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Catusi I, Recalcati MP, Bestetti I, Garzo M, Valtorta C, Alfonsi M, Alghisi A, Cappellani S, Casalone R, Caselli R, Ceccarini C, Ceglia C, Ciaschini AM, Coviello D, Crosti F, D'Aprile A, Fabretto A, Genesio R, Giagnacovo M, Granata P, Longo I, Malacarne M, Marseglia G, Montaldi A, Nardone AM, Palka C, Pecile V, Pessina C, Postorivo D, Redaelli S, Renieri A, Rigon C, Tiberi F, Tonelli M, Villa N, Zilio A, Zuccarello D, Novelli A, Larizza L, Giardino D. Testing single/combined clinical categories on 5110 Italian patients with developmental phenotypes to improve array-based detection rate. Mol Genet Genomic Med 2019; 8:e1056. [PMID: 31851782 PMCID: PMC6978242 DOI: 10.1002/mgg3.1056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 07/25/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023] Open
Abstract
Background Chromosomal microarray analysis (CMA) is nowadays widely used in the diagnostic path of patients with clinical phenotypes. However, there is no ascertained evidence to date on how to assemble single/combined clinical categories of developmental phenotypic findings to improve the array‐based detection rate. Methods The Italian Society of Human Genetics coordinated a retrospective study which included CMA results of 5,110 Italian patients referred to 17 genetics laboratories for variable combined clinical phenotypes. Results Non‐polymorphic copy number variants (CNVs) were identified in 1512 patients (30%) and 615 (32%) present in 552 patients (11%) were classified as pathogenic. CNVs were analysed according to type, size, inheritance pattern, distribution among chromosomes, and association to known syndromes. In addition, the evaluation of the detection rate of clinical subgroups of patients allowed to associate dysmorphisms and/or congenital malformations combined with any other single clinical sign to an increased detection rate, whereas non‐syndromic neurodevelopmental signs and non‐syndromic congenital malformations to a decreased detection rate. Conclusions Our retrospective study resulted in confirming the high detection rate of CMA and indicated new clinical markers useful to optimize their inclusion in the diagnostic and rehabilitative path of patients with developmental phenotypes.
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Affiliation(s)
- Ilaria Catusi
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | | | - Ilaria Bestetti
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Maria Garzo
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Chiara Valtorta
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Melissa Alfonsi
- U.O.C. di Genetica medica, Ospedale SS Annunziata, Chieti, Italy
| | - Alberta Alghisi
- U.O.S. Genetica e Biologia Molecolare, Azienda ULSS 6, Vicenza, Italy
| | | | - Rosario Casalone
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Rossella Caselli
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Carlo Ceglia
- UOSD Genetica Medica, AORN "SG Moscati", Avellino, Italy
| | - Anna Maria Ciaschini
- A.O.U. Ospedali Riuniti Umberto I - G.M.Lancisi - G.Salesi, Lab. Genetica Medica SOS Malattie Rare, Ancona, Italy
| | - Domenico Coviello
- Lab. di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Francesca Crosti
- U.S. Genetica Medica, Ospedale San Gerardo ASST Monza, Monza, Italy
| | | | | | - Rita Genesio
- U.O.C. di Citogenetica, A.O.U. Federico II, Napoli, Italy
| | | | - Paola Granata
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Ilaria Longo
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Michela Malacarne
- Lab. di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | | | | | - Chiara Palka
- Dipartimento di Pediatria, Università G. D'Annunzio, Chieti-Pescara, Italy
| | - Vanna Pecile
- S.C. Genetica Medica, IRCCS Burlo Garofolo, Trieste, Italy
| | - Chiara Pessina
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Diana Postorivo
- U.O.C. Lab. di Genetica Medica, Policlinico Tor Vergata, Roma, Italy
| | - Serena Redaelli
- Dipartimento di Medicina e Chirurgia, Università di Milano-Bicocca, Monza, Italy
| | - Alessandra Renieri
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Chiara Rigon
- U.O.C. Genetica e Epidemiologia Clinica, A.O.U. di Padova, Padova, Italy
