Cytogenomic Microarray Testing

Cytogenomic microarray testing allows the detection of submicroscopic genomic rearrangements, commonly denominated copy number variations (CNVs) that are implicated with many neurodevelopmental disorders, dysmorphic features, multiple congenital anomalies, hematological and solid tumors, and complex disorders and traits in both humans and animals. On the other hand, this approach is also widely used for the identification of structural variations that are applied as a biomarker in pharmacogenomics, agriculture, and animal selection and breeding. The chromosomal microarray analysis (CMA) has been applied for over a decade to screen for submicroscopic genomic gains and losses in DNA sample in both diagnostic and functional scenarios. Herein, we present an overview of the fundamental concepts of cytogenomics and its potential application in human genetic diagnosis, agrigenomics, mutagenesis, and pharmacogenomics

Diagnosis of de novo 17p11.2 microduplication - potocki-lupski syndrome identified by chromosomal microarray analysis: a case report / Diagnóstico de novo 17p11.2 microduplicação - potocki-lupski síndrome identificada por análise de microarray chromosomal: um relatório de caso

Potocki-Lupski Syndrome is a continuous gene syndrome caused by the microduplication of 3.7 Mb segment at 17p11.2 characterized by developmental delay, intellectual disability, the developmental deficit for psychomotor and expressive speech, autistic features, obsessive-compulsive behaviors, and attention deficit. Using CMA, we detected the first de novo 3.7 Mb microduplication at 17p11.2 in a boy with an intellectual disability from Central Brazil

Diagnostic of Chormosome 7Q11,23 Duplication Syndrome - a case report

Resumo: a Síndrome da Duplicação do Cromossomo 7q11.23, também conhecida como Síndrome da duplicação de WBS, é uma desordem rara causada pela duplicação de um segmento de 1.5 Mb e caracterizada por deficiência intelectual, dificuldade na fala e anomalias craniofaciais moderadas. Ao realizar a técnica de CMA em amostras de uma família que tem uma criança com deficiência intelectual, foi observado uma microduplicação de novo de 1.428,9 Kbp no cromossomo 7q11.3. Palavras-chave: CNV. Deficiência Intelectual. Microarranjo. Síndrome da Duplicação de Williams-Beuren

Increased rate of genetic diagnosis of patients from the identification of CNVs, by CMA, involving genes implicated in the clinical manifestation of intellectual disability

