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1.
Clin Epigenetics ; 16(1): 62, 2024 May 07.
Article in English | MEDLINE | ID: mdl-38715103

ABSTRACT

BACKGROUND: Temple syndrome (TS14) is a rare imprinting disorder caused by maternal UPD14, imprinting defects or paternal microdeletions which lead to an increase in the maternal expressed genes and a silencing the paternally expressed genes in the 14q32 imprinted domain. Classical TS14 phenotypic features include pre- and postnatal short stature, small hands and feet, muscular hypotonia, motor delay, feeding difficulties, weight gain, premature puberty along and precocious puberty. METHODS: An exon array comparative genomic hybridization was performed on a patient affected by psychomotor and language delay, muscular hypotonia, relative macrocephaly, and small hand and feet at two years old. At 6 years of age, the proband presented with precocious thelarche. Genes dosage and methylation within the 14q32 region were analyzed by MS-MLPA. Bisulfite PCR and pyrosequencing were employed to quantification methylation at the four known imprinted differentially methylated regions (DMR) within the 14q32 domain: DLK1 DMR, IG-DMR, MEG3 DMR and MEG8 DMR. RESULTS: The patient had inherited a 69 Kb deletion, encompassing the entire DLK1 gene, on the paternal allele. Relative hypermethylation of the two maternally methylated intervals, DLK1 and MEG8 DMRs, was observed along with normal methylation level at IG-DMR and MEG3 DMR, resulting in a phenotype consistent with TS14. Additional family members with the deletion showed modest methylation changes at both the DLK1 and MEG8 DMRs consistent with parental transmission. CONCLUSION: We describe a girl with clinical presentation suggestive of Temple syndrome resulting from a small paternal 14q32 deletion that led to DLK1 whole-gene deletion, as well as hypermethylation of the maternally methylated DLK1-DMR.


Subject(s)
Calcium-Binding Proteins , Chromosomes, Human, Pair 14 , DNA Methylation , Genomic Imprinting , Intercellular Signaling Peptides and Proteins , Humans , Calcium-Binding Proteins/genetics , DNA Methylation/genetics , Chromosomes, Human, Pair 14/genetics , Intercellular Signaling Peptides and Proteins/genetics , Genomic Imprinting/genetics , Membrane Proteins/genetics , Child , Male , Comparative Genomic Hybridization/methods , Female , Chromosome Deletion , Child, Preschool , Phenotype , Abnormalities, Multiple/genetics , Imprinting Disorders , Muscle Hypotonia , Facies
2.
Genes (Basel) ; 14(3)2023 03 13.
Article in English | MEDLINE | ID: mdl-36980980

ABSTRACT

Neurodevelopmental disorders (NDDs) affect 2-5% of the population and approximately 50% of cases are due to genetic factors. Since de novo pathogenic variants account for the majority of cases, a gene panel including 460 dominant and X-linked genes was designed and applied to 398 patients affected by intellectual disability (ID)/global developmental delay (GDD) and/or autism (ASD). Pathogenic variants were identified in 83 different genes showing the high genetic heterogeneity of NDDs. A molecular diagnosis was established in 28.6% of patients after high-depth sequencing and stringent variant filtering. Compared to other available gene panel solutions for NDD molecular diagnosis, our panel has a higher diagnostic yield for both ID/GDD and ASD. As reported previously, a significantly higher diagnostic yield was observed: (i) in patients affected by ID/GDD compared to those affected only by ASD, and (ii) in females despite the higher proportion of males among our patients. No differences in diagnostic rates were found between patients affected by different levels of ID severity. Interestingly, patients harboring pathogenic variants presented different phenotypic features, suggesting that deep phenotypic profiling may help in predicting the presence of a pathogenic variant. Despite the high performance of our panel, whole exome-sequencing (WES) approaches may represent a more robust solution. For this reason, we propose the list of genes included in our customized gene panel and the variant filtering procedure presented here as a first-tier approach for the molecular diagnosis of NDDs in WES studies.