| | - Fabiola Tiberi
- A.O.U. Ospedali Riuniti Umberto I - G.M.Lancisi - G.Salesi, Lab. Genetica Medica SOS Malattie Rare, Ancona, Italy
| | - Mariella Tonelli
- LCGM Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Nicoletta Villa
- U.S. Genetica Medica, Ospedale San Gerardo ASST Monza, Monza, Italy
| | - Anna Zilio
- U.O.S. Genetica e Biologia Molecolare, Azienda ULSS 6, Vicenza, Italy
| | - Daniela Zuccarello
- U.O.C. Genetica e Epidemiologia Clinica, A.O.U. di Padova, Padova, Italy
| | - Antonio Novelli
- U.O.C. Laboratorio di Genetica Medica, Ospedale Pediatrico del Bambino Gesù, Roma, Italy
| | - Lidia Larizza
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Daniela Giardino
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
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Lombardo B, Ceglia C, Verdesca F, Vitale A, Perrotta C, Leggiero E, Pastore L. CGH array for the identification of a compound heterozygous mutation in the CYP1B1 gene in a patient with bilateral anterior segment dysgenesis. Clin Chem Lab Med 2019; 57:e63-e66. [PMID: 30207287 DOI: 10.1515/cclm-2017-1106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/21/2018] [Indexed: 11/15/2022]
Affiliation(s)
- Barbara Lombardo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", Naples, Italy.,CEINGE-Biotecnologie Avanzate Scarl, Naples, Italy
| | - Carlo Ceglia
- CEINGE-Biotecnologie Avanzate Scarl, Naples, Italy
| | - Francesco Verdesca
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", Naples, Italy.,CEINGE-Biotecnologie Avanzate Scarl, Naples, Italy
| | - Andrea Vitale
- CEINGE-Biotecnologie Avanzate Scarl, Naples, Italy.,Dipartimento di Scienze Motorie e del Benessere, Università di Napoli "Parthenope", Naples, Italy
| | - Carla Perrotta
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", Naples, Italy.,CEINGE-Biotecnologie Avanzate Scarl, Naples, Italy
| | | | - Lucio Pastore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", Naples, Italy.,CEINGE-Biotecnologie Avanzate Scarl, Naples, Italy
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Lombardo B, Zarrilli F, Ceglia C, Vitale A, Keller S, Sarchiapone M, Carli V, Stuppia L, Chiariotti L, Castaldo G, Pastore L. Two novel genomic rearrangements identified in suicide subjects using a-CGH array. Clin Chem Lab Med 2015; 53:e245-8. [PMID: 25719327 DOI: 10.1515/cclm-2014-1255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/08/2015] [Indexed: 11/15/2022]
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Iossa S, Costa V, Corvino V, Auletta G, Barruffo L, Cappellani S, Ceglia C, Cennamo G, D'Adamo AP, D'Amico A, Di Paolo N, Forte R, Gasparini P, Laria C, Lombardo B, Malesci R, Vitale A, Marciano E, Franzè A. Phenotypic and genetic characterization of a family carrying two Xq21.1-21.3 interstitial deletions associated with syndromic hearing loss. Mol Cytogenet 2015; 8:18. [PMID: 25821518 PMCID: PMC4376344 DOI: 10.1186/s13039-015-0120-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 09/29/2014] [Accepted: 02/17/2015] [Indexed: 11/21/2022] Open
Abstract
Background Sensorineural hearing impairment is a common pathological manifestation in patients affected by X-linked intellectual disability. A few cases of interstitial deletions at Xq21 with several different phenotypic characteristics have been described, but to date, a complete molecular characterization of the deletions harboring disease-causing genes is still missing. Thus, the aim of this study is to realize a detailed clinical and molecular analysis of a family affected by syndromic X-linked hearing loss with intellectual disability. Results Clinical analyses revealed a very complex phenotype that included inner ear malformations, vestibular problems, choroideremia and hypotonia with a peculiar pattern of phenotypic variability. Genomic analysis revealed, for the first time, the presence of two close interstitial deletions in the Xq21.1-21.3, harboring 11 protein coding, 9 non-coding genes and 19 pseudogenes. Among these, 3 protein coding genes have already been associated with X-linked hearing loss, intellectual disability and choroideremia. Conclusions In this study we highlighted the presence of peculiar genotypic and phenotypic details in a family affected by syndromic X-linked hearing loss with intellectual disability. We identified two, previously unreported, Xq21.1-21.3 interstitial deletions. The two rearrangements, containing several genes, segregate with the clinical features, suggesting their role in the pathogenicity. However, not all the observed phenotypic features can be clearly associated with the known genes thus, further study is necessary to determine regions involved. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0120-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra Iossa
