Investigation of changes in the number of DNA copies (Copy Number Variations, CNVs) in patients with clinical suspicion of Velocardiofacial Syndrome

Orientadores: Vera Lúcia Gil da Silva Lopes, Milena SimioniTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências MédicasResumo: A Síndrome Velocardiofacial (SVCF) tem prevalência de ~1:4.000 nascimentos e apresenta espectro fenotípico variável, incluindo defeitos cardíacos congênitos (DCC). Microdeleções de ~3 Mb em 22q11.2 representam a principal causa, entretanto deleções atípicas nesta região têm sido relatadas, assim como fenótipos similares associados a variações no número de cópias do DNA (Copy number variations, CNVs) em outras regiões cromossômicas. Esta proposta objetiva mapear os pontos de quebra da região 22q11.2 e investigar CNVs em outras regiões do genoma em pacientes com a deleção 22q11.2 confirmada previamente (Grupo I) e investigar CNVs no genoma de pacientes sem a deleção 22q11.2 (Grupo II). Foram investigados 108 pacientes (30 do Grupo I e 78 do Grupo II) com suspeita clínica da SVCF e DCC por Hibridação Genômica em arrays (array Genomic Hybridization- aGH). Para o Grupo I, o tamanho da deleção 22q11.2 proximal variou de 1,8 Mb a 3,3 Mb em 28 casos, sendo que um apresentou a deleção entre as LCRs (Low Copy Repeats) A-B e os demais 27 entre as LCRs A-D (região tipicamente deletada). Dois casos apresentaram deleções atípicas em 22q11.2: 3,6 Mb entre as LCRs B-F, elvolvendo as regiões 22q11.2 proximal e distal; e 1,5 Mb entre as LCRs D-E, envolvendo a região 22q11.2 distal. Além disso, foram observadas dez CNVs ? 300 kb relevantes fora da região 22q11.2, incluindo uma deleção em 11q14.3 e duplicações em 2q24.1-q24.2, 3p22.1, 5p15.2, 5q11.1, 6p21.2, 7p11.2, 15q13.3, 16q23.3 e Xp21.1. Para o Grupo II, foi observado um total de 25 CNVs ? 300 Kb relevantes. Destas, nove CNVs já foram descritas na literatura, incluindo deleções em 4q35.1-q35.2, 5p15.1-p15.33, 8p23.1, 10q22.3-q23.2, 16p11.2, 17q12 e 22q13.33; e duplicações em 3p26.3 e 3q26.2. As variações gênicas dentro dos pontos de quebra da região deletada 22q11.2, bem como as CNVs observadas em outras regiões cromossômicas contribuem para a variabilidade fenotípica observada nesta síndrome e confirmam a sobreposição desta com diferentes condições clínicasAbstract: The Velocardiofacial Syndrome (VCFS) has a prevalence of ~1:4.000 births and shows variable phenotypic spectrum, including congenital heart defects (CHD). Microdeletions of ~3 Mb in 22q11.2 represent the main cause, however atypical deletions in this region have been reported, as well as similar phenotypes associated with changes in the number of DNA copies (Copy number variations, CNVs) in other chromosomal regions. This work aims to map the breakpoints of the 22q11.2 region and investigate CNVs in other regions of the genome in patients with the 22q11.2 deletion previously confirmed (Group I) and investigate CNVs on the genome of patients without the 22q11.2 deletion (Group II). We investigated 108 patients (30 from Group I and 78 from Group II) with clinical suspicion of VCFS and CHD for array Genomic Hybridization (aGH). For Group I, the size of proximal 22q11.2 deletion ranged from 1.8 Mb to 3.3 Mb in 28 cases, of these, one case had the deletion between LCRs (Low Copy Repeats) A-B and the other 27 between LCRs A-D (typically deleted region). Two cases had atypical deletions at 22q11.2: 3.6 Mb between LCRs B-F, involving proximal and distal 22q11.2 regions; and 1.5 Mb between LCRs D-E, involving distal 22q11.2 region. Additionally, we observed ten relevant CNVs ? 300 kb outside of 22q11.2 region, including a deletion in 11q14.3 and duplications in 2q24.1-q24.2, 3p22.1, 5p15.2, 5q11.1, 6p21.2, 7p11.2, 15q13.3, 16q23.3 and Xp21.1. For Group II, a total of 25 relevant CNVs ? 300 Kb was observed. Of these, nine CNVs have been described in the literature, including deletions in 4q35.1-q35.2, 5p15.1-p15.33, 8p23.1, 10q22.3-q23.2, 16p11.2, 17q12 and 22q13.33; and duplications in 3p26.3 and 3q26.2. Gene variations within the break points of the 22q11.2 deleted region and CNVs observed in other chromosomal regions contribute to phenotypic variability observed in this syndrome and confirm the overlapp with different clinical conditionsDoutoradoCiencias BiomedicasDoutora em Ciências Médica

Frequency and genetic profile of compound heterozygous Friedreich's ataxia patients-the brazilian experience

Friedreich ataxia (FRDA) is the most common autosomal recessive ataxia in Caucasian populations. It is caused by a homozygous GAA expansion in the first intron of the frataxin gene (FXN) (OMIM: 606829) in 96% of the affected individuals. The remaining patients have a GAA expansion in one allele and a point mutation in the other. Little is known about compound heterozygous patients outside Europe and North America. We have thus designed a study to determine the frequency and mutational profile of these patients in Brazil. To accomplish that, we recruited all patients with ataxia and at least one expanded GAA allele at FXN from 3 national reference centers. We identified those subjects with a single expansion and proceeded with further genetic testing (Sanger sequencing and CGH arrays) for those. There were 143 unrelated patients (128 families), five of which had a single expanded allele. We identified point mutations in three out of these five (3/128 = 2.34%). Two patients had the c.157delC variant, whereas one individual had the novel variant c.482+1G>T. These results indicate that FXN point mutations are rare, but exist in Brazilian patients with FRDA. This has obvious implications for diagnostic testing and genetic counseling.18611431146CAPES - Coordenação de Aperfeiçoamento de Pessoal e Nível SuperiorFAPESP – Fundação de Amparo à Pesquisa Do Estado De São PauloSem informação2013/01766-

Atypical Copy Number Abnormalities In 22q11.2 Region: Report Of Three Cases.