Subject(s)
Autistic Disorder , Intellectual Disability , Neurodevelopmental Disorders , Male , Female , Humans , Genes, X-Linked , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/genetics , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Genetic Testing , Autistic Disorder/genetics
3.
Am J Med Genet A ; 191(1): 135-143, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36271811

ABSTRACT

We describe the phenotype of 22 male patients (20 probands) carrying a hemizygous missense variant in MED12. The phenotypic spectrum is very broad ranging from nonspecific intellectual disability (ID) to the three well-known syndromes: Opitz-Kaveggia syndrome, Lujan-Fryns syndrome, or Ohdo syndrome. The identified variants were randomly distributed throughout the gene (p = 0.993, χ2 test), but mostly outside the functional domains (p = 0.004; χ2 test). Statistical analyses did not show a correlation between the MED12-related phenotypes and the locations of the variants (p = 0.295; Pearson correlation), nor the protein domain involved (p = 0.422; Pearson correlation). In conclusion, establishing a genotype-phenotype correlation in MED12-related diseases remains challenging. Therefore, we think that patients with a causative MED12 variant are currently underdiagnosed due to the broad patients' clinical presentations.


Subject(s)
Blepharophimosis , Intellectual Disability , Mental Retardation, X-Linked , Male , Humans , Mediator Complex/genetics , Mental Retardation, X-Linked/genetics , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Blepharophimosis/genetics , Mutation, Missense/genetics , Phenotype , Syndrome
4.
J Mol Diagn ; 24(5): 529-542, 2022 05.
Article in English | MEDLINE | ID: mdl-35569879

ABSTRACT

Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%).


Subject(s)
Genomics , Rare Diseases , Computational Biology , Exome , Humans , Rare Diseases/diagnosis , Rare Diseases/genetics , Exome Sequencing
5.
Biology (Basel) ; 12(1)2022 Dec 30.
Article in English | MEDLINE | ID: mdl-36671762

ABSTRACT

Semen quality has a direct relation to male fertility. Whether sperm variables in humans have decreased over the last years is still uncertain, with some studies showing a decline and others reporting no changes. In this regard, previous research has suggested that lifestyle and environmental conditions may contribute to this variability, calling for regional studies. The present work is a retrospective, unicentric study that includes semen samples analyzed between 1997 and 2017 at the Parc Taulí Hospital (Barcelona metropolitan area). First, a multivariate analysis including the age as a confounding factor showed a statistically significant decrease in semen volume, pH, progressive motility, morphology and total motile sperm over time. Contrarily, no significant variation in sperm count or concentration was observed. Mean reductions per year were -0.02 mL for volume, -0.57% for progressively motile sperm and -0.72% for sperm with normal morphology. Interestingly, the average annual temperature registered by the Spanish Meteorology Agency negatively correlated to sperm morphology and sperm count (Rs = -0.642; p = 0.002 and Rs = -0.435; p = 0.049, respectively). In conclusion, the present study based on infertile patients from the Barcelona area found a decline in sperm motility and morphology, without effects on sperm count. Changes in temperature appeared to be associated to this decline, but further studies are needed to address the mechanisms linked to the observed variations.

6.
PLoS One ; 16(10): e0258766, 2021.
Article in English | MEDLINE | ID: mdl-34653234

ABSTRACT

Angelman syndrome (AS) is a neurogenetic disorder characterized by severe developmental delay with absence of speech, happy disposition, frequent laughter, hyperactivity, stereotypies, ataxia and seizures with specific EEG abnormalities. There is a 10-15% of patients with an AS phenotype whose genetic cause remains unknown (Angelman-like syndrome, AS-like). Whole-exome sequencing (WES) was performed on a cohort of 14 patients with clinical features of AS and no molecular diagnosis. As a result, we identified 10 de novo and 1 X-linked pathogenic/likely pathogenic variants in 10 neurodevelopmental genes (SYNGAP1, VAMP2, TBL1XR1, ASXL3, SATB2, SMARCE1, SPTAN1, KCNQ3, SLC6A1 and LAS1L) and one deleterious de novo variant in a candidate gene (HSF2). Our results highlight the wide genetic heterogeneity in AS-like patients and expands the differential diagnosis.