Submitted by Luciana Ferreira ([email protected]) on 2019-06-07T13:57:58Z No. of bitstreams: 2 Tese - Irene Plaza Pinto - 2019.pdf: 6618641 bytes, checksum: 30719194565b9fbbb50b2c5986253787 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Approved for entry into archive by Luciana Ferreira ([email protected]) on 2019-06-10T14:47:32Z (GMT) No. of bitstreams: 2 Tese - Irene Plaza Pinto - 2019.pdf: 6618641 bytes, checksum: 30719194565b9fbbb50b2c5986253787 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Made available in DSpace on 2019-06-10T14:47:32Z (GMT). No. of bitstreams: 2 Tese - Irene Plaza Pinto - 2019.pdf: 6618641 bytes, checksum: 30719194565b9fbbb50b2c5986253787 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2019-05-27Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESConselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPqFundação de Amparo à Pesquisa do Estado de Goiás - FAPEGIntellectual disability (ID) is characterized by significant impairment in both cognitive and adaptive functions, originating before the age of 18 years. In addition, it is a common phenotype sign in a cluster of heterogeneous syndromic or non-syndromic disorders, associated with some comorbidities such as autism and congenital malformations. In the worldwide, ID affects around 1–3% of the general population and in Brazil ID affects approximately 0.8% of the population. The Copy number variations account for about 15– 20% of children with unexplained ID, compromising the functioning of several genes, with more than 1,416 genes described as causative of this phenotype sign. The aim of the study was to evaluate the occurrence of CNVs, identified by CMA with the size filter of < 100 kb, harboring genes functionally associated with ID in patients from SUS with a clinical diagnosis of ID referred for the genetic diagnosis. During January 2013 to December 2016, GTG banding karyotype was performed in 325 patients with ID, achieve the genetic diagnostic in 57.2%, demonstrating to be an important screening approach for patients with DI. However, 42,8% of the patients showed the karyotype with no visible numerical or structural alterations. The CMA analysis with the size filter of ≥ 100 kb was performed in these patients, where it was possible to elucidate the genetic diagnose in 29.8% of the patients, demonstrating 7,1 % of the increment on the diagnostic. All the cases remained without a diagnosis were submitted to the CMA analysis with size filter of < 100 kb, where it was identified loss CNVs in regions harboring CNTNAP2, FGF13, MID1, MID2, SHANK3, IL1RAPL1, DMD, and PAK3 genes. The reduction of the size filter demonstrated an increase of 12% in the ratio of diagnosis, expanding the spectrum of CNVs identification in regions which harboring genes related to the clinical manifestation of ID. The application of both GTG banding and CMA with the size filter of ≥ 100 kb and later the size filter of < 100 kb allowed an increase in the genetic diagnosis of ID and comorbidities, giving a broad understanding of the genetic aspects related to these conditions and allowing the adequate management of families. Finally, the genetic counseling provides a better understanding of the genetic causes of ID, the familial implications of the genetic contribution and the chance of recurrence.Deficiência intelectual (DI) é reconhecida como um transtorno do desenvolvimento neurológico, caracterizado por diminuição significativa em ambas funções cognitivas e adaptativas, originada antes dos 18 anos de idade. Estima-se que em torno de 1–3% das crianças ao redor do mundo são afetadas pela DI e que no Brasil acomete aproximadamente 0,8% da população. As variações no número de cópias (CNVs) são responsáveis por cerca de 15–20% dos casos de DI, que podem comprometer o funcionamento de diversos genes. O objetivo do estudo foi avaliar a ocorrência de CNVs, identificadas pelo CMA com filtro de tamanho < 100 kb, que abrigassem genes funcionalmente associados à DI em pacientes do SUS com diagnóstico clínico de DI. Durante o período de janeiro 2013 a dezembro de 2016, foi realizado o cariótipo por bandeamento GTG em 325 pacientes com indicação clínica de DI, chegando ao diagnóstico genético em 57,2% dos pacientes, demonstrando ser uma importante metodologia de triagem para os pacientes com DI. No entanto, 42,8% dos pacientes apresentaram o cariótipo sem alterações estruturais ou numéricas. Foi realizado nestes pacientes o CMA com filtro de tamanho ≥ 100 kb, onde foi possível elucidar o diagnóstico genético em 29,8% dos casos, apresentando um incremento na taxa de diagnóstico de 7,1%. Os casos que permaneceram sem elucidação, foram submetidos ao CMA com filtro de tamanho < 100 kb, no qual foram identificadas CNVs de perda em regiões que continham os genes CNTNAP2, FGF13, MID1, MID2, SHANK3, IL1RAPL1, DMD e PAK3. A redução do filtro de tamanho demonstrou um incremento na taxa de diagnóstico em 12%, ampliando o espectro de identificação de CNVs presentes em regiões que abrigam genes implicados à manifestação clínica da DI. A aplicação em conjunto das metodologias cariótipo por bandeamento GTG e CMA com filtro de tamanho ≥ 100 kb e posteriormente filtro de tamanho < 100 kb, permitiu um aumento no diagnóstico genético da DI e outras comorbidades, promovendo uma compreensão mais ampla dos aspectos genéticos relacionados à essas afecções e possibilitando um manejo adequado das famílias. Finalmente, o acesso ao aconselhamento genético proporciona uma melhor compreensão das causas genéticas da DI, as implicações familiares da contribuição genética e a chance de recorrência

A importância dos resultados do CMA no aconselhamento genético das famílias com probandos apresentando deficiência intelectual.

