van den Brand MAM, Leenders AM, Rodenburg RJ, Reljić B, Compton AG, Frazier AE, Bruno DL, Christodoulou J, Endo H, Ryan MT, Nijtmans LG, Huynen MA, Thorburn DR. Mutations in the UQCC1-interacting protein, UQCC2, cause human complex III deficiency associated with perturbed cytochrome b protein expression. PLoS Genet 2013; 9:e1004034. [PMID: 24385928 PMCID: PMC3873243 DOI: 10.1371/journal.pgen.1004034] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/29/2013] [Indexed: 12/01/2022] Open
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) is responsible for generating the majority of cellular ATP. Complex III (ubiquinol-cytochrome c oxidoreductase) is the third of five OXPHOS complexes. Complex III assembly relies on the coordinated expression of the mitochondrial and nuclear genomes, with 10 subunits encoded by nuclear DNA and one by mitochondrial DNA (mtDNA). Complex III deficiency is a debilitating and often fatal disorder that can arise from mutations in complex III subunit genes or one of three known complex III assembly factors. The molecular cause for complex III deficiency in about half of cases, however, is unknown and there are likely many complex III assembly factors yet to be identified. Here, we used Massively Parallel Sequencing to identify a homozygous splicing mutation in the gene encoding Ubiquinol-Cytochrome c Reductase Complex Assembly Factor 2 (UQCC2) in a consanguineous Lebanese patient displaying complex III deficiency, severe intrauterine growth retardation, neonatal lactic acidosis and renal tubular dysfunction. We prove causality of the mutation via lentiviral correction studies in patient fibroblasts. Sequence-profile based orthology prediction shows UQCC2 is an ortholog of the Saccharomyces cerevisiae complex III assembly factor, Cbp6p, although its sequence has diverged substantially. Co-purification studies show that UQCC2 interacts with UQCC1, the predicted ortholog of the Cbp6p binding partner, Cbp3p. Fibroblasts from the patient with UQCC2 mutations have deficiency of UQCC1, while UQCC1-depleted cells have reduced levels of UQCC2 and complex III. We show that UQCC1 binds the newly synthesized mtDNA-encoded cytochrome b subunit of complex III and that UQCC2 patient fibroblasts have specific defects in the synthesis or stability of cytochrome b. This work reveals a new cause for complex III deficiency that can assist future patient diagnosis, and provides insight into human complex III assembly by establishing that UQCC1 and UQCC2 are complex III assembly factors participating in cytochrome b biogenesis. Mitochondrial complex III deficiency is a devastating disorder that impairs energy generation, and leads to variable symptoms such as developmental regression, seizures, kidney dysfunction and frequently death. The genetic basis of complex III deficiency is not fully understood, with around half of cases having no known cause. This lack of genetic diagnosis is partly due to an incomplete understanding of the genes required for complex III assembly and function. We have identified two key proteins required for complex III, UQCC1 and UQCC2, and have elucidated the role of these inter-dependent proteins in the biogenesis of cytochrome b, the only complex III subunit that is encoded by mitochondrial DNA. We have shown that mutations in UQCC2 cause human complex III deficiency in a patient with neonatal lactic acidosis and renal tubulopathy. This work contributes to an improved understanding of complex III biogenesis, and will aid future molecular diagnoses of complex III deficiency.
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Affiliation(s)
- Elena J. Tucker
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Bas F. J. Wanschers
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Radek Szklarczyk
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hayley S. Mountford
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Xiaonan W. Wijeyeratne
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Mariël A. M. van den Brand
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anne M. Leenders
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Richard J. Rodenburg
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Boris Reljić
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Alison G. Compton
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ann E. Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Damien L. Bruno
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - John Christodoulou
- Genetic Metabolic Disorders Research Unit, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Disciplines of Paediatrics & Child Health and Genetic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Hitoshi Endo
- Department of Biochemistry, Jichi Medical University, Tochigi, Japan
| | - Michael T. Ryan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- ARC Centre of Excellence for Coherent X-ray Science, La Trobe University, Melbourne, Australia
| | - Leo G. Nijtmans
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- * E-mail: (MAH); (DRT)
| | - David R. Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
- * E-mail: (MAH); (DRT)
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Lonardo F. Genomic microarrays in prenatal diagnosis. World J Med Genet 2013; 3:14-21. [DOI: 10.5496/wjmg.v3.i4.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/13/2013] [Accepted: 08/09/2013] [Indexed: 02/06/2023] Open
Abstract
The application of microarray-based techniques for the diagnosis of genomic rearrangements has been steadily growing in popularity since its introduction in 2004. Given the many advantages of these techniques over conventional cytogenetics, there is increasing pressure towards their application in prenatal diagnosis. However, there remain several important issues that must be addressed. For example, microarray-based techniques (comparative genomic hybridization-based arrays and single nucleotide polymorphism-based arrays) allow detection of even very small genomic imbalances that can determine pathological clinical conditions. In addition, there are other copy number variations which represent normal variation, with no detectable effects on phenotype. Given the still incomplete knowledge of the changes in our genome and the associated phenotypes, microarray-based diagnosis is likely to find variants of uncertain and unknown clinical significance. The interpretation of these variants is now a major challenge for the medical geneticist, who often find it difficult to establish precise correlations between genotype and phenotype. There is sufficient available evidence to justify the use of microarray-based diagnostics for a select number of specific conditions, but there is also an inevitable trend towards ever wider application. It is very important that this drift does not progress in an unchecked and uncontrolled manner under the thrust of commercial interests. Therefore, we recommend that scientific societies be vigilant and take an advisory role in the adopting of these technologies as new scientific knowledge becomes available.