Subject(s)
Angelman Syndrome/genetics , Exome Sequencing/methods , Gene Regulatory Networks , Adolescent , Adult , Child , Female , Genetic Association Studies , Genetic Predisposition to Disease , Heat-Shock Proteins , Humans , Infant , Male , Matrix Attachment Region Binding Proteins/genetics , Receptors, Cytoplasmic and Nuclear/genetics , Repressor Proteins/genetics , Transcription Factors/genetics , Vesicle-Associated Membrane Protein 2/genetics , Young Adult
7.
Front Neurosci ; 15: 618098, 2021.
Article in English | MEDLINE | ID: mdl-34121983

ABSTRACT

KIF1A is a microtubule-dependent motor protein responsible for fast anterograde transport of synaptic vesicle precursors in neurons. Pathogenic variants in KIF1A have been associated with a wide spectrum of neurological disorders. Here, we report a patient presenting a severe neurodevelopmental disorder carrying a novel de novo missense variant p.Arg169Thr (R169T) in the KIF1A motor domain. The clinical features present in our patient match with those reported for NESCAV syndrome including severe developmental delay, spastic paraparesis, motor sensory neuropathy, bilateral optic nerve atrophy, progressive cerebellar atrophy, epilepsy, ataxia, and hypotonia. Here, we demonstrate that the microtubule-stimulated ATPase activity of the KIF1A is strongly reduced in the motor domain of the R169T variant. Supporting this, in silico structural modeling suggests that this variant impairs the interaction of the KIF1A motor domain with microtubules. The characterization of the molecular effect of the R169T variant on the KIF1A protein together with the presence of the typical clinical features indicates its causal pathogenic effect.

8.
Genes (Basel) ; 11(1)2020 01 02.
Article in English | MEDLINE | ID: mdl-31906484

ABSTRACT

X-linked intellectual disability (XLID) is known to contribute up to 10% of intellectual disability (ID) in males and could explain the increased ratio of affected males observed in patients with ID. Over the past decade, next-generation sequencing has clearly stimulated the gene discovery process and has become part of the diagnostic procedure. We have performed targeted next-generation sequencing of 82 XLID genes on 61 non-related male patients with suggestive non-syndromic XLID. These patients were initially referred to the molecular genetics laboratory to exclude Fragile X Syndrome. The cohort includes 47 male patients with suggestive X-linked family history of ID meaning that they had half-brothers or maternal cousins or uncles affected; and 14 male patients with ID and affected brothers whose mothers show skewed X-inactivation. Sequencing data analysis identified 17 candidate variants in 16 patients. Seven families could be re-contacted and variant segregation analysis of the respective eight candidate variants was performed: HUWE1, IQSEC2, MAOA, MED12, PHF8, SLC6A8, SLC9A6, and SYN1. Our results show the utility of targeted next-generation sequencing in unravelling the genetic origin of XLID, especially in retrospective cases. Variant segregation and additional studies like RNA sequencing and biochemical assays also helped in re-evaluating and further classifying the genetic variants found.


