Yield of clinically reportable genetic variants in unselected cerebral palsy by whole genome sequencing.

Cerebral palsy (CP) is the most common cause of childhood physical disability, with incidence between 1/500 and 1/700 births in the developed world. Despite increasing evidence for a major contribution of genetics to CP aetiology, genetic testing is currently not performed systematically. We assessed the diagnostic rate of genome sequencing (GS) in a clinically unselected cohort of 150 singleton CP patients, with CP confirmed at >4 years of age. Clinical grade GS was performed on the proband and variants were filtered, and classified according to American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines. Variants classified as pathogenic or likely pathogenic (P/LP) were further assessed for their contribution to CP. In total, 24.7% of individuals carried a P/LP variant(s) causing or increasing risk of CP, with 4.7% resolved by copy number variant analysis and 20% carrying single nucleotide or indel variants. A further 34.7% carried one or more rare, high impact variants of uncertain significance (VUS) in variation intolerant genes. Variants were identified in a heterogeneous group of genes, including genes associated with hereditary spastic paraplegia, clotting and thrombophilic disorders, small vessel disease, and other neurodevelopmental disorders. Approximately 1/2 of individuals were classified as likely to benefit from changed clinical management as a result of genetic findings. In addition, no significant association between genetic findings and clinical factors was detectable in this cohort, suggesting that systematic sequencing of CP will be required to avoid missed diagnoses.

Generation of induced pluripotent stem cells (iPSCs) by retroviral transduction of skin fibroblasts from four patients suffering Williams-Beuren syndrome (7q11.23 deletion).

Skin fibroblasts were obtained from four patients with Williams-Beuren syndrome (WBS) carrying the typical 1.5 Mb or 1.8 Mb deletion at the 7q11.23 genomic region. Induced pluripotent stem cells (iPSCs) were generated by retroviral infection of fibroblasts with polycystronic vectors. The generated iPSC clones ESi059A, ESi060B and ESi068A had the 1.5 Mb deletion of 7q11.23 and ESi069A the 1.8 Mb, with no novel additional genomic alterations, stable karyotype, expressed pluripotency markers and could differentiate towards the three germ layers in vitro via embryoid body formation and in vivo by teratoma formation. WBS patient's lines are a valuable resource for in vitro modelling of WBS.

Derivation of induced pluripotent stem cells (iPSCs) by retroviral transduction of skin fibroblasts from four patients suffering 7q11.23 microduplication syndrome.

Skin fibroblasts were obtained from four patients with 7q11.23 microduplication syndrome carrying the reciprocal rearrangement of Williams-Beuren syndrome at the 7q11.23 genomic region. Induced pluripotent stem cells (iPSCs) were generated by retroviral infection of fibroblasts with polycystronic vectors. The generated iPSC clones ESi058B, ESi057B, ESi070A and ESi071A had the 7q11.23 duplication with no additional genomic alterations, a stable karyotype, expressed pluripotency markers and could differentiate towards the three germ layers in vitro via embryoid body formation and in vivo by teratoma formation. Patient's derived iPSCs are a valuable resource for in vitro modeling of 7q11.23 microduplication syndrome. Resource Table.

Clinical implication of FMR1 intermediate alleles in a Spanish population.

FMR1 premutation carriers (55-200 CGGs) are at risk of developing Fragile X-associated primary ovarian insufficiency as well as Fragile X-associated tremor/ataxia syndrome. FMR1 premutation alleles are also associated with a variety of disorders, including psychiatric, developmental, and neurological problems. However, there is a major concern regarding clinical implications of smaller CGG expansions known as intermediate alleles (IA) or gray zone alleles (45-54 CGG). Although several studies have hypothesized that IA may be involved in the etiology of FMR1 premutation associated phenotypes, this association still remains unclear. The aim of this study was to provide new data on the clinical implications of IA. We reviewed a total of 17 011 individuals: 1142 with primary ovarian insufficiency, 478 with movement disorders, 14 006 with neurodevelopmental disorders and 1385 controls. Similar IA frequencies were detected in all the cases and controls (cases 1.20% vs controls 1.39%, P = .427). When comparing the allelic frequencies of IA ≥ 50CGGs, a greater, albeit not statistically significant, number of alleles were detected in all the cohorts of patients. Therefore, IA below 50 CGGs should not be considered as risk factors for FMR1 premutation-associated phenotypes, at least in our population. However, the clinical implication of IA ≥ 50CGGs remains to be further elucidated.

