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Stevelink R, Campbell C, Chen S, Abou-Khalil B, Adesoji OM, Afawi Z, Amadori E, Anderson A, Anderson J, Andrade DM, Annesi G, Auce P, Avbersek A, Bahlo M, Baker MD, Balagura G, Balestrini S, Barba C, Barboza K, Bartolomei F, Bast T, Baum L, Baumgartner T, Baykan B, Bebek N, Becker AJ, Becker F, Bennett CA, Berghuis B, Berkovic SF, Beydoun A, Bianchini C, Bisulli F, Blatt I, Bobbili DR, Borggraefe I, Bosselmann C, Braatz V, Bradfield JP, Brockmann K, Brody LC, Buono RJ, Busch RM, Caglayan H, Campbell E, Canafoglia L, Canavati C, Cascino GD, Castellotti B, Catarino CB, Cavalleri GL, Cerrato F, Chassoux F, Cherny SS, Cheung CL, Chinthapalli K, Chou IJ, Chung SK, Churchhouse C, Clark PO, Cole AJ, Compston A, Coppola A, Cosico M, Cossette P, Craig JJ, Cusick C, Daly MJ, Davis LK, de Haan GJ, Delanty N, Depondt C, Derambure P, Devinsky O, Di Vito L, Dlugos DJ, Doccini V, Doherty CP, El-Naggar H, Elger CE, Ellis CA, Eriksson JG, Faucon A, Feng YCA, Ferguson L, Ferraro TN, Ferri L, Feucht M, Fitzgerald M, Fonferko-Shadrach B, Fortunato F, Franceschetti S, Franke A, French JA, Freri E, Gagliardi M, Gambardella A, Geller EB, Giangregorio T, Gjerstad L, Glauser T, Goldberg E, Goldman A, Granata T, Greenberg DA, Guerrini R, Gupta N, Haas KF, Hakonarson H, Hallmann K, Hassanin E, Hegde M, Heinzen EL, Helbig I, Hengsbach C, Heyne HO, Hirose S, Hirsch E, Hjalgrim H, Howrigan DP, Hucks D, Hung PC, Iacomino M, Imbach LL, Inoue Y, Ishii A, Jamnadas-Khoda J, Jehi L, Johnson MR, Kälviäinen R, Kamatani Y, Kanaan M, Kanai M, Kantanen AM, Kara B, Kariuki SM, Kasperavičiūte D, Kasteleijn-Nolst Trenite D, Kato M, Kegele J, Kesim Y, Khoueiry-Zgheib N, King C, Kirsch HE, Klein KM, Kluger G, Knake S, Knowlton RC, Koeleman BPC, Korczyn AD, Koupparis A, Kousiappa I, Krause R, Krenn M, Krestel H, Krey I, Kunz WS, Kurki MI, Kurlemann G, Kuzniecky R, Kwan P, Labate A, Lacey A, Lal D, Landoulsi Z, Lau YL, Lauxmann S, Leech SL, Lehesjoki AE, Lemke JR, Lerche H, Lesca G, Leu C, Lewin N, Lewis-Smith D, Li GHY, Li QS, Licchetta L, Lin KL, Lindhout D, Linnankivi T, Lopes-Cendes I, Lowenstein DH, Lui CHT, Madia F, Magnusson S, Marson AG, May P, McGraw CM, Mei D, Mills JL, Minardi R, Mirza N, Møller RS, Molloy AM, Montomoli M, Mostacci B, Muccioli L, Muhle H, Müller-Schlüter K, Najm IM, Nasreddine W, Neale BM, Neubauer B, Newton CRJC, Nöthen MM, Nothnagel M, Nürnberg P, O’Brien TJ, Okada Y, Ólafsson E, Oliver KL, Özkara C, Palotie A, Pangilinan F, Papacostas SS, Parrini E, Pato CN, Pato MT, Pendziwiat M, Petrovski S, Pickrell WO, Pinsky R, Pippucci T, Poduri A, Pondrelli F, Powell RHW, Privitera M, Rademacher A, Radtke R, Ragona F, Rau S, Rees MI, Regan BM, Reif PS, Rhelms S, Riva A, Rosenow F, Ryvlin P, Saarela A, Sadleir LG, Sander JW, Sander T, Scala M, Scattergood T, Schachter SC, Schankin CJ, Scheffer IE, Schmitz B, Schoch S, Schubert-Bast S, Schulze-Bonhage A, Scudieri P, Sham P, Sheidley BR, Shih JJ, Sills GJ, Sisodiya SM, Smith