Subject(s)
High-Throughput Nucleotide Sequencing/methods , Mental Retardation, X-Linked/diagnosis , Mental Retardation, X-Linked/genetics , Adolescent , Adult , Child , Child, Preschool , Cohort Studies , Exome/genetics , Fragile X Syndrome , Genes, X-Linked/genetics , Guanine Nucleotide Exchange Factors/genetics , Humans , Infant , Intellectual Disability/genetics , Male , Mediator Complex/genetics , Monoamine Oxidase/genetics , Mutation/genetics , Nerve Tissue Proteins/genetics , Pedigree , Plasma Membrane Neurotransmitter Transport Proteins/genetics , Retrospective Studies , Sodium-Hydrogen Exchangers/genetics , Transcription Factors , Exome Sequencing/methods
9.
J Psychiatr Res ; 110: 74-82, 2019 03.
Article in English | MEDLINE | ID: mdl-30597424

ABSTRACT

DDR1 has been linked to schizophrenia (SZ) and myelination. Here, we tested whether DDR1 variants in people at risk for SZ influence white matter (WM) structural variations and cognitive processing speed (PS). First, following a case-control design (Study 1), SZ patients (N = 1193) and controls (N = 1839) were genotyped for rs1264323 and rs2267641 at DDR1, and the frequencies were compared. We replicated the association between DDR1 and SZ (rs1264323, adjusted P = 0.015). Carriers of the rs1264323AA combined with the rs2267641AC or CC genotype are at risk to develop SZ compared to the other genotype combinations. Second, SZ patients (Study 2, N = 194) underwent an evaluation of PS using the Trail Making Test (TMT) and DDR1 genotyping. To compare PS between DDR1 genotype groups, we conducted an analysis of covariance (including rs1264323 as a covariate) and found that SZ patients with the rs2267641CC genotype had decreased PS compared to patients with the AA and AC genotypes. Third, 54 patients (Study 3) from Study 2 were selected based on rs1264323 genotype to undergo reevaluation, including a DTI-MRI brain scan. To test for associations between PS, WM microstructure and DDR1 genotype, we first localized those WM regions where fractional anisotropy (FA) was correlated with PS and tested whether FA showed differences between the rs1264323 genotypes. SZ patients with the rs1264323AA genotype showed decreased FA in WM regions associated with decreased PS. We conclude that DDR1 variants may confer a risk of SZ through WM microstructural alterations leading to cognitive dysfunction.


Subject(s)
Cognitive Dysfunction/physiopathology , Discoidin Domain Receptor 1/genetics , Schizophrenia/genetics , Schizophrenia/pathology , Schizophrenia/physiopathology , White Matter/pathology , Adult , Case-Control Studies , Female , Humans , Magnetic Resonance Imaging , Male , Middle Aged , Polymorphism, Single Nucleotide , Spain , White Matter/diagnostic imaging
10.
Mol Genet Genomic Med ; 7(1): e00511, 2019 01.
Article in English | MEDLINE | ID: mdl-30548424

ABSTRACT

BACKGROUND: Patients affected by Angelman syndrome (AS) present severe intellectual disability, lack of speech, ataxia, seizures, abnormal electroencephalography (EEG), and a characteristic behavioral phenotype. Around 10% of patients with a clinical diagnosis of AS (AS-like) do not have an identifiable molecular defect. Some of these patients harbor alternative genetic defects that present overlapping features with AS. METHODS: Trio whole-exome sequence was performed on patient and parent's DNA extracted from peripheral blood. Exome data were filtered according to a de novo autosomal dominant inheritance. cDNA analysis was carried out to assess the effect of the splice site variant. RESULTS: We identified a novel heterozygous SMARCE1 splicing variant that leads to an exon skipping in a patient with an Angelman-like phenotype. Missense variants in the SMARCE1 gene are known to cause Coffin-Siris syndrome (CSS), which is a rare congenital syndrome. Clinical reevaluation of the patient confirmed the presence of characteristic clinical features of CSS, many of them overlapping with AS. CONCLUSIONS: Taking into account the novel finding reported in this study, we consider that CSS should be added to the expanding list of differential diagnoses for AS.


