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Girardi ACDS, van Opstal Takahashi VN, Vadasz E, Costa CIS, Zachi EC, Vianna-Morgante AM, Passos-Bueno MR. FMR1 premutation in children with autism spectrum disorders: Should additional diagnostic tests be performed? Am J Med Genet A 2022; 188:1334-1337. [PMID: 34981645 DOI: 10.1002/ajmg.a.62624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/15/2021] [Accepted: 12/05/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Cristina De Sanctis Girardi
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Vanessa Naomi van Opstal Takahashi
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Estevão Vadasz
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Claudia Ismania Samogi Costa
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Elaine Cristina Zachi
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto de Psicologia Universidade de São Paulo, São Paulo, Brazil
| | - Angela M Vianna-Morgante
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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2
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Priya PK, Mishra VV, Liehr T, Ziegler M, Tiwari S, Patel A, Chettiar SS, Patel H. Characterization of a complex chromosomal rearrangement involving chromosomes 1, 3, and 4 in a slightly affected male with bad obstetrics history. J Assist Reprod Genet 2018; 35:721-725. [PMID: 29359264 DOI: 10.1007/s10815-018-1117-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022] Open
Affiliation(s)
- Pritti K Priya
- Genetic Division, Department of Obstetrics and Gynaecology, Institute of Kidney Diseases and Research Centre (IKDRC-ITS), Ahmedabad, 380016, India.
| | - Vineet V Mishra
- Department of Obstetrics and Gynaecology, IKDRC, Ahmedabad, Gujarat, India
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Kollegiengasse 10, 07743, Jena, Germany
| | - Monika Ziegler
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Kollegiengasse 10, 07743, Jena, Germany
| | - Stuti Tiwari
- All India Child Development and Genetic Centre, Lawyers Colony, Agra, 282005, India
| | - Alpesh Patel
- Geneexplore Diagnostics and Research Centre Pvt. Ltd., Ahmedabad, India
| | | | - Hetvi Patel
- Department of Obstetrics and Gynaecology, IKDRC, Ahmedabad, Gujarat, India
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3
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Selection of Suitable Reference Genes for Analysis of Salivary Transcriptome in Non-Syndromic Autistic Male Children. Int J Mol Sci 2016; 17:ijms17101711. [PMID: 27754318 PMCID: PMC5085743 DOI: 10.3390/ijms17101711] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 02/08/2023] Open
Abstract
Childhood autism is a severe form of complex genetically heterogeneous and behaviorally defined set of neurodevelopmental diseases, collectively termed as autism spectrum disorders (ASD). Reverse transcriptase quantitative real-time PCR (RT-qPCR) is a highly sensitive technique for transcriptome analysis, and it has been frequently used in ASD gene expression studies. However, normalization to stably expressed reference gene(s) is necessary to validate any alteration reported at the mRNA level for target genes. The main goal of the present study was to find the most stable reference genes in the salivary transcriptome for RT-qPCR analysis in non-syndromic male childhood autism. Saliva samples were obtained from nine drug naïve non-syndromic male children with autism and also sex-, age-, and location-matched healthy controls using the RNA-stabilizer kit from DNA Genotek. A systematic two-phased measurement of whole saliva mRNA levels for eight common housekeeping genes (HKGs) was carried out by RT-qPCR, and the stability of expression for each candidate gene was analyzed using two specialized algorithms, geNorm and NormFinder, in parallel. Our analysis shows that while the frequently used HKG ACTB is not a suitable reference gene, the combination of GAPDH and YWHAZ could be recommended for normalization of RT-qPCR analysis of salivary transcriptome in non-syndromic autistic male children.
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Hemmat M, Yang X, Chan P, McGough RA, Ross L, Mahon LW, Anguiano AL, Boris WT, Elnaggar MM, Wang JCJ, Strom CM, Boyar FZ. Characterization of a complex chromosomal rearrangement using chromosome, FISH, and microarray assays in a girl with multiple congenital abnormalities and developmental delay. Mol Cytogenet 2014; 7:50. [PMID: 25478007 PMCID: PMC4255717 DOI: 10.1186/1755-8166-7-50] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/27/2014] [Indexed: 11/10/2022] Open
Abstract
Complex chromosomal rearrangements (CCRs) are balanced or unbalanced structural rearrangements involving three or more cytogenetic breakpoints on two or more chromosomal pairs. The phenotypic anomalies in such cases are attributed to gene disruption, superimposed cryptic imbalances in the genome, and/or position effects. We report a 14-year-old girl who presented with multiple congenital anomalies and developmental delay. Chromosome and FISH analysis indicated a highly complex chromosomal rearrangement involving three chromosomes (3, 7 and 12), seven breakpoints as a result of one inversion, two insertions, and two translocations forming three derivative chromosomes. Additionally, chromosomal microarray study (CMA) revealed two submicroscopic deletions at 3p12.3 (467 kb) and 12q13.12 (442 kb). We postulate that microdeletion within the ROBO1 gene at 3p12.3 may have played a role in the patient’s developmental delay, since it has potential activity-dependent role in neurons. Additionally, factors other than genomic deletions such as loss of function or position effects may also contribute to the abnormal phenotype in our patient.
