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Ferrari L, Mangano E, Bonati MT, Monterosso I, Capitanio D, Chiappori F, Brambilla I, Gelfi C, Battaglia C, Bordoni R, Riva P. Digenic inheritance of subclinical variants in Noonan Syndrome patients: an alternative pathogenic model? Eur J Hum Genet 2020; 28:1432-1445. [PMID: 32514133 PMCID: PMC7608271 DOI: 10.1038/s41431-020-0658-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/21/2020] [Accepted: 05/22/2020] [Indexed: 11/22/2022] Open
Abstract
Noonan syndrome (NS) is an autosomal-dominant disorder with variable expressivity and locus heterogeneity. Despite several RAS pathway genes were implicated in NS, 20–30% of patients remain without molecular diagnosis, suggesting the involvement of further genes or multiple mechanisms. Eight patients out of 60, negative for conventional NS mutation analysis, with heterogeneous NS phenotype were investigated by means of target resequencing of 26 RAS/MAPK pathway genes. A trio was further characterized by means of whole-exome sequencing. Protein modeling and in silico prediction of protein stability allowed to identify possible pathogenic RAS pathway variants in four NS patients. A new c.355T>C variant in LZTR1 was found in patient 43. Two patients co-inherited variants in LRP1 and LZTR1 (patient 53), or LRP1 and SOS1 genes (patient 67). The forth patient (56) carried a compound heterozygote of RASAL3 gene variants and also an A2ML1 variant. While these subclinical variants are singularly present in healthy parents, they co-segregate in patients, suggesting their addictive effect and supporting a digenic inheritance, as alternative model to a more common monogenic transmission. The ERK1/2 and SAPK/JNK activation state, assessed on immortalized lymphocytes from patients 53 and 67 showed highest phosphorylation levels compared to their asymptomatic parents. These findings together with the lack of their co-occurrence in the 1000Genomes database strengthen the hypothesis of digenic inheritance in a subset of NS patients. This study suggests caution in the exclusion of subclinical variants that might play a pathogenic role providing new insights for alternative hereditary mechanisms.
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Affiliation(s)
- Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale (BIOMETRA), Università degli Studi di Milano, Segrate, Italy
| | - Eleonora Mangano
- Istituto di Tecnologie Biomediche (ITB) Centro Nazionale delle Ricerche (CNR), ITB-CNR, Segrate, Milano, Italy
| | - Maria Teresa Bonati
- Ambulatorio di Genetica Medica, IRCCS Istituto Auxologico Italiano, Milano, Italy.
| | - Ilaria Monterosso
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale (BIOMETRA), Università degli Studi di Milano, Segrate, Italy
| | - Daniele Capitanio
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milano, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Federica Chiappori
- Istituto di Tecnologie Biomediche (ITB) Centro Nazionale delle Ricerche (CNR), ITB-CNR, Segrate, Milano, Italy
| | | | - Cecilia Gelfi
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milano, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Cristina Battaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale (BIOMETRA), Università degli Studi di Milano, Segrate, Italy.,Istituto di Tecnologie Biomediche (ITB) Centro Nazionale delle Ricerche (CNR), ITB-CNR, Segrate, Milano, Italy
| | - Roberta Bordoni
- Istituto di Tecnologie Biomediche (ITB) Centro Nazionale delle Ricerche (CNR), ITB-CNR, Segrate, Milano, Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale (BIOMETRA), Università degli Studi di Milano, Segrate, Italy.
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Zhou L, Zheng Z, Wu L, Xu C, Wu H, Xu X, Tang S. Molecular delineation of small supernumerary marker chromosomes using a single nucleotide polymorphism array. Mol Cytogenet 2020; 13:19. [PMID: 32514314 PMCID: PMC7251855 DOI: 10.1186/s13039-020-00486-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022] Open
Abstract
Background Defining the phenotype-genotype correlation of small supernumerary marker chromosomes (sSMCs) remains a challenge in prenatal diagnosis. We karyotyped 20,481 amniotic fluid samples from pregnant women and explored the molecular characteristics of sSMCs using a single nucleotide polymorphism (SNP) array. Results Out of the 20,481 samples, 15 abnormal karyotypes with sSMC were detected (frequency: 0.073%) and the chromosomal origin was successfully identified by SNP array in 14 of them. The origin of sSMCs were mainly acrocentric-derived chromosomes and the Y chromosome. Two cases of sSMC combined with uniparental disomy (UPD) were detected, UPD(1) and UPD(22). More than half of the cases of sSMC involved mosaicism (8/15) and pathogenicity (9/15) in prenatal diagnosis. A higher prevalence of mosaicism for non-acrocentric chromosomes than acrocentric chromosomes was also revealed. One sSMC derived from chromosome 3 with a neocentromere revealed a 24.99-Mb pathogenic gain of the 3q26.31q29 region on the SNP array, which presented as an abnormal ultrasound indicating nasal bone hypoplasia. Conclusion The clinical phenotypes of sSMCs are variable and so further genetic testing and parental karyotype analysis are needed to confirm the characteristics of sSMCs. The SNP array used here allows a detailed characterisation of the sSMC and establishes a stronger genotype-phenotype correlation, thus allowing detailed genetic counselling for prenatal diagnosis.
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Affiliation(s)
- Lili Zhou
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Zhaoke Zheng
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Lianpeng Wu
- Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325000 People's Republic of China
| | - Chenyang Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Hao Wu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Xueqin Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Shaohua Tang
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China.,Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325000 People's Republic of China
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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] [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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