Subject(s)
Angelman Syndrome/genetics , Chromosomal Proteins, Non-Histone/genetics , DNA-Binding Proteins/genetics , Phenotype , Adolescent , Angelman Syndrome/pathology , Exome , Humans , Male , Mutation, Missense , RNA Splicing
11.
Actas Esp Psiquiatr ; 46(5): 174-82, 2018 Sep.
Article in English | MEDLINE | ID: mdl-30338774

ABSTRACT

INTRODUCTION: The Edinburgh Postnatal Depression Scale (EPDS) is considered the gold standard in screening for postpartum depression. Although the Spanish version has been widely used, its factorial structure has not yet been studied . METHODS: A total of 1,204 women completed the EPDS 32 weeks after delivery. To avoid multiple testing, we split the sample into two halves, randomly drawing two subsamples of 602 participants each. We conducted exploratory factor analysis (EFA), followed by an oblimin rotation with the first sub-sample. Confirmatory factor analysis (CFA) was conducted using a Weighted Least Squares Means and Variance (WLSMV) estimation of the data. We explored different solutions between two and four factors. We compared the factors between two groups with depression and non-depression (evaluated with the Diagnostic Interview for Genetic Studies (DIGS) for the DSM-IV). RESULTS: The EFA indicated a three-factor model consisting of anxiety, depression and anhedonia. The results of the CFA confirmed the three-factor model (χ2=99.203, p<0.001; RMSEA=0.06, 90% CI=0.04/0.07, CFI=0.87 and TLI=0.82). Women with depression in the first 32 weeks obtained higher scores for anxiety, depression and anhedonia dimensions (p<0.001). CONCLUSIONS: This is the first study of confirmatory analysis with the Spanish version of EPDS in a large sample of women without psychiatric care during pregnancy. A three-factor model consisting of anxiety, depression and anhedonia was used. Women with depression had a higher score in the three dimensions of the EPDS.


Subject(s)
Depression, Postpartum/diagnosis , Psychiatric Status Rating Scales , Adult , Diagnostic Self Evaluation , Factor Analysis, Statistical , Female , Humans , Translations
12.
Actas esp. psiquiatr ; 46(5): 174-182, sept.-oct. 2018. tab, graf
Article in Spanish | IBECS | ID: ibc-174685

ABSTRACT

Introducción. La Escala de Depresión Postnatal de Edimburgo (EPDS) es considerada el gold standard para el cribado de depresión postparto. Aunque la versión española ha sido ampliamente utilizada, su estructura factorial no ha sido todavía analizada. Metodología. Un total de 1.204 mujeres completaron la EPDS a las 32 semanas del parto. Para evitar pruebas múltiples dividimos la muestra en dos mitades de 602 participantes. Se realizó un análisis factorial exploratorio (AFE) con rotación oblimin con la primera sub-muestra. Posteriormente, con la segunda de las muestras se realizó un análisis factorial confirmatorio (AFC) mediante la estimación Weighted Least Squares Means and Variance (WLSMV). Se exploraron diferentes soluciones entre dos y cuatro factores. Comparamos los factores en dos grupos de participantes con depresión y sin depresión (evaluados con la Entrevista Diagnóstica para Estudios Genéticos (DIGS) para el DSM-IV). Resultados. El AFE mostró un modelo de tres factores compuesto por ansiedad, depresión y anhedonia. Los resultados del AFC confirmaron el modelo de tres factores (χ2=99,203, p<0,001; RMSEA=0,06, 90% CI=0,04/0,07, CFI=0,87 y TLI=0,82). Mujeres con depresión a las 32 semanas tuvieron puntuaciones más elevadas en ansiedad, depresión y anhedonia (p<0,001). Conclusiones. Primer estudio de análisis confirmatorio de la versión española de la EPDS, en una amplia muestra de mujeres sin tratamiento psiquiátrico durante el embarazo. Un modelo de tres factores compuesto por ansiedad, depresión y anhedonia ha sido obtenido. Mujeres con depresión tuvieron una mayor puntuación en las tres dimensiones de la EPDS