MC, Smith PE, Sonsma ACM, Speed D, Sperling MR, Stefansson H, Stefansson K, Steinhoff BJ, Stephani U, Stewart WC, Stipa C, Striano P, Stroink H, Strzelczyk A, Surges R, Suzuki T, Tan KM, Taneja RS, Tanteles GA, Taubøll E, Thio LL, Thomas GN, Thomas RH, Timonen O, Tinuper P, Todaro M, Topaloğlu P, Tozzi R, Tsai MH, Tumiene B, Turkdogan D, Unnsteinsdóttir U, Utkus A, Vaidiswaran P, Valton L, van Baalen A, Vetro A, Vining EPG, Visscher F, von Brauchitsch S, von Wrede R, Wagner RG, Weber YG, Weckhuysen S, Weisenberg J, Weller M, Widdess-Walsh P, Wolff M, Wolking S, Wu D, Yamakawa K, Yang W, Yapıcı Z, Yücesan E, Zagaglia S, Zahnert F, Zara F, Zhou W, Zimprich F, Zsurka G, Zulfiqar Ali Q. GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture. Nat Genet 2023; 55:1471-1482. [PMID: 37653029 PMCID: PMC10484785 DOI: 10.1038/s41588-023-01485-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment.
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Marconi C, Pecci A, Palombo F, Melazzini F, Bottega R, Nardi E, Bozzi V, Faleschini M, Barozzi S, Giangregorio T, Magini P, Balduini CL, Savoia A, Seri M, Noris P, Pippucci T. Exome sequencing in 116 patients with inherited thrombocytopenia that remained of unknown origin after systematic phenotype-driven diagnostic workup. Haematologica 2023; 108:1909-1919. [PMID: 36519321 PMCID: PMC10316235 DOI: 10.3324/haematol.2022.280993] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/29/2022] [Indexed: 11/01/2023] Open
Abstract
Inherited thrombocytopenias (IT) are genetic diseases characterized by low platelet count, sometimes associated with congenital defects or a predisposition to develop additional conditions. Next-generation sequencing has substantially improved our knowledge of IT, with more than 40 genes identified so far, but obtaining a molecular diagnosis remains a challenge especially for patients with non-syndromic forms, having no clinical or functional phenotypes that raise suspicion about specific genes. We performed exome sequencing (ES) in a cohort of 116 IT patients (89 families), still undiagnosed after a previously validated phenotype-driven diagnostic algorithm including a targeted analysis of suspected genes. ES achieved a diagnostic yield of 36%, with a gain of 16% over the diagnostic algorithm. This can be explained by genetic heterogeneity and unspecific genotype-phenotype relationships that make the simultaneous analysis of all the genes, enabled by ES, the most reasonable strategy. Furthermore, ES disentangled situations that had been puzzling because of atypical inheritance, sex-related effects or false negative laboratory results. Finally, ES-based copy number variant analysis disclosed an unexpectedly high prevalence of RUNX1 deletions, predisposing to hematologic malignancies. Our findings demonstrate that ES, including copy number variant analysis, can substantially contribute to the diagnosis of IT and can solve diagnostic problems that would otherwise remain a challenge.
