Interstitial deletion of the long arm of chromosome 5 in a boy with multiple congenital anomalies and mental retardation: Molecular characterization of the deleted region to 5q22.3q23.3

Novel Genetic Diagnoses in Septo-Optic Dysplasia

Septo-optic dysplasia (SOD) is a developmental phenotype characterized by midline neuroradiological anomalies, optic nerve hypoplasia, and pituitary anomalies, with a high degree of variability and additional systemic anomalies present in some cases. While disruption of several transcription factors has been identified in SOD cohorts, most cases lack a genetic diagnosis, with multifactorial risk factors being thought to play a role. Exome sequencing in a cohort of families with a clinical diagnosis of SOD identified a genetic diagnosis in 3/6 families, de novo variants in SOX2, SHH, and ARID1A, and explored variants of uncertain significance in the remaining three. The outcome of this study suggests that investigation for a genetic etiology is warranted in individuals with SOD, particularly in the presence of additional syndromic anomalies and when born to older, multigravida mothers. The identification of causative variants in SHH and ARID1A further expands the phenotypic spectra associated with these genes and reveals novel pathways to explore in septo-optic dysplasia.

Severe congenital contractural arachnodactyly caused by biallelic pathogenic variants in FBN2

Fibrillin-2, encoded by FBN2, plays an important role in the early process of elastic fiber assembly. To date, heterozygous pathogenic variants in FBN2 have been shown to cause congenital contractural arachnodactyly (CCA; Beals-Hecht syndrome). Classical CCA is characterized by long and slender fingers and toes, ear deformities, joint contractures at birth, clubfeet, muscular hypoplasia and often tall stature. In individuals with a severe CCA form, different cardiovascular or gastrointestinal anomalies have been described. Here, we report on a 15-year-old girl with a severe form of CCA and novel biallelic variants in FBN2. The girl inherited the missense variant c.3563G > T/p.(Gly1188Val) from her unaffected father and the nonsense variant c.6831C > A/p.(Cys2277*) from her healthy mother. We could detect only a small amount of FBN2 transcripts harboring the nonsense variant in leukocyte-derived mRNA from the patient and mother suggesting nonsense-mediated mRNA decay. As the father did not show any clinical signs of CCA we hypothesize the missense variant c.3563G > T to be a hypomorphic allele. Taken together, our data suggests that severe CCA can be inherited in an autosomal-recessive manner by compound heterozygosity of a hypomorphic and a null allele of the FBN2 gene.

Chromosomal microarray analysis in fetuses with central nervous system anomalies: An 8-year long observational study from a tertiary care university hospital

OBJECTIVES

To evaluate the prevalence of DNA copy number variants (CNVs) detected with array comparative genomic hybridization (CGH) in fetuses with central nervous system (CNS) anomalies. Secondary objectives were to describe the prevalence of CNV in specific CNS abnormalities, in isolated defects or associated with other malformations or fetal growth restriction (FGR).

METHODS

Observational cohort study in 238 fetuses with CNS anomalies in which an array-CGH had been performed between January 2009 and December 2017. Pathogenic CNV and variants of unknown significance (VUS) were reported.

RESULTS

Pathogenic CNVs were found in 16/238 cases (6.7%), VUS in 18/238 (7.6%), and normal result in 204/238 (85.7%) cases. Pathogenic CNVs were more frequent in posterior fossa anomalies (cerebellar hypoplasia 33%, megacisterna magna 20%), moderate ventriculomegaly (11%) and spina bifida (3.7%). Pathogenic CNVs and VUS were found in 7/182 (3.8%) and 14/182 (7.7%) cases of isolated anomalies, in 9/49 (18.4%) and 4/49 (8.2%) presenting another malformation, and in 0/7 and 0/7 cases with associated FGR (P = .001, P = .741, respectively).

CONCLUSION

These results provide strong evidence toward performing array in fetuses with CNS anomalies, particular in cases of posterior fossa anomalies. The prevalence of pathogenic CNVs is higher in association with other malformations.

Interstitial Deletion of 5q22.2q23.1 Including APC and TSSK1B in a Patient with Adenomatous Polyposis and Asthenoteratozoospermia

Interstitial 5q22 deletions are relatively rare and usually represented by severe clinical features such as developmental delay and growth retardation. Here, we report a 23-year-old male patient, referred to our laboratory for genetic confirmation of possible familial adenomatous polyposis. MLPA and the subsequent array CGH identified an approximately 8-Mb-sized deletion in the 5q22.2q23.1 locus. Further analysis of the deleted region and the genes within suggested a possible role for the TSSK1B (testis-specific serine/threonine kinase 1) gene in the patient's reproductive capacity. Semen analysis confirmed that the patient's reproductive capability was impaired, and that he suffered from asthenoteratozoospermia. Analysis of the azoospermia factor region on the Y chromosome revealed no microdeletions. Further sequencing tests could not find an alternative explanation for the patient's infertility. This case demonstrates a possible role of TSSK1B in male reproduction.