Made available in DSpace on 2016-08-10T10:38:52Z (GMT). No. of bitstreams: 1 IRENE PLAZA PINTO.pdf: 6549908 bytes, checksum: 3185800a3487b8801d64b261984cf289 (MD5) Previous issue date: 2015-02-10Intellectual disability is characterized by a significant decrease in both cognitive and adaptive functions, affecting 1-3% of the general population. Worldwide is a major socioeconomic problem, with a highly heterogeneous and variable etiology, which may include environmental factors, disorders Mendelian and chromosomal abnormalities, presented alone or in combination. Single gene and chromosomal disorders are considered the cause of intellectual deficiency in 7-37% of cases, while submicroscopic copy number variation occur in 5-15% of cases, especially when associated with multiple congenital abnormalities, and-or dysmorphisms. Genomic microarrays have been extensively used in the studying the genetic causes of intellectual disability, and the chromosomal microarray analysis is recommended as the first-tier cytogenetic diagnostic test for patients with intellectual disability-global developmental delay, autism spectrum disorders and-or multiple congenital anomalies. Genetic counseling is a process that deals with the occurrence or risk of occurrence of a genetic disorder in a family, helping them to understand the contribution of this heritage, involving education and reproductive aspects. The goals include facilitation of informed autonomous choices, education, which includes information on options (available, risks and limitations of those options), as well as provision of emotional support. Promoting, thus, autonomy and adaptation to the diagnosis, with the central tenet the nondirectiveness, requiring the genetic counselor to maintain a neutral stance, supporting and respecting the patient s personal values and decisions. Families of people diagnosed with genetic disorders need to be aware of the importance of going through the process of genetic counseling, and this should be done continuously and according to the need that the facts indicate, with the primary objective the promotion of health and the quality of life.Deficiência intelectual é caracterizada por uma diminuição significativa em ambas funções cognitivas e adaptativas, afetando de 1 3 % da população em geral. É mundialmente um dos principais problemas sócio-econômicos, com uma etiologia altamente heterogênea e variável, podendo incluir fatores ambientais, desordens mendelianas e anormalidades cromossômicas, apresentados sozinhos ou combinados. Desordens de um único gene e cromossômicas são consideradas a causa de deficiência intelectual em 7-37% dos casos, enquanto que variação número de cópias submicroscópicas ocorrem em 5-15% dos casos, especialmente quando estão associadas com anormalidades congênitas múltiplas e-ou dismorfismos. Microarranjos genômicos têm sido extensivamente usados no estudo das causas genéticas da deficiência intelectual, sendo a análise cromossômica em microarranjos recomendada como teste diagnóstico de primeira escolha para pacientes com deficiência intelectual-atraso no desenvolvimento global, desordem do espectro do autista e-ou anormalidades congênitas múltiplas. Aconselhamento genético é um processo que lida com a ocorrência ou o risco de ocorrência de uma doença genética na família, ajudando-a a compreender a contribuição desta herança, envolvendo aspectos educacionais e reprodutivos. Sua prática visa a facilitação de escolhas autônomas informadas, num processo educacional, incluindo informações sobres as opções (disponibilidade, riscos e limitações destas opções), bem como o fornecimento de um suporte emocional. Promovendo, dessa forma, autonomia e adaptação ao diagnóstico, tendo como dogma central a não diretividade, exigindo do conselheiro geneticista uma posição neutra, apoiando e respeitando valores e decisões pessoais do paciente. Famílias de pessoas diagnosticadas com doenças genéticas precisam ser esclarecidas sobre a importância de passarem pelo processo de aconselhamento genético, e este deve ser feito de forma contínua e de acordo com a necessidade que os fatos indicarem, tendo o objetivo primário a promoção da saúde e a qualidade de vida

The genetic counseling service in Brazil: A scoping review

Scoping review to evaluate the current scenario of the genetic counseling service in Brazil. To conduct this review, there will be used PRISMA-ScR and JBI as references. The search for bibliographic content will be carried out in the following databases: Bibliotéca Virtual da Saúde (BVS), PubMed, Web of Science (WofS) and Scopus. To filter the articles, the advanced search tool of all selected databases will be used, applying the Title/Abstract filter to the following descriptors: Genetic counseling/genetic counselling/aconselhamento genético and Brasil/Brazil. The obtained studies will be exported to Rayyan software to remove the duplicated and apply the eligibility criteria. The data extraction will be performed by two more researschers in order to assure the extracted evidence. A qualitative (narrative) synthesis of the selected studies’ data will be provided, describing the results that each author found about the service of genetic counseling in Brazil. All the data will be grouped according to the type of evidence and date of publication

Mosaic Tetrasomy of 9p24.3q21.11 postnatally identified in an infant born with multiple congenital malformations: a case report