Introduction. The Edinburgh Postnatal Depression Scale (EPDS) is considered the gold standard in screening for postpartum depression. Although the Spanish version has been widely used, its factorial structure has not yet been studied. Methods. A total of 1,204 women completed the EPDS 32 weeks after delivery. To avoid multiple testing, we split the sample into two halves, randomly drawing two subsamples of 602 participants each. We conducted exploratory factor analysis (EFA), followed by an oblimin rotation with the first sub-sample. Confirmatory factor analysis (CFA) was conducted using a Weighted Least Squares Means and Variance (WLSMV) estimation of the data. We explored different solutions between two and four factors. We compared the factors between two groups with depression and non-depression (evaluated with the Diagnostic Interview for Genetic Studies (DIGS) for the DSM-IV). Results. The EFA indicated a three-factor model consisting of anxiety, depression and anhedonia. The results of the CFA confirmed the three-factor model (χ2=99.203, p<0.001) RMSEA=0.06, 90% CI=0.04/0.07, CFI=0.87 and TLI=0.82). Women with depression in the first 32 weeks obtained higher scores for anxiety, depression and anhedonia dimensions (p<0.0101). Conclusions. This is the first study of confirmatory analysis with the Spanish version of EPDS in a large sample of women without psychiatric care during pregnancy. A three-factor model consisting of anxiety, depression and anhedonia was used. Women with depression had a higher score in the three dimensions of the EPDS


Subject(s)
Humans , Female , Pregnancy , Adult , Depression/epidemiology , Factor Analysis, Statistical , Depression, Postpartum/epidemiology , Psychiatric Status Rating Scales , Anxiety Disorders/epidemiology , Depression/psychology , Depression, Postpartum/psychology , Pregnancy Complications/psychology , Anhedonia , Anxiety Disorders/complications , Anxiety Disorders/psychology
14.
Behav Genet ; 48(4): 323-336, 2018 07.
Article in English | MEDLINE | ID: mdl-29882083

ABSTRACT

A genetic analysis of unexplained mild-moderate intellectual disability and co-morbid psychiatric or behavioural disorders is not systematically conducted in adults. A cohort of 100 adult patients affected by both phenotypes were analysed in order to identify the presence of copy number variants (CNVs) responsible for their condition identifying a yield of 12.8% of pathogenic CNVs (19% when including clinically recognizable microdeletion syndromes). Moreover, there is a detailed clinical description of an additional 11% of the patients harbouring possible pathogenic CNVs-including a 7q31 deletion (IMMP2L) in two unrelated patients and duplications in 3q29, 9p24.2p24.1 and 15q14q15.1-providing new evidence of its contribution to the phenotype. This study adds further proof of including chromosomal microarray analysis (CMA) as a mandatory test to improve the diagnosis in the adult patients in psychiatric services.


Subject(s)
DNA Copy Number Variations , Intellectual Disability/epidemiology , Intellectual Disability/genetics , Mental Disorders/epidemiology , Mental Disorders/genetics , Adolescent , Adult , Comorbidity , Female , Genotype , Humans , Incidence , Intellectual Disability/diagnosis , Male , Mental Disorders/diagnosis , Middle Aged , Oligonucleotide Array Sequence Analysis , Phenotype , Prospective Studies , Spain , Statistics, Nonparametric , Young Adult
15.
Br J Psychiatry ; 212(5): 287-294, 2018 05.
Article in English | MEDLINE | ID: mdl-29693535