Genetic and epigenetic methylation defects and implication of the ERMN gene in autism spectrum disorders.

Autism spectrum disorders (ASD) are highly heritable and genetically complex conditions. Although highly penetrant mutations in multiple genes have been identified, they account for the etiology of <1/3 of cases. There is also strong evidence for environmental contribution to ASD, which can be mediated by still poorly explored epigenetic modifications. We searched for methylation changes on blood DNA of 53 male ASD patients and 757 healthy controls using a methylomic array (450K Illumina), correlated the variants with transcriptional alterations in blood RNAseq data, and performed a case-control association study of the relevant findings in a larger cohort (394 cases and 500 controls). We found 700 differentially methylated CpGs, most of them hypomethylated in the ASD group (83.9%), with cis-acting expression changes at 7.6% of locations. Relevant findings included: (1) hypomethylation caused by rare genetic variants (meSNVs) at six loci (ERMN, USP24, METTL21C, PDE10A, STX16 and DBT) significantly associated with ASD (q-value <0.05); and (2) clustered epimutations associated to transcriptional changes in single-ASD patients (n=4). All meSNVs and clustered epimutations were inherited from unaffected parents. Resequencing of the top candidate genes also revealed a significant load of deleterious mutations affecting ERMN in ASD compared with controls. Our data indicate that inherited methylation alterations detectable in blood DNA, due to either genetic or epigenetic defects, can affect gene expression and contribute to ASD susceptibility most likely in an additive manner, and implicate ERMN as a novel ASD gene.

Lateral preference in Williams-Beuren syndrome is associated with cognition and language.

Williams-Beuren syndrome (WBS) is a genetically defined neurodevelopmental disorder presenting with intellectual disability associated with a specific neurocognitive profile characterized by anxiety, hypersociability, poor visuospatial skills and relatively preserved language. We have defined the lateral preference in 69 individuals (40 males and 29 females, age range 5-47 years) with WBS confirmed by molecular testing, and explored its correlation with cognition, behavior problems, the main aspects of the behavioral phenotype, and specific molecular variants (parental origin and size of the 7q11.23 deletion). Lateral preference (hand, foot, eye and ear) and neurobehavioral features [intelligence quotient (IQ), sociability, visuospatial construction, narrative skills and behavior] were assessed by a battery of tests and parental interviews. A large proportion of WBS individuals showed either left or mixed handedness (26 and 19%, respectively). Hand, foot and ear lateral preference showed significant association with IQ, with individuals with mixed lateral preference presenting lower general IQ, especially verbal IQ, with respect to subjects with well-defined laterality. Approachability, visuospatial ability, behavior problems or molecular variants were not associated with lateral preference. Our results indicate that, as in other neurodevelopmental disorders, laterality is poorly defined in a significant proportion of WBS individuals, and reinforces the idea that a correct definition of lateral preference is important for cognition and language.

[Blood cell chimerism in dizygotic twins conceived by in vitro fertilization]. / Quimerismo hemático en gemelos dicigóticos concebidos por fertilización in vitro.