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Affiliation(s)
- Morteza Hemmat
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Xiaojing Yang
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Patricia Chan
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Robert A McGough
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Leslie Ross
- Quest Diagnostics, 695 South Broadway, Denver, Colorado 80209, USA
| | - Loretta W Mahon
- Quest Diagnostics, 8401 Fallbrook Avenue , West, Hills, California 91304, USA
| | - Arturo L Anguiano
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Wang T Boris
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Mohamed M Elnaggar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Jia-Chi J Wang
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Charles M Strom
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
| | - Fatih Z Boyar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, San Juan Capistrano, California 92675, USA
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Moreira DP, Griesi-Oliveira K, Bossolani-Martins AL, Lourenço NCV, Takahashi VNO, da Rocha KM, Moreira ES, Vadasz E, Meira JGC, Bertola D, Halloran EO, Magalhães TR, Fett-Conte AC, Passos-Bueno MR. Investigation of 15q11-q13, 16p11.2 and 22q13 CNVs in autism spectrum disorder Brazilian individuals with and without epilepsy. PLoS One 2014; 9:e107705. [PMID: 25255310 PMCID: PMC4177849 DOI: 10.1371/journal.pone.0107705] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 08/21/2014] [Indexed: 11/18/2022] Open
Abstract
Copy number variations (CNVs) are an important cause of ASD and those located at 15q11-q13, 16p11.2 and 22q13 have been reported as the most frequent. These CNVs exhibit variable clinical expressivity and those at 15q11-q13 and 16p11.2 also show incomplete penetrance. In the present work, through multiplex ligation-dependent probe amplification (MLPA) analysis of 531 ethnically admixed ASD-affected Brazilian individuals, we found that the combined prevalence of the 15q11-q13, 16p11.2 and 22q13 CNVs is 2.1% (11/531). Parental origin could be determined in 8 of the affected individuals, and revealed that 4 of the CNVs represent de novo events. Based on CNV prediction analysis from genome-wide SNP arrays, the size of those CNVs ranged from 206 kb to 2.27 Mb and those at 15q11-q13 were limited to the 15q13.3 region. In addition, this analysis also revealed 6 additional CNVs in 5 out of 11 affected individuals. Finally, we observed that the combined prevalence of CNVs at 15q13.3 and 22q13 in ASD-affected individuals with epilepsy (6.4%) was higher than that in ASD-affected individuals without epilepsy (1.3%; p<0.014). Therefore, our data show that the prevalence of CNVs at 15q13.3, 16p11.2 and 22q13 in Brazilian ASD-affected individuals is comparable to that estimated for ASD-affected individuals of pure or predominant European ancestry. Also, it suggests that the likelihood of a greater number of positive MLPA results might be found for the 15q13.3 and 22q13 regions by prioritizing ASD-affected individuals with epilepsy.
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MESH Headings
- Adolescent
- Base Sequence
- Brazil
- Child
- Child Development Disorders, Pervasive/complications
- Child Development Disorders, Pervasive/genetics
- Chromosomes, Human/genetics
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 22/genetics
- DNA Copy Number Variations
- Epilepsy/complications
- Female
- Genomics
- Humans
- Male
- Pedigree
- Polymorphism, Single Nucleotide
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Affiliation(s)
- Danielle P. Moreira
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Karina Griesi-Oliveira
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Ana L. Bossolani-Martins
- Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brasil
| | - Naila C. V. Lourenço
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Vanessa N. O. Takahashi
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Kátia M. da Rocha
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Eloisa S. Moreira
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Estevão Vadasz
- Instituto de Psiquiatria do Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brasil
| | - Joanna Goes Castro Meira
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
| | - Debora Bertola
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
- Instituto da Criança da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brasil
| | - Eoghan O’ Halloran
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Tiago R. Magalhães
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Dublin, Ireland
| | - Agnes C. Fett-Conte
- Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brasil
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brasil
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Guilherme RS, Cernach MCSP, Sfakianakis TE, Takeno SS, Nardozza LMM, Rossi C, Bhatt SS, Liehr T, Melaragno MI. A complex chromosome rearrangement involving four chromosomes, nine breakpoints and a cryptic 0.6-Mb deletion in a boy with cerebellar hypoplasia and defects in skull ossification. Cytogenet Genome Res 2013; 141:317-23. [PMID: 23817307 DOI: 10.1159/000353302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2013] [Indexed: 11/19/2022] Open
Abstract
Constitutional complex chromosomal rearrangements (CCRs) are considered rare cytogenetic events. Most apparently balanced CCRs are de novo and are usually found in patients with abnormal phenotypes. High-resolution techniques are unveiling genomic imbalances in a great percentage of these cases. In this paper, we report a patient with growth and developmental delay, dysmorphic features, nervous system anomalies (pachygyria, hypoplasia of the corpus callosum and cerebellum), a marked reduction in the ossification of the cranial vault, skull base sclerosis, and cardiopathy who presents a CCR with 9 breakpoints involving 4 chromosomes (3, 6, 8 and 14) and a 0.6-Mb deletion in 14q24.1. Although the only genomic imbalance revealed by the array technique was a deletion, the clinical phenotype of the patient most likely cannot be attributed exclusively to haploinsufficiency. Other events must also be considered, including the disruption of critical genes and position effects. A combination of several different investigative approaches (G-banding, FISH with different probes and SNP array techniques) was required to describe this CCR in full, suggesting that CCRs may be more frequent than initially thought. Additionally, we propose that a chain chromosome breakage mechanism may have occurred as a single rearrangement event resulting in this CCR. This study demonstrates the importance of applying different cytogenetic and molecular techniques to detect subtle rearrangements and to delineate the rearrangements at a more accurate level, providing a better understanding of the mechanisms involved in CCR formation and a better correlation with phenotype.
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Affiliation(s)
- R S Guilherme
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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