ABSTRACT

BACKGROUND: Copy number variants (CNVs) are established risk factors for neurodevelopmental disorders. To date the study of CNVs in psychiatric illness has focused on single disorder populations. The role of CNVs in individuals with intellectual disabilities and psychiatric comorbidities are less well characterised.AimsTo determine the type and frequency of CNVs in adults with intellectual disabilities and comorbid psychiatric disorders. METHOD: A chromosomal microarray analysis of 599 adults recruited from intellectual disabilities psychiatry services at three European sites. RESULTS: The yield of pathogenic CNVs was high - 13%. Focusing on established neurodevelopmental disorder risk loci we find a significantly higher frequency in individuals with intellectual disabilities and comorbid psychiatric disorder (10%) compared with healthy controls (1.2%, P<0.0001), schizophrenia (3.1%, P<0.0001) and intellectual disability/autism spectrum disorder (6.5%, P < 0.00084) populations. CONCLUSIONS: In the largest sample of adults with intellectual disabilities and comorbid psychiatric disorders to date, we find a high rate of pathogenic CNVs. This has clinical implications for the use of genetic investigations in intellectual disability psychiatry.Declaration of interestNone.


Subject(s)
Child Development Disorders, Pervasive/genetics , DNA Copy Number Variations/genetics , Intellectual Disability/genetics , Mental Disorders/genetics , Schizophrenia/genetics , Adult , Child Development Disorders, Pervasive/epidemiology , Comorbidity , Europe/epidemiology , Female , Humans , Intellectual Disability/epidemiology , Male , Mental Disorders/epidemiology , Microarray Analysis , Middle Aged , Schizophrenia/epidemiology
17.
BMC Med Genet ; 18(1): 137, 2017 11 21.
Article in English | MEDLINE | ID: mdl-29162042

ABSTRACT

BACKGROUND: Patients with Angelman syndrome (AS) are affected by severe intellectual disability with absence of speech, distinctive dysmorphic craniofacial features, ataxia and a characteristic behavioral phenotype. AS is caused by the lack of expression in neurons of the UBE3A gene, which is located in the 15q11.2-q13 imprinted region. Functional loss of UBE3A is due to 15q11.2-q13 deletion, mutations in the UBE3A gene, paternal uniparental disomy and genomic imprinting defects. CASE PRESENTATION: We report here two patients with clinical features of AS referred to our hospital for clinical follow-up and genetic diagnosis. Methylation Specific-Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) of the 15q11.2-q13 region was carried out in our laboratory as the first diagnostic tool detecting two novel UBE3A intragenic deletions. Subsequently, the MLPA P336-A2 kit was used to confirm and determine the size of the UBE3A deletion in the two patients. A review of the clinical features of previously reported patients with whole UBE3A gene or partial intragenic deletions is presented here together with these two new patients. CONCLUSION: Although rare, UBE3A intragenic deletions may represent a small fraction of AS patients without a genetic diagnosis. Testing for UBE3A intragenic exonic deletions should be performed in those AS patients with a normal methylation pattern and no mutations in the UBE3A gene.


Subject(s)
Angelman Syndrome/genetics , Base Sequence , Chromosomes, Human, Pair 15 , Genomic Imprinting , Sequence Deletion , Ubiquitin-Protein Ligases/genetics , Angelman Syndrome/diagnosis , Angelman Syndrome/pathology , Child, Preschool , Exons , Female , Gene Dosage , Humans , Neurons/metabolism , Neurons/pathology , Nucleic Acid Amplification Techniques , Reagent Kits, Diagnostic , Ubiquitin-Protein Ligases/deficiency
18.
Nat Commun ; 8(1): 467, 2017 09 07.
Article in English | MEDLINE | ID: mdl-28883545

ABSTRACT

It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our observations in primary tumors. Imprinted differentially methylated regions (DMRs) regulate parent-of-origin monoallelic expression of neighboring transcripts in cis. Unlike single-copy CpG islands that may be prone to hypermethylation, imprinted DMRs can either loose or gain methylation during tumorigenesis. Here, we show that methylation profiles at imprinted DMRs often not represent genuine epigenetic changes but simply the accumulation of underlying copy-number aberrations (CNAs), which is independent of the genome methylation state inferred from cancer susceptible loci. Our results reveal that CNAs also influence allelic expression as loci with copy-number neutral loss-of-heterozygosity or amplifications may be expressed from the appropriate parental chromosomes, which is indicative of maintained imprinting, although not observed as a single expression foci by RNA FISH.Altered genomic imprinting is frequently reported in cancer. Here, the authors analyze copy number and methylation in cancer cell lines and primary tumors to show that imprinted methylation profiles represent the accumulation of copy number alteration, rather than epigenetic alterations.