We present a case of hematopoietic chimerism in dizygotic twins (male and female) conceived by in vitro fertilization (IVF). At 8 years of age a blood karyotype was performed on the female due to the presence of clitoromegaly. Two different lines: 46,XX (53%) and 46,XY (47%) were found. FISH studies confirmed the presence of the SRY gene in 46,XY cells. Karyotyping of the male showed two different lines: 46,XY (58%) and 46,XX (42%). SRY gene was present in 46,XY cells. Microsatellite analyses of blood DNA revealed tetra-allelic contribution at some autosomal loci with similar proportions of maternal and paternal alleles and X/Y chromosome dose. FISH in buccal mucous showed that all cells from the female were 46,XX and those from the male 46,XY. The gonadal karyotype in the female was 46,XX without SRY. Hence, we report 46,XX/46,XY chimerism in dizygotic twins. Blood chimerism was confirmed by performing FISH on the buccal cells of the patients.

Behavioral features of Williams Beuren syndrome compared to Fragile X syndrome and subjects with intellectual disability without defined etiology.

Williams-Beuren syndrome (WBS) is a genetically determined neurodevelopmental disorder caused by a heterozygous deletion of 26-28 genes on chromosome band 7q11.23. During the past few years, researchers and clinicians have significantly contributed to define the phenotype of the syndrome, including its cognitive and behavioral aspects. However, it is not well known yet whether the psychological problems are specific to the syndrome or secondary to the intellectual disability (ID). The aim of our study was to better define the psychopathological profile of WBS and whether or not it is related with IQ or anxiety symptoms. Twenty-five subjects (12 girls, 13 boys) with a diagnosis of WBS were compared to 27 boys with Fragile X Syndrome and to 24 boys with ID of non-specific etiology using the Child Behavior Checklist. Anxiety, depression and attention problems were the main behavioral problems found in WBS with no gender differences. Significant differences between cohorts were observed in somatic complaints, delinquent behavior, aggressive behavior, and externalizing problems. Some associations between IQ and anxiety items were found. The findings are discussed in terms of behavioral phenotypes, genetic implications and ID.

Partial 7q11.23 deletions further implicate GTF2I and GTF2IRD1 as the main genes responsible for the Williams-Beuren syndrome neurocognitive profile.

BACKGROUND: Williams-Beuren syndrome (WBS) is a developmental disorder with multisystemic manifestations mainly characterised by vascular stenoses, distinctive craniofacial features, mental retardation with a characteristic neurocognitive profile, and some endocrine and connective tissue abnormalities, caused by a recurrent deletion of 1.55 Mb including 26-28 genes at chromosomal region 7q11.23. The analysis of clinical-molecular correlations in a few reported atypical patients has been useful to propose several deleted genes as main contributors to specific aspects of the WBS phenotype. PATIENTS AND METHODS: Two additional families with partial phenotypes and atypical 7q11.23 deletions were studied. Deletions were precisely defined at the nucleotide level, and the expression levels of some affected and flanking genes were assessed in lymphoblastoid cell lines. RESULTS: Affected individuals presented variable cardiovascular and connective tissue manifestations, subtle craniofacial features, normal visuospatial construction abilities with low average IQ and no endocrine abnormalities. The deletion in family NW1 encompassed 817 kb with 11 genes (CLDN3-GTF2IRD1), and 610 kb with 14 genes (VPS37D-RFC2) in family NW2. All deleted genes in typical and atypical deletions revealed low expression levels in lymphoblastoid cell lines, except for GTF2IRD1. CLIP2 was also underexpressed in all patients despite being outside the deletion in NW2, while no other flanking non-deleted gene showed significantly different expression compared to controls. CONCLUSIONS: Along with previously reported cases, clinical-molecular correlations in these two families further confirm that the functional hemizygosity for the GTF2I and GTF2IRD1 genes is the main cause of the neurocognitive profile and some aspects of the gestalt phenotype of WBS.

Association of common copy number variants at the glutathione S-transferase genes and rare novel genomic changes with schizophrenia.