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Affiliation(s)
- Caterina Marconi
- Department of Medical and Surgical Science, University of Bologna, Bologna
| | - Alessandro Pecci
- Department of Internal Medicine, University of Pavia, Pavia, Italy; Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Flavia Palombo
- Department of Medical and Surgical Science, University of Bologna, Bologna
| | - Federica Melazzini
- Department of Internal Medicine, University of Pavia, Pavia, Italy; Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Roberta Bottega
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste
| | - Elena Nardi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna
| | - Valeria Bozzi
- Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | | | - Serena Barozzi
- Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | | | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna
| | | | - Anna Savoia
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy; Department of Medical Sciences, University of Trieste, Trieste
| | - Marco Seri
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy; Medical Genetics Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna.
| | - Patrizia Noris
- Department of Internal Medicine, University of Pavia, Pavia, Italy; Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Tommaso Pippucci
- Medical Genetics Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna
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3
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Cani I, Pondrelli F, Licchetta L, Minardi R, Giangregorio T, Mostacci B, Muccioli L, Di Vito L, Fetta A, Barba C, Castioni CA, Bordugo A, Tinuper P, Bisulli F. Epilepsy and inborn errors of metabolism in adults: The diagnostic odyssey of a young woman with medium-chain acyl-coenzyme A dehydrogenase deficiency. Epilepsia Open 2022; 7:810-816. [PMID: 35869793 PMCID: PMC9712474 DOI: 10.1002/epi4.12630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022] Open
Abstract
We describe a case of epileptic encephalopathy in a young woman with undiagnosed medium-chain acyl-coenzyme A dehydrogenase deficiency (MCADD), who presented with an early-onset focal motor status epilepticus (SE) then followed by permanent left hemiplegia and drug-resistant epilepsy with neurodevelopmental delay. Throughout her clinical history, recurrent episodes of lethargy, feeding difficulties, and clustering seizures occurred, progressing into a super refractory SE and death at the age of 25 years. Although epilepsy is not a distinctive feature of MCADD, we advise considering this metabolic disease as a possible etiology of epileptic encephalopathy and hemiconvulsion-hemiplegia-epilepsy syndrome of unknown origin, on the chance to provide a timely and targeted treatment preventing development delay and evolution to SE. Adult patients with epilepsy of unknown etiology not screened at birth for inborn errors of metabolism, such as MCADD, should be promptly investigated for these treatable conditions.
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Affiliation(s)
- Ilaria Cani
- Department of Biomedical and Neuromotor SciencesUniversity of BolognaBolognaItaly
| | - Federica Pondrelli
- Department of Biomedical and Neuromotor SciencesUniversity of BolognaBolognaItaly
| | - Laura Licchetta
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Full member of the European Reference Network EpiCAREBolognaItaly
| | - Raffaella Minardi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Full member of the European Reference Network EpiCAREBolognaItaly
| | - Tania Giangregorio
- Department of Medical and Surgical SciencesUniversity of BolognaBolognaItaly
| | - Barbara Mostacci
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Full member of the European Reference Network EpiCAREBolognaItaly
| | - Lorenzo Muccioli
- Department of Biomedical and Neuromotor SciencesUniversity of BolognaBolognaItaly
| | - Lidia Di Vito
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Full member of the European Reference Network EpiCAREBolognaItaly
| | - Anna Fetta
- Department of Medical and Surgical SciencesUniversity of BolognaBolognaItaly
| | - Carmen Barba
- Neuroscience DepartmentMeyer Children's HospitalFirenzeItaly,University of FlorenceFlorenceItaly
| | - Carlo Alberto Castioni
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Full member of the European Reference Network EpiCAREBolognaItaly
| | - Andrea Bordugo
- Inherited Metabolic Diseases Unit and Regional Centre for Newborn Screening, Diagnosis and Treatment of Inherited Metabolic Diseases and Congenital Endocrine DiseasesAzienda Ospedaliera Universitaria IntegrataVeronaItaly
| | - Paolo Tinuper
- Department of Biomedical and Neuromotor SciencesUniversity of BolognaBolognaItaly,IRCCS Istituto delle Scienze Neurologiche di Bologna, Full member of the European Reference Network EpiCAREBolognaItaly
| | - Francesca Bisulli
