Duplication 9p and their implication to phenotype

Background: Trisomy 9p is one of the most common partial trisomies found in newborns. We report the clinical features and cytogenomic findings in five patients with different chromosome rearrangements resulting in complete 9p duplication, three of them involving 9p centromere alterations.Methods: the rearrangements in the patients were characterized by G-banding, SNP-array and fluorescent in situ hybridization (FISH) with different probes.Results: Two patients presented de novo dicentric chromosomes: der(9; 15)t(9; 15)(p11.2;p13) and der(9; 21)t(9; 21) (p13.1;p13.1). One patient presented two concomitant rearranged chromosomes: a der(12)t(9; 12)(q21.13;p13.33) and an psu i(9)(p10) which showed FISH centromeric signal smaller than in the normal chromosome 9. Besides the duplication 9p24.3p13.1, array revealed a 7.3 Mb deletion in 9q13q21.13 in this patient. the break in the psu i(9) (p10) probably occurred in the centromere resulting in a smaller centromere and with part of the 9q translocated to the distal 12p with the deletion 9q occurring during this rearrangement. Two patients, brother and sister, present 9p duplication concomitant to 18p deletion due to an inherited der(18)t(9; 18)(p11.2; p11.31) mat.Conclusions: the patients with trisomy 9p present a well-recognizable phenotype due to facial appearance, although the genotype-phenotype correlation can be difficult due to concomitant partial monosomy of other chromosomes. the chromosome 9 is rich in segmental duplication, especially in pericentromeric region, with high degree of sequence identity to sequences in 15p, 18p and 21p, chromosomes involved in our rearrangements. Thus, we suggest that chromosome 9 is prone to illegitimate recombination, either intrachromosomal or interchromosomal, which predisposes it to rearrangements, frequently involving pericentromeric regions.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo, Dept Morphol & Genet, BR-04023900 São Paulo, BrazilUniv São Paulo, Dept Pathol, Lab Citogen, BR-05403000 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Morphol & Genet, BR-04023900 São Paulo, BrazilFAPESP: 2012/51150-0FAPESP: 2012/15572-7Web of Scienc

Cytogenomic study and evaluation of gene expression in patients with 22q11.2 deletion

Introdução: A síndrome da deleção 22q11.2 é decorrente de perdas de segmentos de DNA do cromossomo 22, delimitadas na maioria das vezes por regiões com low copy repeats (LCRs), sendo mais frequentes as deleções de 3 e 1,5 Mb. O fenótipo pode ser variável em pacientes com deleções de extensões semelhantes, podendo também ser observados fenótipos similares em pacientes com deleções distintas na região 22q11.2, mesmo não sobrepostas. Objetivos: Investigação citogenômica de pacientes com o espectro clínico da síndrome da deleção 22q11.2 quanto à presença da deleção. Determinar a extensão das deleções identificadas. Avaliar a expressão gênica global. Analisar as interações entre genes diferencialmente expressos e processos biológicos enriquecidos. Casuística e Métodos: Uma amostra de 53 pacientes com o fenótipo sugestivo da síndrome da deleção 22q11.2 foi analisada quanto ao cariótipo e MLPA (Multiplex Ligation-dependent Probe Amplification). Dentre esses, seis apresentaram deleção. A esse grupo foram incluídos 24 pacientes com deleção previamente detectada, totalizando uma amostra de 30 pacientes. Em 29 pacientes, a extensão da deleção foi refinada por microarray genômico, e em 14, a expressão gênica foi avaliada em relação aos seus respectivos controles, pareados por idade e sexo. As interações entre genes e os processos biológicos enriquecidos foram investigados pelos softwares GeneMania e Enrichr. Resultados: Todos os pacientes apresentaram cariótipos normais, com exceção de uma que apresentou translocação não equilibrada t(6;22), resultando em deleção 22q11.2. A MLPA revelou deleções em seis dentre os 53 pacientes com fenótipo sugestivo da síndrome da deleção 22q11.2. As deleções encontradas na amostra de 30 pacientes foram de 3 Mb (22 pacientes), de 1,5 Mb (4 pacientes) e deleções atípicas (4 pacientes). Os microarrays genômicos revelaram variação dos pontos de quebra entre as deleções. O estudo da expressão gênica por microarray identificou redução da expressão de 48 transcritos, correspondentes tanto a genes da região deletada, quanto a genes das regiões que flanqueiam a região da deleção, e de outros cromossomos. Conclusões: A MLPA identificou deleções tanto típicas como atípicas. A redução da expressão de genes da região deletada, mas também de genes flanqueadores da deleção e de genes de outros cromossomos, indicam que mecanismos relacionados a um efeito de posição e ao reposicionamento da cromatina no núcleo devem estar relacionados à alteração da expressão desses genes. A avaliação da coexpressão mostrou uma relação entre os genes da região deletada e aqueles adjacentes a ela, entre genes das regiões das deleções de 1,5 e 3 Mb, bem como entre genes do cromossomo 22 e de outras regiões genômicas, revelando uma possível relação biológica, que poderia esclarecer a similaridade fenotípica entre pacientes com diferentes deleções. Dessa forma, este estudo contribuiu para uma melhor compreensão tanto dos mecanismos moleculares quanto da participação de genes na complexa rede de regulação gênica responsável pelo fenótipo característico da síndrome da deleção 22q11.Introduction: 22q11.2 deletion syndrome results from a hemizygous deletion of chromosome 22 usually flanked by low copy repeat (LCR) regions, the 3 and 1.5 Mb deletions being the most frequent. The phenotype may be variable in patients with similar deletions, and similar phenotypes may also be observed in patients with different size deletions in the 22q11.2 region, even without overlap. Objective: Cytogenomic investigation of the presence of deletion in patients with the 22q11.2 deletion syndrome clinical spectrum. In patients where the deletion was detected, determination of deletion size, of gene expression, and analysis of gene interactions and enriched biological processes. Methods: Karyotyping and MLPA was performed in 53 patients with a phenotype suggestive of 22q11.2 deletion syndrome, for deletion screening, from which six patients were found to have deletion. These were added to 24 previously deletion detected patients, totaling 30 for the study. From these, 29 patients had the size of deletion assessed by genomic microarray and 14 were evaluated for gene expression relative to their respective controls, who were matched for age and sex. Interactions between genes and evaluation of enriched biological processes were conducted by GeneMania and Enrichr software. Results: Karyotypes were normal in most patients, with only one showing a translocation involving chromosomes 6 and 22, resulting in 22q11.2 deletion. MLPA revealed deletions in six patients out of 53 patients with phenotype suggestive of 22q11.2 deletion syndrome. The deletions found in the sample of 30 patients were: 3 Mb (22 patients), 1.5 Mb (4 patients) and atypical deletions (4 patients). Variable breakpoints among the deletions were revealed by genomic microarray. The study of gene expression by microarray identified reduced expression of 48 transcripts corresponding to genes of the 22q deleted region, and also of genes flanking the deleted region or genes located in other chromosomes. Conclusions: Most patients had normal karyotypes, and only one had a translocation. The MLPA detected deletions in patients, both typical and atypical, providing an advantage over FISH, which does not identify atypical deletions. Deletions had their size refined by genomic microarray, confirming breakpoint variations among deletions. In addition to the reduced expression of the hemizygous genes, there was a reduction in the expression of genes flanking the deletion, and also of genes of other chromosomes. These data indicate a position effect and the chromatin repositioning in the nucleus, mechanisms possibly related to the altered expression of these genes. The coexpression evaluation showed a relationship between the genes of the deleted region and those adjacent to it, between the genes of 1.5 and 3 Mb deletions regions, and between genes of chromosome 22 and of other genomic regions. These data revealed a possible biological relationship, which could explain the phenotypic similarity between patients with different size deletions. This study contributes to the understanding of the molecular mechanisms involved in the complex network of gene regulation, which is responsible for the characteristic phenotype of the 22q11.2 deletion syndrome.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