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Stutterd C, Savoia H, Fink AM, Stark Z. Severe fetal ischaemic brain injury caused by homozygous protein C deficiency. Prenat Diagn 2013; 34:192-4. [DOI: 10.1002/pd.4251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/22/2013] [Accepted: 09/29/2013] [Indexed: 11/07/2022]
Affiliation(s)
- C. Stutterd
- Victorian Clinical Genetics Service; Murdoch Childrens Research Institute; Parkville Victoria Australia
| | - H. Savoia
- Department of Haematology; Royal Women's Hospital; Parkville Victoria Australia
| | - A. M. Fink
- Department of Radiology; University of Melbourne; Parkville Victoria Australia
- Medical Imaging Department; Royal Children's Hospital; Parkville Victoria Australia
| | - Z. Stark
- Victorian Clinical Genetics Service; Murdoch Childrens Research Institute; Parkville Victoria Australia
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Homozygous truncating mutation of the KBP gene, encoding a KIF1B-binding protein, in a familial case of fetal polymicrogyria. Neurogenetics 2013; 14:215-24. [DOI: 10.1007/s10048-013-0373-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/28/2013] [Indexed: 01/12/2023]
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29
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Howell KB, Kornberg AJ, Harvey AS, Ryan MM, Mackay MT, Freeman JL, Rodriguez Casero MV, Collins KJ, Hayman M, Mohamed A, Ware TL, Clark D, Bruno DL, Burgess T, Slater H, McGillivray G, Leventer RJ. High resolution chromosomal microarray in undiagnosed neurological disorders. J Paediatr Child Health 2013; 49:716-24. [PMID: 23731025 DOI: 10.1111/jpc.12256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2013] [Indexed: 12/17/2022]
Abstract
AIM Despite advances in medical investigation, many children with neurological conditions remain without a diagnosis, although a genetic aetiology is often suspected. Chromosomal microarray (CMA) screens for copy number variants (CNVs) and long continuous stretches of homozygosity (LCSH) and may further enhance diagnostic yield. Although recent studies have identified pathogenic CNVs in intellectual disability, autism and epilepsy, the utility of CMA testing in a broader cohort of children with neurologic disorders has not been reported. METHODS Two hundred fifteen patients with neurological conditions of unknown aetiology were seen over a 6-month period and were prospectively tested by CMA using high-resolution single nucleotide polymorphism (SNP) microarrays (Illumina HumanCytoSNP-12 v2.1 or Affymetrix 2.7M). RESULTS Thirty of 215 (14%) patients tested had an abnormal CMA. Twenty-nine had CNVs (13%) and one (0.5%) a clinically significant stretch of homozygosity. Twenty (9.3%) had a CMA finding considered to be pathogenic or involved in susceptibility to the condition of interest, and 10 (4.7%) had findings of unknown significance. Their phenotypes included infantile spasms and other epilepsies, neuromuscular conditions, ataxia, movement disorders, microcephaly and malformations of cortical development. At least one third of patients did not meet national funding criteria for CMA at the time of presentation. CONCLUSIONS CMA detected clinically significant abnormalities in a broad range of neurologic phenotypes of unknown aetiology. This test should be considered a first-tier investigation of children with neurologic disorders in whom the initial clinical assessment does not indicate a likely aetiology, especially those with severe epilepsies and neurologically abnormal neonates.