- Department of Biomedical and Neuromotor SciencesUniversity of BolognaBolognaItaly,IRCCS Istituto delle Scienze Neurologiche di Bologna, Full member of the European Reference Network EpiCAREBolognaItaly
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4
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Gozzelino L, Kochlamazashvili G, Baldassari S, Mackintosh AI, Licchetta L, Iovino E, Liu YC, Bennett CA, Bennett MF, Damiano JA, Zsurka G, Marconi C, Giangregorio T, Magini P, Kuijpers M, Maritzen T, Norata GD, Baulac S, Canafoglia L, Seri M, Tinuper P, Scheffer IE, Bahlo M, Berkovic SF, Hildebrand MS, Kunz WS, Giordano L, Bisulli F, Martini M, Haucke V, Hirsch E, Pippucci T. OUP accepted manuscript. Brain 2022; 145:2313-2331. [PMID: 35786744 PMCID: PMC9337808 DOI: 10.1093/brain/awac082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/13/2022] [Accepted: 02/12/2022] [Indexed: 11/20/2022] Open
Abstract
Epilepsy is one of the most frequent neurological diseases, with focal epilepsy accounting for the largest number of cases. The genetic alterations involved in focal epilepsy are far from being fully elucidated. Here, we show that defective lipid signalling caused by heterozygous ultra-rare variants in PIK3C2B, encoding for the class II phosphatidylinositol 3-kinase PI3K-C2β, underlie focal epilepsy in humans. We demonstrate that patients’ variants act as loss-of-function alleles, leading to impaired synthesis of the rare signalling lipid phosphatidylinositol 3,4-bisphosphate, resulting in mTORC1 hyperactivation. In vivo, mutant Pik3c2b alleles caused dose-dependent neuronal hyperexcitability and increased seizure susceptibility, indicating haploinsufficiency as a key driver of disease. Moreover, acute mTORC1 inhibition in mutant mice prevented experimentally induced seizures, providing a potential therapeutic option for a selective group of patients with focal epilepsy. Our findings reveal an unexpected role for class II PI3K-mediated lipid signalling in regulating mTORC1-dependent neuronal excitability in mice and humans.
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Affiliation(s)
| | | | | | - Albert Ian Mackintosh
- Department of Molecular Pharmacology and Cell Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Laura Licchetta
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Epilepsy Center (Reference Center for Rare and Complex Epilepsies—EpiCARE), Bologna, Italy
| | - Emanuela Iovino
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Yu Chi Liu
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VictoriaAustralia
| | - Caitlin A Bennett
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Mark F Bennett
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VictoriaAustralia
| | - John A Damiano
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Gábor Zsurka
- Department of Experimental Epileptology and Cognition Research and Department of Epileptology, University Bonn Medical Center, Venusberg Campus 1, D-53105 Bonn, Germany
| | - Caterina Marconi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Tania Giangregorio
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Pamela Magini
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Marijn Kuijpers
- Department of Molecular Pharmacology and Cell Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Tanja Maritzen
- Department of Molecular Pharmacology and Cell Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
- Department of Nanophysiology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Giuseppe Danilo Norata
- Department of Excellence in Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan and Center for the Study of Atherosclerosis, SISA Bassini Hospital Cinisello B, Italy
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau—Paris Brain Institute—ICM, Inserm, CNRS, F-75013 Paris, France
| | - Laura Canafoglia
- Unit of Integrated Diagnostics for Epilepsy, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Marco Seri
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Paolo Tinuper
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Epilepsy Center (Reference Center for Rare and Complex Epilepsies—EpiCARE), Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Melbourne, Victoria, Australia
- Florey Institute for Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- Spedali Civili, Neuropsychiatric Department, Brescia, Italy
- Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Melbourne, Victoria, Australia
| | - Wolfram S Kunz
- Department of Experimental Epileptology and Cognition Research and Department of Epileptology, University Bonn Medical Center, Venusberg Campus 1, D-53105 Bonn, Germany
| | - Lucio Giordano
- Spedali Civili, Neuropsychiatric Department, Brescia, Italy
| | - Francesca Bisulli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Epilepsy Center (Reference Center for Rare and Complex Epilepsies—EpiCARE), Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Volker Haucke
- Volker Haucke Robert-Roessle-Strasse 10, 13125 Berlin, Germany E-mail:
