Novel rearrangements between different chromosomes with direct impact on the diagnosis of 5p- syndrome

Objectives: Copy Number Variations (CNVs) in the human genome account for common populational variations but can also be responsible for genetic syndromes depending on the affected region. Although a deletion in 5p is responsible for a syndrome with highly recognizable phenotypical features, other chromosomal abnormalities might overlap phenotypes, especially considering that most studies in 5p use traditional cytogenetic techniques and not molecular techniques. Methods: The authors have investigated 29 patients with clinical suspicion of 5p- syndrome using Chromosomal Microarray (CMA), and have gathered information on previous tests, clinical signs, symptoms, and development of the patients. Results: The results showed 23 pure terminal deletions, one interstitial deletion, one deletion followed by a 3 Mb duplication in 5p, three cases of 5p deletion concomitant to duplications larger than 20 Mb in chromosomes 2, 9, and 18, and one 5p deletion with a chromosome Y deletion. CMA showed relevant CNVs not typically associated with 5p- that may have contributed to the final phenotype in these patients. Conclusions: The authors have identified three novel rearrangements between chromosomes 5 and 2 (Patient 27), 5 and 18 (Patient 11), and 5 and Y (Patient 22), with breakpoints and overlapped phenotypes that were not previously described. The authors also highlight the need for further molecular investigation using CMA, in different chromosomes beyond chromosome 5 (since those cases did not show only the typical deletion expected for the 5p- syndrome) to explain discordant chromosomal features and overlapped phenotypes to unravel the cause of the syndrome in atypical cases

Cytogenomic assessment of the diagnosis of 93 patients with developmental delay and multiple congenital abnormalities: The Brazilian experience

OBJECTIVE: The human genome contains several types of variations, such as copy number variations, that can generate specific clinical abnormalities. Different techniques are used to detect these changes, and obtaining an unequivocal diagnosis is important to understand the physiopathology of the diseases. The objective of this study was to assess the diagnostic capacity of multiplex ligation-dependent probe amplification and array techniques for etiologic diagnosis of syndromic patients. METHODS: We analyzed 93 patients with developmental delay and multiple congenital abnormalities using multiplex ligation-dependent probe amplifications and arrays. RESULTS: Multiplex ligation-dependent probe amplification using different kits revealed several changes in approximately 33.3% of patients. The use of arrays with different platforms showed an approximately 53.75% detection rate for at least one pathogenic change and a 46.25% detection rate for patients with benign changes. A concomitant assessment of the two techniques showed an approximately 97.8% rate of concordance, although the results were not the same in all cases. In contrast with the array results, the MLPA technique detected ∼70.6% of pathogenic changes. CONCLUSION: The obtained results corroborated data reported in the literature, but the overall detection rate was higher than the rates previously reported, due in part to the criteria used to select patients. Although arrays are the most efficient tool for diagnosis, they are not always suitable as a first-line diagnostic approach because of their high cost for large-scale use in developing countries. Thus, clinical and laboratory interactions with skilled technicians are required to target patients for the most effective and beneficial molecular diagnosis

Molecular-genetic profile of patients with epidermolysis bullosa using next-generation sequencing

