Burden of Rare Copy Number Variants in Microcephaly: A Brazilian Cohort of 185 Microcephalic Patients and Review of the Literature.

Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment.

Copy number variations in a Brazilian cohort with autism spectrum disorders highlight the contribution of cell adhesion genes.

Prediction of pathogenicity of rare copy number variations (CNVs), a genomic alteration known to contribute to the etiology of autism spectrum disorder (ASD), represents a serious limitation to interpreting genetic tests, particularly for genetic counseling purposes. Chromosomal microarray analysis (CMA) was conducted in a unique collection of 144 Brazilian individuals with ASD of strong European and African ancestries. Rare CNVs were detected in 39 patients: 41 of unknown significance (VUS), four pathogenic and one likely pathogenic CNVs (clinical yield of 4.1%; 5/122). Based on gene content and recurrence in three large cohorts [a Brazilian neurodevelopmental disorder cohort, the autism MSSNG cohort, and the Canadian-based Centre for Applied Genomics microarray database], this work strengthened the pathogenicity of 14 genes (FAT1, CAMK4, BIRC6, DPP6, CSMD1, CTNNA3, CDH8/CDH11, CDH13, OR1C1, CNTN6, CNTNAP4, FGF2 and PTPRN2) within 14 CNVs. Notably, enrichment of cell adhesion proteins to ASD etiology was identified (p < 0.05), highlighting the importance of these gene families in the etiology of ASD.

Investigating Genetic Factors Contributing to Variable Expressivity of Class I 17p13.3 Microduplication.

17p13.3 microduplications are rare copy number variations (CNVs) associated with variable phenotypes, including facial dysmorphism, developmental delay, intellectual disability, and autism. Typically, when a recognized pathogenic CNV is identified, other genetic factors are not considered. We investigated via whole-exome sequencing the presence of additional variants in four carriers of class I 17p13.3 microduplications. A 730 kb 17p13.3 microduplication was identified in two half-brothers with intellectual disability, but not in a third affected half-brother or blood cells from their normal mother (Family A), thus leading to the hypothesis of maternal germline mosaicism. No additional pathogenic variants were detected in Family A. Two affected siblings carried maternally inherited 450 kb 17p13.3 microduplication (Family B); the three carriers of the microduplication exhibited microcephaly and learning disability/speech impairment of variable degrees. Exome analysis revealed a variant of uncertain significance in RORA, a gene already linked to autism, in the autistic boy; his sister was heterozygous for a CYP1B1 pathogenic variant that could be related to her congenital glaucoma. Besides, both siblings carried a loss-of-function variant in DIP2B, a candidate gene for intellectual disability, which was inherited from their father, who also exhibited learning disability in childhood. In conclusion, additional pathogenic variants were revealed in two affected carriers of class I 17p13.3 microduplication (Family B), probably adding to their phenotypes. These results provided new evidence regarding the contribution of RORA and DIP2B to neurocognitive deficits, and highlighted the importance of full genetic investigation in carriers of CNV syndromes with variable expressivity. Finally, we suggest that microcephaly may be a rare clinical feature also related to the presence of the class I 17p13.3 microduplication.

10q23.31 microduplication encompassing PTEN decreases mTOR signalling activity and is associated with autosomal dominant primary microcephaly.

BACKGROUND: Hereditary primary microcephaly (MCPH) is mainly characterised by decreased occipitofrontal circumference and variable degree of intellectual disability. MCPH with a dominant pattern of inheritance is a rare condition, so far causally linked to pathogenic variants in the ALFY, DPP6, KIF11 and DYRK1A genes. OBJECTIVE: This study aimed at identifying the causative variant of the autosomal dominant form of MCPH in a Brazilian family with three affected members. METHODS: Following clinical evaluation of two sibs and their mother presenting with autosomal dominant MCPH, array comparative genome hybridisation was performed using genomic DNA from peripheral blood of the family members. Gene and protein expression studies were carried out in cultured skin fibroblasts. RESULTS: A 382 kb microduplication at 10q23.31 was detected, encompassing the entire PTEN, KLLN and ATAD1 genes. PTEN haploinsufficiency has been causally associated with macrocephaly and autism spectrum disorder and, therefore, was considered the most likely candidate gene to be involved in this autosomal dominant form of MCPH. In the patients' fibroblasts, PTEN mRNA and protein were found to be overexpressed, and the phosphorylation patterns of upstream and downstream components of the mammalian target of rapamycin (mTOR) signalling pathway were dysregulated. CONCLUSIONS: Taken together, our results demonstrate that the identified submicroscopic 10q23.31 duplication in a family with MCPH leads to markedly increased expression of PTEN and reduced activity of the mTOR signalling pathway. These results suggest that the most probable pathomechanism underlying the microcephaly phenotype in this family involves downregulation of the mTOR pathway through overexpression of PTEN.

Two distinct regions in 2q24.2-q24.3 associated with idiopathic epilepsy.