| | - Emilio Hirsch
- Correspondence may also be addressed to: Emilio Hirsch via Nizza 52, 10126 Torino (TO), Italy E-mail:
| | - Tommaso Pippucci
- Correspondence to: Tommaso Pippucci Via Giuseppe Massarenti 9, 40138 Bologna (BO), Italy E-mail:
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5
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Faleschini M, Papa N, Morel-Kopp MC, Marconi C, Giangregorio T, Melazzini F, Bozzi V, Seri M, Noris P, Pecci A, Savoia A, Bottega R. Dysregulation of oncogenic factors by GFI1B p32: investigation of a novel GFI1B germline mutation. Haematologica 2021; 107:260-267. [PMID: 33472357 PMCID: PMC8719102 DOI: 10.3324/haematol.2020.267328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Indexed: 11/10/2022] Open
Abstract
GFI1B is a transcription factor essential for the regulation of erythropoiesis and megakaryopoiesis, and pathogenic variants have been associated with thrombocytopenia and bleeding. Analysing thrombocytopenic families by whole exome sequencing, we identified a novel GFI1B variant (c.648+5G>A), which causes exon 9 skipping and overexpression of a shorter p32 isoform. We report the clinical data of our patients and critically review the phenotype observed in individuals with different GFI1B variants leading to the same effect on the p32 expression. Since p32 is increased in acute and chronic leukemia cells, we tested the expression level of genes playing a role in various type of cancers, including hematological tumors and found that they are significantly dysregulated, suggesting a potential role for GFI1B in carcinogenesis regulation. Increasing the detection of individuals with GFI1B variants will allow us to better characterize this rare disease and determine whether it is associated with an increased risk of developing malignancies.
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Affiliation(s)
| | - Nicole Papa
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste
| | - Marie-Christine Morel-Kopp
- Department of Haematology and Transfusion Medicine, Royal North Shore Hospital and Northern Blood Research Centre, Kolling Institute, University of Sydney, Sydney
| | - Caterina Marconi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna
| | | | - Federica Melazzini
- Biotechnology Research Laboratories, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Valeria Bozzi
- Biotechnology Research Laboratories, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Marco Seri
- Department of Medical and Surgical Sciences, University of Bologna, Bologna
| | - Patrizia Noris
- Biotechnology Research Laboratories, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Alessandro Pecci
- Biotechnology Research Laboratories, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Anna Savoia
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy; Department of Medical Sciences, University of Trieste, Trieste.
| | - Roberta Bottega
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste
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6
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Magi A, Giangregorio T, Semeraro R, Carangelo G, Palombo F, Romeo G, Seri M, Pippucci T. AUDACITY: A comprehensive approach for the detection and classification of Runs of Homozygosity in medical and population genomics. Comput Struct Biotechnol J 2020; 18:1956-1967. [PMID: 32774790 PMCID: PMC7394861 DOI: 10.1016/j.csbj.2020.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 11/17/2022] Open
Abstract
Runs of Homozygosity (RoHs) are popular among geneticists as the footprint of demographic processes, evolutionary forces and inbreeding in shaping our genome, and are known to confer risk of Mendelian and complex diseases. Notwithstanding growing interest in their study, there is unmet need for reliable and rapid methods for genomic analyses in large data sets. AUDACITY is a tool integrating novel RoH detection algorithm and autozygosity prediction score for prioritization of mutation-surrounding regions. It processes data in VCF file format, and outperforms existing methods in identifying RoHs of any size. Simulations and analysis of real exomes/genomes show its potential to foster future RoH studies in medical and population genomics.
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Affiliation(s)
- Alberto Magi
- Department of Information Engineering, University of Florence, Florence, Italy
- Corresponding authors.
| | - Tania Giangregorio
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Roberto Semeraro
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Giulia Carangelo
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Flavia Palombo
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Marco Seri
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Medical Genetics Unit, Sant’Orsola-Malpighi University Hospital, Bologna, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, Sant’Orsola-Malpighi University Hospital, Bologna, Italy
- Corresponding authors.