- DMMBM, Università di Napoli "Federico II", Naples, Italy ; Ceinge Biotecnologie Avanzate, Naples, Italy
| | | | - Virginia Corvino
- Istituto di Audiologia, Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università di Napoli "Federico II", Naples, Italy
| | - Gennaro Auletta
- Istituto di Audiologia, Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università di Napoli "Federico II", Naples, Italy
| | - Luigi Barruffo
- Istituto di Audiologia, Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università di Napoli "Federico II", Naples, Italy
| | - Stefania Cappellani
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | | | - Giovanni Cennamo
- Dipartimento di Oftalmologia, Università di Napoli "Federico II", Naples, Italy
| | - Adamo Pio D'Adamo
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy ; University of Trieste, Trieste, Italy
| | - Alessandra D'Amico
- Dipartimento di Scienze Biomediche Avanzate, Università di Napoli "Federico II", Naples, Italy
| | - Nilde Di Paolo
- Dipartimento di Scienze Biomediche Avanzate, Università di Napoli "Federico II", Naples, Italy
| | - Raimondo Forte
- Dipartimento di Oftalmologia Pediatrica, Università di Salerno, Salerno, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy ; University of Trieste, Trieste, Italy
| | - Carla Laria
- Istituto di Audiologia, Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università di Napoli "Federico II", Naples, Italy
| | - Barbara Lombardo
- DMMBM, Università di Napoli "Federico II", Naples, Italy ; Ceinge Biotecnologie Avanzate, Naples, Italy
| | - Rita Malesci
- Istituto di Audiologia, Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università di Napoli "Federico II", Naples, Italy
| | - Andrea Vitale
- Dipartimento di Scienze Motorie e del Benessere, Università di Napoli "Parthenope", Naples, Italy
| | - Elio Marciano
- Istituto di Audiologia, Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università di Napoli "Federico II", Naples, Italy
| | - Annamaria Franzè
- Ceinge Biotecnologie Avanzate, Naples, Italy ; Istituto di Audiologia, Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università di Napoli "Federico II", Naples, Italy
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Tarsitano M, Ceglia C, Novelli A, Capalbo A, Lombardo B, Pastore L, Fioretti G, Vicari L, Pisanti MA, Friso P, Cavaliere ML. Microduplications in 22q11.2 and 8q22.1 associated with mild mental retardation and generalized overgrowth. Gene 2013; 536:213-6. [PMID: 24315824 DOI: 10.1016/j.gene.2013.11.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 09/23/2013] [Revised: 11/04/2013] [Accepted: 11/22/2013] [Indexed: 12/21/2022]
Abstract
The 22q11.2 microduplication is a genomic disorder, characterized from a variable phenotype ranging from different defects to normality. The most common microduplication of 22q11.2 is 3 Mb in size, but there are also cases reported with atypical duplications between 0.8 Mb and 6Mb. Here, we describe a case of a child with macrocephaly, overgrowth with advanced bone age, attention deficits, evidence of mild mental retardation and dysmorphic features. An array-CGH analysis detected a 252 Kb duplication at the 22q11.2 region inherited from mother and 142 Kb duplication at 8q22.1 region inherited from father. Both parents show mild dysmorphic features. The duplicated genes in chromosomes 22q and 8q are TOP3B and PGCP, respectively. We describe for the first time a patient carrying the smaller atypical 22q11.2 duplication who also presents with mild mental retardation and generalized overgrowth. This patient has an additional duplication in 8q22.1 which may act as a genomic modifier of its clinical phenotype.