Copy number variants (CNVs) are a substantial source of human genetic diversity, influencing the variable susceptibility to multifactorial disorders. Schizophrenia is a complex illness thought to be caused by a number of genetic and environmental effects, few of which have been clearly defined. Recent reports have found several low prevalent CNVs associated with the disease. We have used a multiplex ligation-dependent probe amplification-based (MLPA) method to target 140 previously reported and putatively relevant gene-containing CNV regions in 654 schizophrenic patients and 604 controls for association studies. Most genotyped CNVs (95%) showed very low (<1%) population frequency. A few novel rare variants were only present in patients suggesting a possible pathogenic involvement, including 1.39 Mb overlapping duplications at 22q11.23 found in two unrelated patients, and duplications of the somatostatin receptor 5 gene (SSTR5) at 16p13.3 in three unrelated patients. Furthermore, among the few relatively common CNVs observed in patients and controls, the combined analysis of gene copy number genotypes at two glutathione S-transferase (GST) genes, GSTM1 (glutathione S-transferase mu 1) (1p13.3) and GSTT2 (glutathione S-transferase theta 2) (22q11.23), showed a statistically significant association of non-null genotypes at both loci with an additive effect for increased vulnerability to schizophrenia (odds ratio of 1.92; P=0.0008). Our data provide complementary evidences for low prevalent, but highly penetrant chromosomal variants associated with schizophrenia, as well as for common CNVs that may act as susceptibility factors by disturbing glutathione metabolism.

Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome.

BACKGROUND: Recurrent 15q13.3 microdeletions were recently identified with identical proximal (BP4) and distal (BP5) breakpoints and associated with mild to moderate mental retardation and epilepsy. METHODS: To assess further the clinical implications of this novel 15q13.3 microdeletion syndrome, 18 new probands with a deletion were molecularly and clinically characterised. In addition, we evaluated the characteristics of a family with a more proximal deletion between BP3 and BP4. Finally, four patients with a duplication in the BP3-BP4-BP5 region were included in this study to ascertain the clinical significance of duplications in this region. RESULTS: The 15q13.3 microdeletion in our series was associated with a highly variable intra- and inter-familial phenotype. At least 11 of the 18 deletions identified were inherited. Moreover, 7 of 10 siblings from four different families also had this deletion: one had a mild developmental delay, four had only learning problems during childhood, but functioned well in daily life as adults, whereas the other two had no learning problems at all. In contrast to previous findings, seizures were not a common feature in our series (only 2 of 17 living probands). Three patients with deletions had cardiac defects and deletion of the KLF13 gene, located in the critical region, may contribute to these abnormalities. The limited data from the single family with the more proximal BP3-BP4 deletion suggest this deletion may have little clinical significance. Patients with duplications of the BP3-BP4-BP5 region did not share a recognisable phenotype, but psychiatric disease was noted in 2 of 4 patients. CONCLUSIONS: Overall, our findings broaden the phenotypic spectrum associated with 15q13.3 deletions and suggest that, in some individuals, deletion of 15q13.3 is not sufficient to cause disease. The existence of microdeletion syndromes, associated with an unpredictable and variable phenotypic outcome, will pose the clinician with diagnostic difficulties and challenge the commonly used paradigm in the diagnostic setting that aberrations inherited from a phenotypically normal parent are usually without clinical consequences.

Extending the phenotype of recurrent rearrangements of 16p11.2: deletions in mentally retarded patients without autism and in normal individuals.

Array CGH (comparative genomic hybridization) screening of large patient cohorts with mental retardation and/or multiple congenital anomalies (MR/MCA) has led to the identification of a number of new microdeletion and microduplication syndromes. Recently, a recurrent copy number variant (CNV) at chromosome 16p11.2 was reported to occur in up to 1% of autistic patients in three large autism studies. In the screening of 4284 patients with MR/MCA with various array platforms, we detected 22 individuals (14 index patients and 8 family members) with deletions in 16p11.2, which are genomically identical to those identified in the autism studies. Though some patients shared a facial resemblance and a tendency to overweight, there was no evidence for a recognizable phenotype. Autism was not the presenting feature in our series. The assembled evidence indicates that recurrent 16p11.2 deletions are associated with variable clinical outcome, most likely arising from haploinsufficiency of one or more genes. The phenotypical spectrum ranges from MR and/or MCA, autism, learning and speech problems, to a normal phenotype.