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7
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Pecci A, Ragab I, Bozzi V, De Rocco D, Barozzi S, Giangregorio T, Ali H, Melazzini F, Sallam M, Alfano C, Pastore A, Balduini CL, Savoia A. Thrombopoietin mutation in congenital amegakaryocytic thrombocytopenia treatable with romiplostim. EMBO Mol Med 2019; 10:63-75. [PMID: 29191945 PMCID: PMC5760853 DOI: 10.15252/emmm.201708168] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Congenital amegakaryocytic thrombocytopenia (CAMT) is an inherited disorder characterized at birth by thrombocytopenia with reduced megakaryocytes, which evolves into generalized bone marrow aplasia during childhood. Although CAMT is genetically heterogeneous, mutations of MPL, the gene encoding for the receptor of thrombopoietin (THPO), are the only known disease‐causing alterations. We identified a family with three children affected with CAMT caused by a homozygous mutation (p.R119C) of the THPO gene. Functional studies showed that p.R119C affects not only ability of the cytokine to stimulate MPL but also its release, which is consistent with the relatively low serum THPO levels measured in patients. In all the three affected children, treatment with the THPO‐mimetic romiplostim induced trilineage hematological responses, remission of bleeding and infections, and transfusion independence, which were maintained after up to 6.5 years of observation. Recognizing patients with THPO mutations among those with juvenile bone marrow failure is essential to provide them with appropriate substitutive therapy and prevent the use of invasive and unnecessary treatments, such as hematopoietic stem cell transplantation or immunosuppression.
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Affiliation(s)
- Alessandro Pecci
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Iman Ragab
- Hematology-Oncology Unit, Pediatric Hospital, Ain Shams University, Cairo, Egypt
| | - Valeria Bozzi
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Daniela De Rocco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Serena Barozzi
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | | | - Heba Ali
- Hematology-Oncology Unit, Pediatric Hospital, Ain Shams University, Cairo, Egypt
| | - Federica Melazzini
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Mohamed Sallam
- Department of Clinical Pathology, Ain Shams University, Cairo, Egypt
| | - Caterina Alfano
- Maurice Wohl Clinical Neuroscience Institute, King's College, London, UK.,Fondazione Ri.MED, Palermo, Italy
| | - Annalisa Pastore
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Carlo L Balduini
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy .,Department of Medical Sciences, University of Trieste, Trieste, Italy
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8
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Faleschini M, Melazzini F, Marconi C, Giangregorio T, Pippucci T, Cigalini E, Pecci A, Bottega R, Ramenghi U, Siitonen T, Seri M, Pastore A, Savoia A, Noris P. ACTN1 mutations lead to a benign form of platelet macrocytosis not always associated with thrombocytopenia. Br J Haematol 2018; 183:276-288. [PMID: 30351444 DOI: 10.1111/bjh.15531] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/19/2018] [Indexed: 12/27/2022]
Abstract
The inherited thrombocytopenias (IT) are a heterogeneous group of diseases resulting from mutations in more than 30 different genes. Among them, ACTN1-related thrombocytopenia (ACTN1-RT; Online Mendelian Inheritance in Man: 615193) is one of the most recently identified forms. It has been described as a mild autosomal dominant macrothrombocytopenia caused by mutations in ACTN1, a gene encoding for one of the two non-muscle isoforms of α-actinin. We recently identified seven new unrelated families with ACTN1-RT caused by different mutations. Two of them are novel missense variants (p.Trp128Cys and p.Pro233Leu), whose pathogenic role has been confirmed by in vitro studies. Together with the 10 families we have previously described, our cohort of ACTN1-RT now consists of 49 individuals carrying ACTN1 mutations. This is the largest case series ever collected and enabled a critical evaluation of the clinical aspects of the disease. We concluded that ACTN1-RT is the fourth most frequent form of IT worldwide and it is characterized by platelet macrocytosis in all affected subjects and mild thrombocytopenia in less than 80% of cases. The risk of bleeding, either spontaneous or upon haemostatic challenge, is negligible and there are no other associated defects, either congenital or acquired. Therefore, ACTN1-RT is a benign form of IT, whose diagnosis provides affected individuals and their families with a good prognosis.