Ocular Manifestations of a Novel Proximal 19p13.3 Microdeletion

Microdeletions at 19p13.3 are rarely reported in the medical literature with significant phenotypic variability. Among the reported cases, common clinical manifestations have included developmental delay, facial dysmorphism, and hypotonia. Herein we described a child with a de novo 19p13.3 microdeletion, proximal to the reported cases of 19p13.3 microdeletion/duplication, with ocular manifestations of bilateral ocular colobomata complicated with microphthalmos and cataract, associated with short stature. This case highlights the phenotypic heterogeneity of deletions in the 19p13.3 region.

Could APC Gene Screening be Useful in Children with Hepatoblastoma? Early Onset of Adenocarcinoma in a Child with Familial Adenomatous Polyposis and Hepatoblastoma

Familial adenomatous polyposis is an inherited disorder characterized by the development of hundreds of colorectal adenomas during adolescence, which in many cases will transform into colorectal cancer by the fourth decade of life, along with the development of various malignant tumors including hepatoblastoma. We report on a female patient with a de novo interstitial deletion of 5q21.3-q23.3, encompassing the APC gene, associated with adenomatous polyposis and early colorectal cancer, hepatoblastoma, epidermoid cysts, mental retardation, several mild dysmorphic signs and lower limb venous thrombosis.

A syndromic form of Pierre Robin sequence is caused by 5q23 deletions encompassing FBN2 and PHAX

Pierre Robin sequence (PRS) is an aetiologically distinct subgroup of cleft palate. We aimed to define the critical genomic interval from five different 5q22-5q31 deletions associated with PRS or PRS-associated features and assess each gene within the region as a candidate for the PRS component of the phenotype. Clinical array-based comparative genome hybridisation (aCGH) data were used to define a 2.08 Mb minimum region of overlap among four de novo deletions and one mother-son inherited deletion associated with at least one component of PRS. Commonly associated anomalies were talipes equinovarus (TEV), finger contractures and crumpled ear helices. Expression analysis of the orthologous genes within the PRS critical region in embryonic mice showed that the strongest candidate genes were FBN2 and PHAX. Targeted aCGH of the critical region and sequencing of these genes in a cohort of 25 PRS patients revealed no plausible disease-causing mutations. In conclusion, deletion of ∼2 Mb on 5q23 region causes a clinically recognisable subtype of PRS. Haploinsufficiency for FBN2 accounts for the digital and auricular features. A possible critical region for TEV is distinct and telomeric to the PRS region. The molecular basis of PRS in these cases remains undetermined but haploinsufficiency for PHAX is a plausible mechanism.

Multidisciplinary treatment of desmoid tumours in Gardner's syndrome due to a large interstitial deletion of chromosome 5q

BACKGROUND AND AIMS

Classic autosomal-dominant familial adenomatous polyposis (FAP) is clinically defined by the development of hundreds to thousands of colorectal adenomas beginning in childhood and adolescence. A variant of FAP characterized by polyposis in combination with osteomas or soft tissue tumours is called Gardner's syndrome. FAP is caused by germline inactivation of the APC (adenomatous polyposis coli) tumour-suppressor gene located on the long arm of chromosome 5 (5q21-5q22). Cytogenetically visible deletions of chromosome 5q encompassing APC have very rarely been reported. Here, we aimed to phenotypically and genetically characterize a patient with a heterozygous 5q deletion resulting in Gardner's syndrome.

METHODS AND RESULTS

A 26-year-old female patient with mild mental handicap and dysmorphic features due to a cytogenetically visible deletion on chromosome 5q (microscopically estimated region 5q14-5q23) presented at our tertiary referral centre because of mild adenomatous polyposis (<500 polyps). Twenty months after prophylactic proctocolectomy with definitive ileostomy, three rapidly growing desmoids were observed. Tumour-associated complications necessitated a multidisciplinary approach including medical treatment, surgery and radiation therapy. The characterization of the deletion by comparative genomic hybridization identified a large 5q deletion expanding over a 20-Mb region (5q21.3-5q23.3) including the APC gene.

CONCLUSION

Chromosome deletions must be suspected in patients presenting with FAP together with mental handicap and dysmorphic features. This case also impressively shows that FAP-associated desmoids need multimodal treatment taking into account the patient's individual symptoms, disease progression and tumour location.

Prenatal diagnosis of de novo interstitial deletions involving 5q23.1-q23.3 and 18q12.1-q12.3 by array CGH using uncultured amniocytes in a pregnancy with fetal interrupted aortic arch and atrial septal defect

We present prenatal diagnosis of de novo interstitial deletions involving 5q23.1-q23.3 and 18q12.1-q12.3 by aCGH using uncultured amniocytes in pregnancy with interrupted aortic arch and atrial septal defect in a fetus. The fetus postnatally manifested facial dysmorphisms and long slender fingers. We discuss the genotype-phenotype correlation and the consequence of haploinsufficiency of FBN2, DTNA and CELF4 in this case.