Approximately 50% of all carriers of 2q21-q31 deletions present epileptic seizures. The band 2q24 constitutes the smallest commonly deleted segment in these patients, and contains the voltage-gated sodium channel genes SCN1A and SCN2A, associated with Dravet syndrome and benign familial neonatal-infantile seizures, respectively. A further putative locus involving epilepsy in the region was previously identified through disruption of the SLC4A10 gene by translocation. In the course of performing high-resolution DNA copy number analyses on syndromic mentally impaired individuals, we encountered three patients with overlapping deletions in chromosome region 2q24. Two of these patients exhibited epileptic seizures in addition to mental deficiency. The deletion in one of the epileptic patients did not include the SCN cluster, demonstrating that a less severe form of epilepsy maps to an adjacent genomic region. This second region comprises about 3 Mb and contains the candidate gene SLC4A10, providing further support for the potential role of this gene in epilepsy.

Normal male carriers on the Martin-Bell syndrome gene: implications for genetic counseling

A freqüência de comprometimento mental foi estimada entre os parentes de homens normais portadores do gene da SMB. Suas filhas, hetertozigotas certas, säo raramente afetadas e a freqüência de comprometimento mental em suas irmandades é menor do que nas irmandades de homens afetados. Seus netos e netas, entretanto, têm risco de serem afetados semelhantes ao dos filhos e filhas de heterozigotas filhas de mulheres portadoras. Os riscos de afetados na prole de possíveis portadores que näo expressam o X frágil foram calculados nos casos em que o gene pode ser transmitido por um homem normmal

Cytogenetic analysis of first trimester chorionic villi samplings

O cariótipo fetal foi determinado em 65 amostras de vilosidade coriônica obtidas entre as oitava e décima segunda semanas de gestaçäo. A idade materna foi a indicaçäo principal em 40 gravidezes e nesse grupo foram detectadas 4 alteraçöes cromossômicas: 47,XX,+21;45,X/47,XYY;92,XXXX e 47,XX,+mar. Em 8 casos havia uma criança anterior portadora de aberraçäo cromossômica; entre eles, foi diagnosticado um feto triplóide. Cinco exames foram realizados porque ocorrera anteriormente uma criança malformada, cuja constituiçäo cromossômica era desconhecida (2) ou por motivos psicológicos (3); todos revelaram cromossomos normais. Cinco genitores eram portadores de translocaçöes equilibradas e um dos fetos tinha a aberraçäo näo equilibrada. O exame foi realizado para a determinaçäo do sexo em 7 gravidezes com risco de doença de herança recessiva ligada ao X; três fetos masculinos foram identificados. Foram estabelecidas culturas de tecidos fetal e da placenta após o abortamento, nos casos triplóide e tetraplóide; confirmaram-se os resultados obtidos no diagnóstico pré-natal. No caso do cariótipo 47,XX,+mar, o exame cromossômico após amniocentese revelou cariótipo normal

Genetic counseling in Martin-Bell syndrome

A Síndrome de Martin-Bell (MBS) de herança ligada ao X é uma causa importante de retardo mental. A ocorrência de homens normais portadores do gene e a alta freqüência de heterozigotas que manifestam comprometimento mental fazem com que o padräo de herança desta síndrome seja marcadamente diferente do de outras doenças ligadas ao X. Além disso, embora a expressäo do X frágil permita a identificaçäo de portadores normais do gene da MBS, muitos deles säo fra(X)-negativos. Neste trabalho, estimamos o risco de afetados na prole de possíveis portadores do gene da MBS que säo fra(X)-negativos. Estes riscos nunca excederam 10%

Chorionic villi sampling for early prenatal genetic diagnosis

Foram estudadas 11 pacientes submetidas a AVC, para diagnóstico cromossômico, entre a 8ª e a 10ª semana de gestaçäo. Utilizou-se um catéter especial para este tipo de procedimento (Portex LTD, Inglatera) e a colheita do material foi sempre guiada por ultra-sonografia. Três casos näo forneceram metáfases que permitissem análise cromossômica e para estes foi indicada amniocentese posterior. Com exceçäo do primeiro caso onde o material foi colhido em um aborto retido, todas as demais gestaçöes evoluem satisfatoriamente

Dermotoglyphics in patients with the Prader-Willi syndrome and normal Karyotypes

Realizamos estudo dermatoglífico de 8 pacientes com SPW e cariótipo normal, compreendendo as seguintes variáveis: padröes digitais e palmares, pregas palmares e terminaçöes das linhas principais, contagem total de cristas e índices de ulnaridade e da linha principal. A análise da freqüência de padröes digitais, pregas palmares e terminaçöes das linhas principais incluíu os dados da literatura referentes a 24 pacientes com SPW e cariótipo normal. Somente as terminaçöes das linhas principais A e T diferiram significantemente entre os pacientes e o grupo controle; a linha principal A terminou radialmente (posiçäo 1 + 2) mais frequentemente do que no controle e a linha principal T estava deslocada da posiçäo 13 para 11 ou 12 mais frequentemente nos pacientes do que no controle