Subject(s)
Epigenesis, Genetic , Gene Dosage , Genomic Imprinting , Neoplasms/genetics , Alleles , Cell Line, Tumor , DNA Copy Number Variations/genetics , DNA Methylation/genetics , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Genetic Loci , Humans
19.
Am J Med Genet A ; 173(10): 2795-2797, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28815939

ABSTRACT

Fragile X syndrome (FXS) is the most common form of inherited intellectual disability (ID) and autism. In most of cases, the molecular basis of this syndrome is a CGG repeat expansion in the 5' untranslated region of the FMR1 gene. It is inherited as an X linked dominant trait, with a reduced penetrance (80% for males and 30% for females). Full mutation (FM) expansion from premutated alleles (PM) is only acquired via maternal meiosis, while paternal transmission always remains in the PM range. We present a 16-year-old girl with a mild fragile X syndrome phenotype. FMR1 gene study showed that the patient inherited a mosaic premutation-full mutation with an unmethylated uninterrupted allele (175, >200 CGG) from her father. The father showed an 88 CGG uninterrupted unmethylated allele in blood and sperm cells. To our knowledge, this is the first case of a FMR1 mosaic premutation-full mutation allele inherited from a PM father. In our opinion, the most likely explanation could be a postzygotic somatic expansion. We can conclude that in rare cases of a child with a full mutation whose mother does not carry a premutation, the possibility of paternal transmission should be considered.


Subject(s)
Fragile X Mental Retardation Protein/genetics , Fragile X Syndrome/genetics , Mutation , Paternal Inheritance , Adolescent , Adult , Female , Fragile X Syndrome/pathology , Humans , Male , Young Adult
20.
Gene ; 628: 109-116, 2017 Sep 10.
Article in English | MEDLINE | ID: mdl-28710037

ABSTRACT

RNA editing is being recognized as an important post-transcriptional mechanism that may have crucial roles in introducing genetic variation and phenotypic diversity. Despite microRNA editing recurrence, defining its biological relevance is still under extended debate. To better understand microRNA editing function and regulation we performed an exhaustive characterization of the A-to-I site-specific patterns in mir-376a-1, a mammalian microRNA which RNA editing is involved in the regulation of development and in disease. Thorough an integrative approach based on high-throughput small RNA sequencing, Sanger sequencing and computer simulations we explored mir-376a-1 editing in samples from various individuals and primate species including human placenta and macaque, gorilla, chimpanzee and human brain cortex. We observed that mir-376a-1 editing is a common phenomenon in the mature and primary microRNA molecules and it is more frequently detected in brain than in placenta. Primary mir-376a-1 is edited at three positions, -1, +4 and +44. Editing frequency estimations and in silico simulations indicated that editing was not equally recurrent along the three mir-376a-1 sites, nevertheless no epistatic interactions among them were observed. Particularly, the +4 site, located in the seed region of the mature miR-376a-5p, reached the highest editing frequency in all samples. Secondary structure predictions revealed that the +4 position was the one that conferred the highest stability to the mir-376a-1 hairpin. We suggest that molecular stability might partially explain the editing recurrence observed in certain microRNAs and that editing events conferring new functional regulatory roles in particular tissues and species could have been conserved along evolution, as it might be the case of mir-376a-1 in primate brain cortex.


Subject(s)
MicroRNAs/metabolism , RNA Editing , RNA Stability , Animals , Cerebral Cortex/metabolism , Epistasis, Genetic , Female , Gorilla gorilla , Macaca , MicroRNAs/genetics , Nucleic Acid Conformation , Pan troglodytes , Placenta/metabolism , Pregnancy
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