Abstract Background Supernumerary Marker Chromosomes consist in structurally abnormal chromosomes, considered as an extra chromosome in which around 70% occur as a de novo event and about 30% of the cases are mosaic. Tetrasomy 9p is a rare chromosomal abnormality described as the presence of a supernumerary isochromosome 9p. Clinical features of tetrasomy 9p include a variety of physical and developmental abnormalities. Case presentation Herein, we reported a postnatal case of a newborn who died in early infancy with multiple congenital malformations due to a mosaic de novo tetrasomy 9p detected by Chromosomal Microarray Analysis. Conventional cytogenetics analysis of the proband was 47,XY,+mar[45]/46,XY[5]. The parental karyotypes presented no visible numerical or structural alterations. Microarray Analysis of the proband revealed that the marker chromosome corresponded to a mosaic de novo gain at 9p24.3q21.11. Conclusions Chromosomal Microarray Analysis was helpful to identify the origin of the supernumerary marker chromosome and it was a powerful tool to carry out genetic diagnostic, guiding the medical diagnosis. Furthermore, the CMA allowed observing at the first time in Central Brazil the tetrasomy 9p and partial tetrasomy 9q in mosaic, encompassing a large duplicated region with several morbid genes, in an infant with multiple congenital malformations

Diagnostic yield of patients with undiagnosed intellectual disability, global developmental delay and multiples congenital anomalies using karyotype, microarray analysis, whole exome sequencing from Central Brazil

Intellectual Disability (ID) is a neurodevelopmental disorder that affects approximately 3% of children and adolescents worldwide. It is a heterogeneous and multifactorial clinical condition. Several methodologies have been used to identify the genetic causes of ID and in recent years new generation sequencing techniques, such as exome sequencing, have enabled an increase in the detection of new pathogenic variants and new genes associated with ID. The aim of this study was to evaluate exome sequencing with analysis of the ID gene panel as a tool to increase the diagnostic yield of patients with ID/GDD/MCA in Central Brazil, together with karyotype and CMA tests. A retrospective cohort study was carried out with 369 patients encompassing both sexes. Karyotype analysis was performed for all patients. CMA was performed for patients who did not present structural and or numerical alterations in the karyotype. Cases that were not diagnosed after performing karyotyping and CMA were referred for exome sequencing using a gene panel for ID that included 1,252 genes. The karyotype identified chromosomal alterations in 34.7% (128/369). CMA was performed in 83 patients who had normal karyotype results resulting in a diagnostic yield of 21.7% (18/83). Exome sequencing with analysis of the ID gene panel was performed in 19 trios of families that had negative results with previous methodologies. With the ID gene panel analysis, we identified mutations in 63.1% (12/19) of the cases of which 75% (9/12) were pathogenic variants,8.3% (1/12) likely pathogenic and in 16.7% (2/12) it concerned a Variant of Uncertain Significance. With the three methodologies applied, it was possible to identify the genetic cause of ID in 42.3% (156/369) of the patients. In conclusion, our studies show the different methodologies that can be useful in diagnosing ID/GDD/MCA and that whole exome sequencing followed by gene panel analysis, when combined with clinical and laboratory screening, is an efficient diagnostic strategy

The Identification of Microdeletion and Reciprocal Microduplication in 22q11.2 Using High-Resolution CMA Technology

The chromosome 22q11.2 region has long been implicated in genomic diseases. Some genomic regions exhibit numerous low copy repeats with high identity in which they provide increased genomic instability and mediate deletions and duplications in many disorders. DiGeorge Syndrome is the most common deletion syndrome and reciprocal duplications could be occurring in half of the frequency of microdeletions. We described five patients with phenotypic variability that carries deletions or reciprocal duplications at 22q11.2 detected by Chromosomal Microarray Analysis. The CytoScan HD technology was used to detect changes in the genome copy number variation of patients who had clinical indication to global developmental delay and a normal karyotype. We observed in our study three microdeletions and two microduplications in 22q11.2 region with variable intervals containing known genes and unstudied transcripts as well as the LCRs that are often flanking and within this genomic rearrangement. The identification of these variants is of particular interest because it may provide insight into genes or genomic regions that are crucial for specific phenotypic manifestations and are useful to assist in the quest for understanding the mechanisms subjacent to genomic deletions and duplications