X-chromosome tiling path array detection of copy number variants in patients with chromosome X-linked mental retardation.

BACKGROUND: Aproximately 5-10% of cases of mental retardation in males are due to copy number variations (CNV) on the X chromosome. Novel technologies, such as array comparative genomic hybridization (aCGH), may help to uncover cryptic rearrangements in X-linked mental retardation (XLMR) patients. We have constructed an X-chromosome tiling path array using bacterial artificial chromosomes (BACs) and validated it using samples with cytogenetically defined copy number changes. We have studied 54 patients with idiopathic mental retardation and 20 controls subjects. RESULTS: Known genomic aberrations were reliably detected on the array and eight novel submicroscopic imbalances, likely causative for the mental retardation (MR) phenotype, were detected. Putatively pathogenic rearrangements included three deletions and five duplications (ranging between 82 kb to one Mb), all but two affecting genes previously known to be responsible for XLMR. Additionally, we describe different CNV regions with significant different frequencies in XLMR and control subjects (44% vs. 20%). CONCLUSION: This tiling path array of the human X chromosome has proven successful for the detection and characterization of known rearrangements and novel CNVs in XLMR patients.

MAPT gene duplications are not a cause of frontotemporal lobar degeneration.

Recurrent deletions of the 17q21.31 region encompassing the microtubule-associated protein tau (MAPT) gene have recently been described in patients with mental retardation. This region is flanked by segmental duplications that make it prone to inversions, deletions and duplications. Since gain-of-function mutations of the MAPT gene cause frontotemporal lobar degeneration (FTLD) characterized by deposition of tau protein, we hypothesize that MAPT duplication affecting gene dosage could also lead to disease. Gene dosage alterations have already been found to be involved in the etiology of neurodegenerative disorders caused by protein or peptide accumulation, such as Alzheimer's and Parkinson's diseases. To determine whether MAPT gene copy number variation is involved in FTLD, 70 patients with clinical diagnosis of FTLD and no MAPT mutation (including 12 patients with pathologically proven tau-positive FTLD) were screened by using multiplex ligation probe amplification (MLPA) with specific oligonucleotide probes. No copy number variation in the MAPT gene was observed in cases. Although our study was limited by the relatively small number of patients, it does not support the theory that chromosomal rearrangements in this region are a cause of FTLD.

[Clinical guide to the management of patients with Beckwith-Wiedemann syndrome]. / Guía clínica para el seguimiento de pacientes con síndrome de Beckwith-Wiedemann.

Beckwith-Wiedemann syndrome (BWS) is characterized by congenital overgrowth, macroglossia and omphalocele or umbilical hernia. Children with BWS may also have all or some of the following features: asymmetry (hemihypertrophy) of the limbs, torso or face, hypoglycemia, organomegaly, ear pits or creases, and embryonal tumors. The frequency of BWS is approximately 1:14,000 births. We present a guide for the management of children with BWS aimed at helping pediatricians and general practitioners or specialists in the clinical follow-up of these patients. This guide has been structured according to different age groups and is based on published evidence.

[Williams syndrome: its clinical aspects and molecular bases]. / Síndrome de Williams: aspectos clínicos y bases moleculares.