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Affiliation(s)
- Michela Faleschini
- Institute for Maternal and Child Health - "IRCCS Burlo Garofolo", Trieste, Italy
| | - Federica Melazzini
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Caterina Marconi
- Department of Medical Science, Medical Genetics Unit, Policlinico Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | | | - Tommaso Pippucci
- Department of Medical Science, Medical Genetics Unit, Policlinico Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Elena Cigalini
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Alessandro Pecci
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health - "IRCCS Burlo Garofolo", Trieste, Italy
| | - Ugo Ramenghi
- Pediatric Department, Hematology Unit, University of Torino, Torino, Italy
| | - Timo Siitonen
- Department of Medicine, Oulu University Hospital, Oulu, Finland
| | - Marco Seri
- Department of Medical Science, Medical Genetics Unit, Policlinico Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Annalisa Pastore
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health - "IRCCS Burlo Garofolo", Trieste, Italy.,Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Patrizia Noris
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
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9
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Zaninetti C, De Rocco D, Giangregorio T, Bozzi V, Demeter J, Leoni P, Noris P, Ryhänen S, Barozzi S, Pecci A, Savoia A. MYH9-Related Thrombocytopenia: Four Novel Variants Affecting the Tail Domain of the Non-Muscle Myosin Heavy Chain IIA Associated with a Mild Clinical Evolution of the Disorder. Hamostaseologie 2018; 39:87-94. [PMID: 29996171 DOI: 10.1055/s-0038-1645840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
MYH9-related disease (MYH9-RD) is an autosomal-dominant thrombocytopenia caused by mutations in the gene for non-muscle myosin heavy chain IIA (NMMHC-IIA). Patients present congenital macrothrombocytopenia and inclusions of NMMHC-IIA in leukocytes, and have a variable risk of developing kidney damage, sensorineural deafness, presenile cataracts and/or liver enzymes abnormalities. The spectrum of mutations found in MYH9-RD patients is limited and the incidence and severity of the non-congenital features are predicted by the causative MYH9 variant. In particular, different alterations of the C-terminal tail domain of NMMHC-IIA associate with remarkably different disease evolution. We report four novel MYH9 mutations affecting the tail domain of NMMHC-IIA and responsible for MYH9-RD in four families. Two variants cause amino acid substitutions in the coiled-coil region of NMMHC-IIA, while the other two are a splicing variant and a single nucleotide deletion both resulting in frameshift alterations of the short non-helical tailpiece. Characterization of phenotypes of affected individuals shows that all of these novel variants are associated with a mild clinical evolution of the disease.
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Affiliation(s)
- Carlo Zaninetti
- Department of Internal Medicine, IRCCS Policlicnico San Matteo Foundation, University of Pavia, Pavia, Italy.,PhD Programme in Experimental Medicine, University of Pavia, Pavia, Italy
| | - Daniela De Rocco
- Institute for Maternal and Child Health, "IRCCS Burlo Garofolo," Trieste, Italy
| | | | - Valeria Bozzi
- Department of Internal Medicine, IRCCS Policlicnico San Matteo Foundation, University of Pavia, Pavia, Italy
| | - Judit Demeter
- Division of Hematology, First Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Pietro Leoni
- Hematology Clinic, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Patrizia Noris
- Department of Internal Medicine, IRCCS Policlicnico San Matteo Foundation, University of Pavia, Pavia, Italy
| | - Samppa Ryhänen
- Division of Hematology, Oncology, and Stem Cell Transplantation, Children's Hospital, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Serena Barozzi
- Department of Internal Medicine, IRCCS Policlicnico San Matteo Foundation, University of Pavia, Pavia, Italy
| | - Alessandro Pecci
- Department of Internal Medicine, IRCCS Policlicnico San Matteo Foundation, University of Pavia, Pavia, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health, "IRCCS Burlo Garofolo," Trieste, Italy.,Department of Medical Sciences, University of Trieste, Trieste, Italy
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10
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Noris P, Marconi C, De Rocco D, Melazzini F, Pippucci T, Loffredo G, Giangregorio T, Pecci A, Seri M, Savoia A. A new form of inherited thrombocytopenia due to monoallelic loss of function mutation in the thrombopoietin gene. Br J Haematol 2017; 181:698-701. [PMID: 28466964 DOI: 10.1111/bjh.14694] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Patrizia Noris