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Affiliation(s)
- Katherine B Howell
- Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia
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Alsolami R, Knight SJL, Schuh A. Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia? Per Med 2013; 10:361-376. [PMID: 24611071 PMCID: PMC3943176 DOI: 10.2217/pme.13.33] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is low-grade lymphoma of mature B cells and it is considered to be the most common type of hematological malignancy in the western world. CLL is characterized by a chronically relapsing course and clinical and biological heterogeneity. Many patients do not require any treatment for years. Although important progress has been made in the treatment of CLL, none of the conventional treatment options are curative. Recurrent chromosomal abnormalities have been identified and are associated with prognosis and pathogenesis of the disease. More recently, unbiased genome-wide technologies have identified multiple additional recurrent aberrations. The precise predictive value of these has not been established, but it is likely that the genetic heterogeneity observed at least partly reflects the clinical variability. The present article reviews our current knowledge of predictive markers in CLL using whole-genome technologies.
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Affiliation(s)
- Reem Alsolami
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- King Abdulaziz University, Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia
| | - Samantha JL Knight
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anna Schuh
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
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31
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Secondary variants--in defense of a more fitting term in the incidental findings debate. Eur J Hum Genet 2013; 21:1331-4. [PMID: 23695288 DOI: 10.1038/ejhg.2013.89] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/04/2013] [Accepted: 04/02/2013] [Indexed: 11/08/2022] Open
Abstract
New genetic technologies are capable of returning far more information than the single answer to the single question posed when conducting a given genetic test. Genetics contexts consequently stand on the brink of an explosion of what have traditionally been called 'incidental findings'. However, the continued use of this term is controversial. Various replacements for 'incidental findings' have been attempted, but none with widespread success. Agreement on terminology and definitions is vital so that the legal and ethical debate around incidental findings can proceed. We highlight the difficulties raised by the various terms currently used as alternatives, and end by defending our choice for the term 'secondary variants'.
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Ganesamoorthy D, Bruno DL, McGillivray G, Norris F, White SM, Adroub S, Amor DJ, Yeung A, Oertel R, Pertile MD, Ngo C, Arvaj AR, Walker S, Charan P, Palma-Dias R, Woodrow N, Slater HR. Meeting the challenge of interpreting high-resolution single nucleotide polymorphism array data in prenatal diagnosis: does increased diagnostic power outweigh the dilemma of rare variants? BJOG 2013; 120:594-606. [PMID: 23332022 DOI: 10.1111/1471-0528.12150] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2012] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Several studies have already shown the superiority of chromosomal microarray analysis (CMA) compared with conventional karyotyping for prenatal investigation of fetal ultrasound abnormality. This study used very high-resolution single nucleotide polymorphism (SNP) arrays to determine the impact on detection rates of all clinical categories of copy number variations (CNVs), and address the issue of interpreting and communicating findings of uncertain or unknown clinical significance, which are to be expected at higher frequency when using very high-resolution CMA. DESIGN Prospective validation study. SETTING Tertiary clinical genetics centre. POPULATION Women referred for further investigation of fetal ultrasound anomaly. METHODS We prospectively tested 104 prenatal samples using both conventional karyotyping and high-resolution arrays. MAIN OUTCOME MEASURES The detection rates for each clinical category of CNV. RESULTS Unequivocal pathogenic CNVs were found in six cases, including one with uniparental disomy (paternal UPD 14). A further four cases had a 'likely pathogenic' finding. Overall, CMA improved the detection of 'pathogenic' and 'likely pathogenic' abnormalities from 2.9% (3/104) to 9.6% (10/104). CNVs of 'unknown' clinical significance that presented interpretational difficulties beyond results from parental investigations were detected in 6.7% (7/104) of samples. CONCLUSIONS Increased detection sensitivity appears to be the main benefit of high-resolution CMA. Despite this, in this cohort there was no significant benefit in terms of improving detection of small pathogenic CNVs. A potential disadvantage is the high detection rate of CNVs of 'unknown' clinical significance. These findings emphasise the importance of establishing an evidence-based policy for the interpretation and reporting of CNVs, and the need to provide appropriate pre- and post-test counselling.
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Affiliation(s)
- D Ganesamoorthy
- VCGS Cytogenetics Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
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Verhagen JM, Huijmans JG, Williams M, van Ruyven RL, Bergen AA, Wouters CH, Brooks AS. Incidental finding of alpha-methylacyl-CoA racemase deficiency in a patient with oculocutaneous albinism type 4. Am J Med Genet A 2012; 158A:2931-4. [DOI: 10.1002/ajmg.a.35611] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/17/2012] [Indexed: 11/09/2022]
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McGillivray G, Rosenfeld JA, McKinlay Gardner RJ, Gillam LH. Genetic counselling and ethical issues with chromosome microarray analysis in prenatal testing. Prenat Diagn 2012; 32:389-95. [PMID: 22467169 DOI: 10.1002/pd.3849] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Molecular karyotyping using chromosome microarray analysis (CMA) detects more pathogenic chromosomal anomalies than classical karyotyping, making CMA likely to become a first tier test for prenatal diagnosis. Detecting copy number variants of uncertain clinical significance raises ethical considerations. We consider the risk of harm to a woman or her fetus following the detection of a copy number variant of uncertain significance, whether it is ethically justifiable to withhold any test result information from a woman, what constitutes an 'informed choice' when women are offered CMA in pregnancy and whether clinicians are morally responsible for 'unnecessary' termination of pregnancy. Although we are cognisant of the distress associated with uncertain prenatal results, we argue in favour of the autonomy of women and their right to information from genome-wide CMA in order to make informed choices about their pregnancies. We propose that information material to a woman's decision-making process, including uncertain information, should not be withheld, and that it would be paternalistic for clinicians to try to take responsibility for women's decisions to terminate pregnancies. Non-directive pre-test and post-test genetic counselling is central to the delivery of these ethical objectives.