The 22q11.2 Deletion Syndrome (22q11.2DS) is the most common microdeletion syndrome in humans, with a highly variable phenotype. This chromosomal region contains low copy repeat (LCR) sequences that mediate non-allelic homologous recombination which predispose to copy number abnormalities at this locus. This article describes three patients investigated for suspicion of 22q11.2DS presenting atypical copy number abnormalities overlapping or not with the common ∼3 Mb deletion. They were investigated by G-banding karyotype, Multiplex-ligation dependent probe amplification (MLPA) and array Genomic Hibridization (aGH). Clinical and molecular data were compared with literature, in order to contribute to genotype-phenotype correlation. Atypical chromosomal abnormalities were detected: 3.6 Mb deletion at 22q11.21-q11.23 between LCRs B-F in patient 1 and approximately 1.5 Mb deletion at 22q11.21-q11.22 between LCRs D-E in patients 2 and 3. The breakpoints detected in patient 1 have not been previously described. These findings exemplify the complexity and genetic heterogeneity observed in 22q11.2 region and corroborates the idea that genetic modifiers contribute to the phenotypic variability observed in proximal and distal 22q11.2 deletion syndromes.56515-2

Genomic imbalances in syndromic congenital heart disease

Objective: To identify pathogenic genomic imbalances in patients presenting congenital heart disease (CHD) with extra cardiac anomalies and exclusion of 22q11.2 deletion syndrome (22q11.2 DS). Methods: 78 patients negative for the 22q11.2 deletion, previously screened by fluorescence in situ hybridization (FISH) and/or multiplex ligation probe amplification (MLPA) were tested by chromosomal microarray analysis (CMA). Results: Clinically significant copy number variations (CNVs ≥300 kb) were identified in 10% (8/78) of cases. In addition, potentially relevant CNVs were detected in two cases (993 kb duplication in 15q21.1 and 706 kb duplication in 2p22.3). Genes inside the CNV regions found in this study, such as IRX4, BMPR1A, SORBS2, ID2, ROCK2, E2F6, GATA4, SOX7, SEMAD6D, FBN1, and LTPB1 are known to participate in cardiac development and could be candidate genes for CHD. Conclusion: These data showed that patients presenting CHD with extra cardiac anomalies and exclusion of 22q11.2 DS should be investigated by CMA. The present study emphasizes the possible role of CNVs in CHD

Copy number variation in the susceptibility to systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component and etiology characterized by chronic inflammation and autoantibody production. The purpose of this study was to ascertain copy number variation (CNV) in SLE using a case-control design in an admixed Brazilian population. The whole-genome detection of CNV was performed using Cytoscan HD array in SLE patients and healthy controls. The best CNV candidates were then evaluated by quantitative real-time PCR in a larger cohort or validated using droplet digital PCR. Logistic regression models adjusted for sex and ancestry covariates was applied to evaluate the association between CNV with SLE susceptibility. The data showed a synergistic effect between the FCGR3B and ADAM3A loci with the presence of deletions in both loci significantly increasing the risk to SLE (5.9-fold) compared to the deletion in the single FCGR3B locus (3.6-fold). In addition, duplications in these genes were indeed more frequent in healthy subjects, suggesting that high FCGR3B/ADAM3A gene copy numbers are protective factors against to disease development. Overall, 21 rare CNVs were identified in SLE patients using a four-step pipeline created for identification of rare variants. Furthermore, heterozygous deletions overlapping the CFHR4, CFHR5 and HLA-DPB2 genes were described for the first time in SLE patients. Here we present the first genome-wide CNV study of SLE patients in a tri-hybrid population. The results show that novel susceptibility loci to SLE can be found once the distribution of structural variants is analyzed throughout the whole genome

Genomic imbalances in syndromic congenital heart disease,

Abstract Objective: To identify pathogenic genomic imbalances in patients presenting congenital heart disease (CHD) with extra cardiac anomalies and exclusion of 22q11.2 deletion syndrome (22q11.2 DS). Methods: 78 patients negative for the 22q11.2 deletion, previously screened by fluorescence in situ hybridization (FISH) and/or multiplex ligation probe amplification (MLPA) were tested by chromosomal microarray analysis (CMA). Results: Clinically significant copy number variations (CNVs ≥300 kb) were identified in 10% (8/78) of cases. In addition, potentially relevant CNVs were detected in two cases (993 kb duplication in 15q21.1 and 706 kb duplication in 2p22.3). Genes inside the CNV regions found in this study, such as IRX4, BMPR1A, SORBS2, ID2, ROCK2, E2F6, GATA4, SOX7, SEMAD6D, FBN1, and LTPB1 are known to participate in cardiac development and could be candidate genes for CHD. Conclusion: These data showed that patients presenting CHD with extra cardiac anomalies and exclusion of 22q11.2 DS should be investigated by CMA. The present study emphasizes the possible role of CNVs in CHD