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Affiliation(s)
| | - Carlo Ceglia
- CEINGE Advanced Biotechnology, S.c.a.r.l., Naples, Italy
| | - Antonio Novelli
- Mendel Laboratory, Casa Sollievo della Sofferenza IRCCS, Viale Regina Margherita 261, 00198 Rome, Italy
| | - Anna Capalbo
- Mendel Laboratory, Casa Sollievo della Sofferenza IRCCS, Viale Regina Margherita 261, 00198 Rome, Italy
| | - Barbara Lombardo
- CEINGE Advanced Biotechnology, S.c.a.r.l., Naples, Italy; Department Biochemistry and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Lucio Pastore
- CEINGE Advanced Biotechnology, S.c.a.r.l., Naples, Italy; Department Biochemistry and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | | | - Laura Vicari
- Service of Medical Genetics, Cardarelli Hospital, Naples, Italy
| | | | - Patrizia Friso
- Service of Medical Genetics, Cardarelli Hospital, Naples, Italy
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Lombardo B, Ceglia C, Tarsitano M, Pierucci I, Salvatore F, Pastore L. Identification of a deletion in the NDUFS4 gene using array-comparative genomic hybridization in a patient with suspected mitochondrial respiratory disease. Gene 2013; 535:376-9. [PMID: 24295889 DOI: 10.1016/j.gene.2013.10.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [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: 07/11/2013] [Revised: 10/16/2013] [Accepted: 10/30/2013] [Indexed: 11/17/2022]
Abstract
We evaluated a patient, born after a normal 38-week pregnancy, with psychomotor retardation, poor coordination of ocular movements, recurrent vomiting and severe lactic acidosis. The patient was admitted to hospital at 2 months of age because of a mitochondrial-like syndrome and died at the age of 4.5 months. Array-comparative genomic hybridization (a-CGH) analysis revealed a homozygous deletion in 5q11.2 involving NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18 kDa (NADH-coenzyme Q reductase; NDUFS4). Both parents were heterozygous for the mutation. The array revealed a deletion of ~32kb that includes exon 2 of NDUFS4 subsequently confirmed by real time-PCR and multiplex PCR. NDUFS4 was previously correlated to Leigh syndrome since mutations in this gene block the assembly of complex I. This result demonstrates the relevance of a-CGH screening in patients affected by metabolic disorders of unknown etiology.
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Affiliation(s)
- Barbara Lombardo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; CEINGE-Biotecnologie Avanzate, Naples, Italy.
| | | | | | - Ippolito Pierucci
- U.O.C. di Pediatria, Presidio Ospedaliero dell'Immacolata, Sapri, Italy
| | | | - Lucio Pastore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; CEINGE-Biotecnologie Avanzate, Naples, Italy
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Sanna V, Ceglia C, Tarsitano M, Lombardo B, Coppola A, Zarrilli F, Castaldo G, Di Minno G. Aberrant F8 gene intron 1 inversion with concomitant duplication and deletion in a severe hemophilia A patient from Southern Italy. J Thromb Haemost 2013; 11:195-7. [PMID: 23140572 DOI: 10.1111/jth.12061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- V Sanna
- CEINGE-Biotecnologie Avanzate, Naples Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
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Castaldo G, Cerbone AM, Guida A, Tandurella I, Ingino R, Tufano A, Ceglia C, Di Minno MND, Ruocco AL, Di Minno G. Molecular analysis and genotype-phenotype correlation in patients with antithrombin deficiency from Southern Italy. Thromb Haemost 2012; 107:673-80. [PMID: 22398878 DOI: 10.1160/th11-09-0671] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/27/2011] [Indexed: 12/19/2022]
Abstract
We sequenced the SERPINC1 gene in 26 patients (11 males) with antithrombin (AT) deficiency (22 type I, 4 type II), belonging to 18 unrelated families from Southern Italy. Heterozygous mutations were identified in 15/18 (83.3%) families. Of them, eight were novel mutations, each being identified in one family. Seven clearly cause impaired protein synthesis (four frameshift, one non-stop, one splicing and one 21bp deletion). One, present in a single patient, is a missense mutation thought to be causative because: a) it is absent in 100 chromosomes from controls; b) it involves a highly conserved amino acid, whose change is predicted to impair AT activity; c) no other mutation is present in the propositus. Severe mutations (i.e. nonsense, frameshift, deletions) were invariably identified in type I patients. In type II patients, 3/4 were missense mutations; the fourth leads to a 19 nucleotides shift in the stop codon. In addition to the type of mutation, the co-existence of other predisposing factors in most patients helps explain the severity of the present type I cases (age at first event, recurrence during prophylaxis). In the five families in which there was more than one member affected, the same genotype and a concordant clinical expression of the disease were found. We conclude that the molecular bases of AT deficiency in Southern Italy are different as compared to other geographic areas, and that molecular analysis and the study of the effect of the mutation may help predict the clinical expression of the disease.
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Affiliation(s)
- G Castaldo
- CEINGE-Biotecnologie Avanzate, Naples, Italy
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