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Caterina Marconi
- Department of Medical and Surgical Science, Policlinico Sant'Orsola Malpighi and University of Bologna, Bologna, Italy
| | - Daniela De Rocco
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Federica Melazzini
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Tommaso Pippucci
- Department of Medical and Surgical Science, Policlinico Sant'Orsola Malpighi and University of Bologna, Bologna, Italy
| | - Giuseppe Loffredo
- Department of Oncology, Azienda Ospedaliera "Santobono-Pausilipon", Pausilipon Hospital, Naples, Italy
| | - Tania Giangregorio
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Alessandro Pecci
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Marco Seri
- Department of Medical and Surgical Science, Policlinico Sant'Orsola Malpighi and University of Bologna, Bologna, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy.,Department of Medical Sciences, University of Trieste, Trieste, Italy
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11
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Palombo F, Al-Wardy N, Ruscone GAG, Oppo M, Kindi MNA, Angius A, Al Lamki K, Girotto G, Giangregorio T, Benelli M, Magi A, Seri M, Gasparini P, Cucca F, Sazzini M, Al Khabori M, Pippucci T, Romeo G. A novel founder MYO15A frameshift duplication is the major cause of genetic hearing loss in Oman. J Hum Genet 2016; 62:259-264. [PMID: 27734841 DOI: 10.1038/jhg.2016.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 12/16/2022]
Abstract
The increased risk for autosomal recessive disorders is one of the most well-known medical implications of consanguinity. In the Sultanate of Oman, a country characterized by one of the highest rates of consanguineous marriages worldwide, prevalence of genetic hearing loss (GHL) is estimated to be 6/10 000. Families of GHL patients have higher consanguinity rates than the general Omani population, indicating a major role for recessive forms. Mutations in GJB2, the most commonly mutated GHL gene, have been sporadically described. We collected 97 DNA samples of GHL probands, affected/unaffected siblings and parents from 26 Omani consanguineous families. Analyzing a first family by whole-exome sequencing, we identified a novel homozygous frameshift duplication (c.1171_1177dupGCCATCT) in MYO15A, the gene linked to the deafness locus DFNB3. This duplication was then found in a total of 8/26 (28%) families, within a 849 kb founder haplotype. Reconstruction of haplotype structure at MYO15A surrounding genomic regions indicated that the founder haplotype branched out in the past two to three centuries from a haplotype present worldwide. The MYO15A duplication emerges as the major cause of GHL in Oman. These findings have major implications for the design of GHL diagnosis and prevention policies in Oman.
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Affiliation(s)
- Flavia Palombo
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Nadia Al-Wardy
- College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Guido Alberto Gnecchi Ruscone
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department BiGeA University of Bologna, Bologna, Italy
| | - Manuela Oppo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy.,Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
| | | | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy.,Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Parco Scientifico e Tecnologico della Sardegna, Pula, Italy
| | - Khalsa Al Lamki
- College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Giorgia Girotto
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Tania Giangregorio
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Matteo Benelli
- Department Laboratory, Careggi University Hospital, Firenze, Italy
| | - Alberto Magi
- Department of Experimental and Clinical Medicine, University of Florence, Firenze, Italy
| | - Marco Seri
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Paolo Gasparini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy.,Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
| | - Marco Sazzini
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department BiGeA University of Bologna, Bologna, Italy
| | - Mazin Al Khabori
- Department of ENT, Al Nahda Hospital, Ministry of Health, Muscat, Oman
| | - Tommaso Pippucci
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
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