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Affiliation(s)
- George McGillivray
- Royal Women's Hospital, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia.
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Calvo SE, Compton AG, Hershman SG, Lim SC, Lieber DS, Tucker EJ, Laskowski A, Garone C, Liu S, Jaffe DB, Christodoulou J, Fletcher JM, Bruno DL, Goldblatt J, Dimauro S, Thorburn DR, Mootha VK. Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med 2012; 4:118ra10. [PMID: 22277967 DOI: 10.1126/scitranslmed.3003310] [Citation(s) in RCA: 338] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. Although in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic use, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with more than 100 causal genes identified to date. We performed "MitoExome" sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Because patients and healthy control individuals harbored a comparable number of such heterozygous alleles, we could not prioritize dominant-acting genes. However, patients showed a fivefold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23 of 42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. Thirteen patients (31%) had mutations in nuclear genes not previously linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by complementation studies and evidence from multiple patients, respectively. The results underscore the potential and challenges of deploying NGS in clinical settings.
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Affiliation(s)
- Sarah E Calvo
- Center for Human Genetic Research and Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Sixth Floor, Boston, MA 02114, USA
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Abstract
Zusammenfassung
Die molekulare Karyotypisierung durch Array-CGH („comparative genomic hybridization“) und SNP-Arrays (SNP: „single nucleotide polymorphism“) ermöglicht die hochauflösende Untersuchung des gesamten Genoms, um so Gewinne und/oder Verluste (Kopienzahlvarianten, „copy number variants“, CNVs) zu detektieren, die die Ursache einer genetischen Erkrankung sein können. Diese Technik wird in erster Linie zur Ursachenklärung bei syndromalen und nichtsyndromalen (geistigen) Entwicklungsstörungen und zur genetischen Charakterisierung von Tumoren eingesetzt. Auch in der pränatalen Diagnostik könnte die molekulare Karyotypisierung bei auffälligem sonographischem Befund zur Klärung der Ursachen hilfreich sein. Der Artikel gibt eine kurze Übersicht über die grundlegenden Methoden, deren Grenzen und Stärken sowie einen Ausblick in die Zukunft.
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Filges I, Suda L, Weber P, Datta AN, Fischer D, Dill P, Glanzmann R, Benzing J, Hegi L, Wenzel F, Huber AR, Mori AC, Miny P, Röthlisberger B. High resolution array in the clinical approach to chromosomal phenotypes. Gene 2012; 495:163-9. [PMID: 22240311 DOI: 10.1016/j.gene.2011.12.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 12/11/2022]
Abstract
Array genomic hybridization (AGH) has recently been implemented as a diagnostic tool for the detection of submicroscopic copy number variants (CNVs) in patients with developmental disorders. However, there is no consensus regarding the choice of the platform, the minimal resolution needed and systematic interpretation of CNVs. We report our experience in the clinical diagnostic use of high resolution AGH up to 100 kb on 131 patients with chromosomal phenotypes but previously normal karyotype. We evaluated the usefulness in our clinics and laboratories by the detection rate of causal CNVs and CNVs of unknown clinical significance and to what extent their interpretation would challenge the systematic use of high-resolution arrays in clinical application. Prioritizing phenotype-genotype correlation in our interpretation strategy to criteria previously described, we identified 33 (25.2%) potentially pathogenic aberrations. 16 aberrations were confirmed pathogenic (16.4% syndromic, 8.5% non-syndromic patients); 9 were new and individual aberrations, 3 of them were pathogenic although inherited and one is as small as approx 200 kb. 13 of 16 further CNVs of unknown significance were classified likely benign, for 3 the significance remained unclear. High resolution array allows the detection of up to 12.2% of pathogenic aberrations in a diagnostic clinical setting. Although the majority of aberrations are larger, the detection of small causal aberrations may be relevant for family counseling. The number of remaining unclear CNVs is limited. Careful phenotype-genotype correlations of the individual CNVs and clinical features are challenging but remain a hallmark for CNV interpretation.
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