Idiopathic mental retardation: evaluation of a CGH microarray strategy for genetic diagnosis

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The Role of AKT3 Copy Number Changes in Brain Abnormalities and Neurodevelopmental Disorders: Four New Cases and Literature Review

Publication . Lopes, F.; Torres, F.; Soares, G.; van Karnebeek, C.; Martins, C.; Antunes, D.; Silva, J.; Muttucomaroe, L.; Botelho, L.; Sousa, S.; Rendeiro, P.; Tavares, P.; Van Esch, H.; Rajcan-Separovic, E.; Maciel, P.

Microdeletions at 1q43-q44 have been described as resulting in a clinically recognizable phenotype of intellectual disability (ID), facial dysmorphisms and microcephaly (MIC). In contrast, the reciprocal microduplications of 1q43-q44 region have been less frequently reported and patients showed a variable phenotype, including macrocephaly. Reports of a large number of patients with copy number variations involving this region highlighted the AKT3 gene as a likely key player in head size anomalies. We report four novel patients with copy number variations in the 1q43-q44 region: one with a larger deletion (3.7Mb), two with smaller deletions affecting AKT3 and SDCCAG8 genes (0.16 and 0.18Mb) and one with a quadruplication (1Mb) that affects the entire AKT3 gene. All patients with deletions presented MIC without structural brain abnormalities, whereas the patient with quadruplication had macrocephaly, but his carrier father had normal head circumference. Our report also includes a comparison of phenotypes in cases with 1q43-q44 duplications to assist future genotype-phenotype correlations. Our observations implicate AKT3 as a contributor to ID/development delay (DD) and head size but raise doubts about its straightforward impact on the latter aspect of the phenotype in patients with 1q43-q44 deletion/duplication syndrome.

2019Journal article

Open access

Identification of rare de novo epigenetic variations in congenital disorders

Publication . Barbosa, M.; Joshi, R.; Garg, P.; Martin-Trujillo, A.; Patel, N.; Jadhav, B.; Watson, C.; Gibson, W.; Chetnik, K.; Tessereau, C.; Mei, H.; De Rubeis, S.; Reichert, J.; Lopes, F.; Vissers, L.; Kleefstra, T.; Grice, D.; Edelmann, L.; Soares, G.; Maciel, P.; Brunner, H.; Buxbaum, J.; Gelb, B.; Sharp, A.

Certain human traits such as neurodevelopmental disorders (NDs) and congenital anomalies (CAs) are believed to be primarily genetic in origin. However, even after whole-genome sequencing (WGS), a substantial fraction of such disorders remain unexplained. We hypothesize that some cases of ND-CA are caused by aberrant DNA methylation leading to dysregulated genome function. Comparing DNA methylation profiles from 489 individuals with ND-CAs against 1534 controls, we identify epivariations as a frequent occurrence in the human genome. De novo epivariations are significantly enriched in cases, while RNAseq analysis shows that epivariations often have an impact on gene expression comparable to loss-of-function mutations. Additionally, we detect and replicate an enrichment of rare sequence mutations overlapping CTCF binding sites close to epivariations, providing a rationale for interpreting non-coding variation. We propose that epivariations contribute to the pathogenesis of some patients with unexplained ND-CAs, and as such likely have diagnostic relevance.

2018-05-25Journal article

Open access

Genomic imbalances defining novel intellectual disability associated loci

Publication . Lopes, Fátima; Torres, Fátima; Soares, Gabriela; Barbosa, Mafalda; Silva, João; Duque, Frederico; Rocha, Miguel; Sá, Joaquim; Oliveira, Guiomar; Sá, Maria João; Temudo, Teresa; Sousa, Susana; Marques, Carla; Lopes, Sofia; Gomes, Catarina; Barros, Gisela; Jorge, Arminda; Rocha, Felisbela; Martins, Cecília; Mesquita, Sandra; Loureiro, Susana; Cardoso, Elisa Maria; Cálix, Maria José; Dias, Andreia; Martins, Cristina; Mota, Céu R; Antunes, Diana; Dupont, Juliette; Figueiredo, Sara; Figueiroa, Sónia; Gama-de-Sousa, Susana; Cruz, Sara; Sampaio, Adriana; Eijk, Paul; Weiss, Marjan M; Ylstra, Bauke; Rendeiro, Paula; Tavares, Purificação; Reis-Lima, Margarida; Pinto-Basto, Jorge; Fortuna, Ana Maria; Maciel, Patrícia

Background: High resolution genome-wide copy number analysis, routinely used in clinical diagnosis for several years, retrieves new and extremely rare copy number variations (CNVs) that provide novel candidate genes contributing to disease etiology. The aim of this work was to identify novel genetic causes of neurodevelopmental disease, inferred from CNVs detected by array comparative hybridization (aCGH), in a cohort of 325 Portuguese patients with intellectual disability (ID). Results: We have detected CNVs in 30.1% of the patients, of which 5.2% corresponded to novel likely pathogenic CNVs. For these 11 rare CNVs (which encompass novel ID candidate genes), we identified those most likely to be relevant, and established genotype-phenotype correlations based on detailed clinical assessment. In the case of duplications, we performed expression analysis to assess the impact of the rearrangement. Interestingly, these novel candidate genes belong to known ID-related pathways. Within the 8% of patients with CNVs in known pathogenic loci, the majority had a clinical presentation fitting the phenotype(s) described in the literature, with a few interesting exceptions that are discussed. Conclusions: Identification of such rare CNVs (some of which reported for the first time in ID patients/families) contributes to our understanding of the etiology of ID and for the ever-improving diagnosis of this group of patients.

2019Journal article

Open access

Whole Gene Deletion of EBF3 Supporting Haploinsufficiency of This Gene as a Mechanism of Neurodevelopmental Disease

Publication . Lopes, F.; Soares, G.; Gonçalves-Rocha, M.; Pinto-Basto, J.; Maciel, P.

Mutations in early B cell factor 3 (EBF3) were recently described in patients with a neurodevelopmental disorder (NDD) that includes developmental delay/intellectual disability, ataxia, hypotonia, speech impairment, strabismus, genitourinary abnormalities, and mild facial dysmorphisms. Several large 10q terminal and interstitial deletions affecting many genes and including EBF3 have been described in the literature. However, small deletions (<1 MB) affecting almost exclusively EBF3 are not commonly reported. We performed array comparative genomic hybridization (aCGH) (Agilent 180K) and quantitative PCR analysis in a female patient with intellectual disability. A clinical comparison between our patient and overlapping cases reported in the literature was also made. The patient carries a de novo 600 Kb deletion at 10q26.3 affecting the MGMT, EBF3, and GLRX genes. The patient has severe intellectual disability, language impairment, conductive hearing loss, hypotonia, vision alterations, triangular face, short stature, and behavior problems. This presentation overlaps that reported for patients carrying EBF3 heterozygous point mutations, as well as literature reports of patients carrying large 10qter deletions. Our results and the literature review suggest that EBF3 haploinsufficiency is a key contributor to the common aspects of the phenotype presented by patients bearing point mutations and indels in this gene, given that deletions affecting the entire gene (alone or in addition to other genes) are causative of a similar syndrome, including intellectual disability (ID) with associated neurological symptoms and particular facial dysmorphisms.

2017-10-09Journal article

Open access