CEDNIK syndrome in a Brazilian patient with compound heterozygous pathogenic variants.

peer reviewedCEDNIK (Cerebral Dysgenesis, Neuropathy, Ichthyosis, and Keratoderma) syndrome is a neuro ichthyotic syndrome characterized by a clinical constellation of features including severe developmental delay, microcephaly, and facial dysmorphism. Here, we report the clinical and molecular characterization of a patient with CEDNIK syndrome harboring two compound heterozygous variants in the SNAP29 gene. The patient presents a combination of a loss-of-function SNAP29 mutation and a ∼370 kb 22q11.2 deletion, each of these genetic variants inherited from one of the parents. This report provides detailed data of a patient with unprecedented genetic events leading to the CEDNIK phenotype and may contribute to the elucidation of this rare condition

Genetic mechanisms leading to primary amenorrhea in balanced X-autosome translocations

Objective: To map the X-chromosome and autosome breakpoints in women with balanced X-autosome translocations and primary amenorrhea, searching candidate genomic loci for female infertility.Design: Retrospective and case-control study.Setting: University-based research laboratory.Patient(s): Three women with balanced X-autosome translocation and primary amenorrhea.Intervention(s): Conventional cytogenetic methods, genomic array, array painting, fluorescence in situ hybridization, and quantitative reverse transcription-polymerase chain reaction.Main Outcome Measure(s): Karyotype, copy number variation, breakpoint mapping, and gene expression levels.Result(s): All patients presented with breakpoints in the Xq13q21 region. in two patients, the X-chromosome breakpoint disrupted coding sequences (KIAA2022 and ZDHHC15 genes). Although both gene disruptions caused absence of transcription in peripheral blood, there is no evidence that supports the involvement of these genes with ovarian function. the ZDHHC15 gene belongs to a conserved syntenic region that encompasses the FGF16 gene, which plays a role in female germ line development. the break in the FGF16 syntenic block may have disrupted the interaction between the FGF16 promoter and its cis-regulatory element. in the third patient, although both breakpoints are intergenic, a gene that plays a role in the DAX1 pathway (FHL2 gene) flanks distally the autosome breakpoint. the FHL2 gene may be subject to position effect due to the attachment of an autosome segment in Xq21 region.Conclusion(s): the etiology of primary amenorrhea in balanced X-autosome translocation patients may underlie more complex mechanisms than interruption of specific X-linked candidate genes, such as position effect. the fine mapping of the rearrangement breakpoints may be a tool for identifying genetic pathogenic mechanisms for primary amenorrhea. (C) 2015 by American Society for Reproductive Medicine.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo, Dept Morphol & Genet, Div Genet, BR-04023900 São Paulo, SP, BrazilUniversidade Federal de São Paulo, Dept Gynecol, BR-04023900 São Paulo, SP, BrazilHosp Servidor Publ Estado São Paulo, Div Genet, São Paulo, BrazilUniv Jena, Inst Human Genet, Jena Univ Hosp, Jena, GermanyUniversidade Federal de São Paulo, Dept Morphol & Genet, Div Genet, BR-04023900 São Paulo, SP, BrazilUniversidade Federal de São Paulo, Dept Gynecol, BR-04023900 São Paulo, SP, BrazilFAPESP: 2011/51690-1Web of Scienc