INTRODUCTION AND DEVELOPMENT: Williams syndrome is a developmental disorder with an estimated prevalence of 1 in 7,500 newborns. Its phenotype is characterized by distinctive facial features, mild to moderate mental retardation and general cognitive deficits with a non-uniform profile, having problems in some areas (psychomotricity, visuospatial integration) and relative preservation of others (language, musicality), friendly personality, occasional hypercalcemia of infancy, and a vasculopathy with supravalvular aortic stenosis. Williams syndrome is caused by a submicroscopic deletion of 1.55 Mb in the chromosome band 7q11.23, which includes 26-28 genes. The mutational mechanism consists in a misalignment between regions of almost identical sequence and the subsequent unequal recombination. The reciprocal product of this rearrangement is the duplication of this region, causing a language specific disorder. CONCLUSIONS: Clinical-molecular correlations establishment through a good phenotypic characterization and the precise analysis of breakpoints in patients with atypical and typical deletions, altogether with the design of animal models and functional studies in vitro for the genes of the interval will be important to be able to determine the exact contribution of the genes to the phenotype, to know their pathogenesis and physiopathology, and to identify therapeutic methods.

[Transient neonatal diabetes associated with uniparental isodisomy of chromosome 6]. / Diabetes mellitus neonatal transitoria asociada a isodisomía uniparental del cromosoma 6.

A female neonate was born after a 37.4-week pregnancy to a healthy primipara. There was a family history of diabetes on the father's side. The neonate's birth weight was 1,955 g and she was 43 cm long. Physical examination showed bilateral palpebral edema, macroglossia, umbilical hernia and abdominal distension. At 29 hours of life she presented hyperglycemia without acidosis or ketosis. Insulin treatment was started and maintained intermittently until 38 days of life. The patient presented anemia from the second day of life, which required iron therapy and blood transfusion one month after birth. The karyotype was 46, XX with paternal uniparental isodisomy of chromosome 6. Paternal uniparental isodisomy of chromosome 6 has been described as the pathogenic mechanism of transient neonatal diabetes, which provides evidence for an imprinted gene exclusively of paternal expression. In paternal isodisomy (as in regional duplications) there is overexpression due to the existence of two functional copies of the gene, which is responsible for transient neonatal diabetes mellitus. Transient neonatal diabetes associated with macroglossia, umbilical hernia and anemia has been described in only a few cases.

DNA affinity chromatography.

DNA-affinity chromatography has been used for the purification of DNA-binding proteins that control various cellular processes. There have been improvements in coupling methods and choice of supports over the years. The procedure for coupling 5'-aminoethyl-(dT)18 to silica activated with N-hydroxysuccinimide and a carbodiimide has been described. Also, the cyanogen bromide mediated coupling of aminoethyl-(dT)18 to Sepharose is described. Determination of (dT)18-coupling to silica and Sepharose is by 5' end-labeling an oligonucleotide containing a (dA)18 stretch of sequence and determining how much hybridizes with the (dT)18 support. Enzymatic synthesis of a double-stranded DNA-silica or Sepharose prevents modification of nucleotide bases. We have explained the use of DNA and RNA templates for template-directed enzymatic synthesis of affinity columns. DNA-affinity chromatography is a powerful method with broad applicability and we are currently extending this technology for purifying transcription factors, polymerases, and nucleases.

Evaluation of the Stag3 gene and the synaptonemal complex in a rat model (as/as) for male infertility.

Affected males (as/as) from the mutant TT rat strain are sterile due to spermatogenesis impairment with meiotic arrest at the pachytene stage. The as locus is on rat chromosome 12, in a region that shows conserved synteny to cM 74-94 on mouse chromosome 5. Stag3, a new member of the stromalin protein family, is expressed specifically in testis and associates to the synaptonemal complex. Mouse Stag3 gene has been assigned to cM 78 on chromosome 5. In this study, we have characterized the rat Stag3 gene and examined it as a candidate for male infertility in as/as rats. The rat Stag3 cDNA is 4181 nucleotides long, contains a highly polymorphic hexanucleotide repeat in the coding region, and encodes a 1256 amino acid protein with 93 and 77% sequence identity to mouse and human Stag3 proteins, respectively. No mutations or differences in size or abundance of Stag3 mRNA were detected between as/as and control rats, suggesting that Stag3 is not responsible for the aspermic phenotype. In addition, immunohistochemistry with antibodies against SCP1 and SPC3 proteins suggest that the synaptonemal complex structures are not primarily affected in these rats.