Epidermólise bolhosa (EB) hereditária é o nome de um grupo heterogêneo de doenças genéticas raras que levam ao aparecimento recorrente de bolhas que se formam espontaneamente ou como resposta a traumas mínimos. O diagnóstico dos diferentes tipos de EB atualmente é estabelecido a partir da história clínica e do modo de transmissão da doença aliado ao mapeamento antigênico de imunofluorescência ou microscopia eletrônica de transmissão. No entanto, em alguns casos, os resultados dos testes histológicos são inconclusivos, dificultando o diagnóstico preciso. Objetivo: Desenvolver um painel específico de sequenciamento de nova geração (NGS) para os genes associados à Epidermólise Bolhosa. Metodologia: Amostras do sangue periférico de pacientes com diagnóstico clínico de EB foram sequenciadas com a plataforma Illumina® utilizando um painel multigênico customizado (Agilent Technologies). Resultados e discussão: Identificamos 33 variantes distribuídas em 7 genes nos 45 pacientes. As variantes foram classificadas seguindo os critérios do ACMG. Por meio da aplicação do painel foi possível classificar o tipo de EB baseados na avaliação do perfil genético-molecular, sendo ainda realizada a reclassificação de pacientes em casos onde as hipóteses clínicas iniciais e/ou imunomapeamento estavam equivocados. Conclusão: O NGS mostrou-se útil na tarefa de encontrar variantes patológicas, classificar corretamente os tipos de EB, e concluir o diagnóstico genético dos pacientesIntroduction: Hereditary epidermolysis bullosa (EB) is the name of a heterogeneous group of rare genetic diseases that lead to the recurrent appearance of blisters that form spontaneously or in response to minimal trauma. The diagnosis of different types of EB is currently based on the mode of transmission based on the clinical history and the mode of transmission of the disease combined with antigenic or electronic microscogenic mapping of transmission. However, in some cases, the results of histological tests are inconclusive, making accurate diagnosis difficult. Objective: To develop a specific multigene next generation sequencing (NGS) panel for the genes associated with Epidermolysis Bullosa. Methodology: Agilent Technologies. Results and discussion: What are the variants (in genes?) that are different (in?) in 14 patients. Of these, following the ACMG results patients, 13 were classified as pathogenic and 5 application of this panel was possible to diagnose Conclusion: NGS proved to be useful in the task of finding pathological variants, correctly classifying the types and subtypes of EB, and determining the diagnosis. patients genetic

Cytogenetics investigation in 151 Brazilian infertile male patients and genomic analysis in selected cases: experience of 14 years in a public genetic service

Abstract Objectives Male infertility accounts for approximately 30% of cases of reproductive failure. The characterization of genetic variants using cytogenomic techniques is essential for the adequate clinical management of these patients. We aimed to conduct a cytogenetic investigation of numerical and structural rearrangements and a genomic study of Y chromosome microdeletions/microduplications in infertile men derived from a single centre with over 14 years of experience. Results We evaluated 151 infertile men in a transversal study using peripheral blood karyotypes and 15 patients with normal karyotypes through genomic investigation by multiplex ligation-dependent probe amplification (MLPA) or polymerase chain reaction of sequence-tagged sites (PCR-STS) techniques. Out of the 151 patients evaluated by karyotype, 13 presented chromosomal abnormalities: two had numerical alterations, and 11 had structural chromosomal rearrangements. PCR-STS detected a BPY2 gene region and RBMY2DP pseudogene region microdeletion in one patient. MLPA analysis allowed the identification of one patient with CDY2B_1 and CDY2B_2 probe duplications (CDY2B and NLGN4Y genes) and one patient with BPY2_1, BPY2_2, and BPY2_4 probe duplications (PRY and RBMY1J genes)

Cytogenomic assessment of the diagnosis of 93 patients with developmental delay and multiple congenital abnormalities: The Brazilian experience

OBJECTIVE: The human genome contains several types of variations, such as copy number variations, that can generate specific clinical abnormalities. Different techniques are used to detect these changes, and obtaining an unequivocal diagnosis is important to understand the physiopathology of the diseases. The objective of this study was to assess the diagnostic capacity of multiplex ligation-dependent probe amplification and array techniques for etiologic diagnosis of syndromic patients. METHODS: We analyzed 93 patients with developmental delay and multiple congenital abnormalities using multiplex ligation-dependent probe amplifications and arrays. RESULTS: Multiplex ligation-dependent probe amplification using different kits revealed several changes in approximately 33.3% of patients. The use of arrays with different platforms showed an approximately 53.75% detection rate for at least one pathogenic change and a 46.25% detection rate for patients with benign changes. A concomitant assessment of the two techniques showed an approximately 97.8% rate of concordance, although the results were not the same in all cases. In contrast with the array results, the MLPA technique detected ∼70.6% of pathogenic changes. CONCLUSION: The obtained results corroborated data reported in the literature, but the overall detection rate was higher than the rates previously reported, due in part to the criteria used to select patients. Although arrays are the most efficient tool for diagnosis, they are not always suitable as a first-line diagnostic approach because of their high cost for large-scale use in developing countries. Thus, clinical and laboratory interactions with skilled technicians are required to target patients for the most effective and beneficial molecular diagnosis