Mutation of Semaphorin-6A disrupts limbic and cortical connectivity and models neurodevelopmental psychopathology

Psychiatric disorders such as schizophrenia and autism are characterised by cellular disorganisation and dysconnectivity across the brain and can be caused by mutations in genes that control neurodevelopmental processes. To examine how neurodevelopmental defects can affect brain function and behaviour, we have comprehensively investigated the consequences of mutation of one such gene, Semaphorin-6A, on cellular organisation, axonal projection patterns, behaviour and physiology in mice. These analyses reveal a spectrum of widespread but subtle anatomical defects in Sema6A mutants, notably in limbic and cortical cellular organisation, lamination and connectivity. These mutants display concomitant alterations in the electroencephalogram and hyper-exploratory behaviour, which are characteristic of models of psychosis and reversible by the antipsychotic clozapine. They also show altered social interaction and deficits in object recognition and working memory. Mice with mutations in Sema6A or the interacting genes may thus represent a highly informative model for how neurodevelopmental defects can lead to anatomical dysconnectivity, resulting, either directly or through reactive mechanisms, in dysfunction at the level of neuronal networks with associated behavioural phenotypes of relevance to psychiatric disorders. The biological data presented here also make these genes plausible candidates to explain human linkage findings for schizophrenia and autism.

Copy number variations and primary open-angle glaucoma

PURPOSE

This study sought to investigate the role of rare copy number variation (CNV) in age-related disorders of blindness, with a focus on primary open-angle glaucoma (POAG). Data are reported from a whole-genome copy number screen in a large cohort of 400 individuals with POAG and 500 age-matched glaucoma-free subjects.

METHODS

DNA samples from patients and controls were tested for CNVs using a combination of two microarray platforms. The signal intensity data generated from these arrays were then analyzed with multiple CNV detection programs including CNAG version 2.0, PennCNV, and dChip.

RESULTS

A total of 11 validated CNVs were identified as recurrent in the POAG set and absent in the age-matched control set. This set included CNVs on 5q23.1 (DMXL1, DTWD2), 20p12 (PAK7), 12q14 (C12orf56, XPOT, TBK1, and RASSF3), 12p13.33 (TULP3), and 10q34.21 (PAX2), among others. The CNVs presented here are exceedingly rare and are not found in the Database of Genomic Variants. Moreover, expression data from ocular tissue support the role of these CNV-implicated genes in vision-related processes. In addition, CNV locations of DMXL1 and PAK7 overlap previously identified linkage signals for glaucoma on 5p23.1 and 20p12, respectively.

CONCLUSIONS

The data are consistent with the hypothesis that rare CNV plays a role in the development of POAG.

A new microdeletion syndrome of 5q31.3 characterized by severe developmental delays, distinctive facial features, and delayed myelination

Chromosomal deletion including 5q31 is rare and only a few patients have been reported to date. We report here the first two patients with a submicroscopic deletion of 5q31.3 identified by microarray-based comparative genomic hybridization. The common clinical features of both patients were marked hypotonia,feeding difficulty in infancy, severe developmental delay, and epileptic/nonepileptic encephalopathy associated with delayed myelination. Both patients also shared characteristic facial features,including narrow forehead, low-set and dysmorphic ears, bilateral ptosis, anteverted nares, long philtrum, tented upper vermilion,edematous cheeks, and high arched palate. The deleted region contains clustered PCDHs, including PCDHA [corrected]. and PCDHG, which are highly expressed in the brain where they function to guide neurons during brain development, neuronal differentiation, and synaptogenesis. The common deletion also contains neuregulin 2(NRG2), a major gene for neurodevelopment. We suggest that 5q31.3 deletion is responsible for severe brain developmental delay and distinctive facial features, and that the common findings in these two patients should be recognized as a new microdeletion syndrome. We need further investigations to determine which genes are really responsible for patients' characteristic features

CHERI: time to identify the syndrome?

Chiari I malformations are congenital abnormalities that are etiologically heterogeneous. Some studies recognize a probable association between Chiari 1 malformation, delayed language or motor development, and mental retardation with or without epilepsy. The present patient appeared to have an isolated cleft palate and Chiari 1 malformation with co-existing functional and behavioral disorders (i.e., speech delay, mental retardation, and deviant electroencephalography [EEG]). In consideration of the cleft palate population, the implication of the present case study is that more attention should be paid to the developmental milestones in children with cleft palate. Because several cases of Chiari I anomaly co-occurring with mental retardation and deviant EEG or epilepsy have been recognized, it appears justified to identify a syndrome, which is here called CHERI (Chiari 1 malformation with or without cleft palate, deviant EEG or epilepsy, and retarded intelligence with delayed language development). It will be important in the future to describe those cases identified to delineate the clinical picture and to estimate the frequency of the occurrence of various characteristics.

Fortuitous FISH diagnosis of an interstitial microdeletion (5)(q31.1q31.2) in a girl suspected to present a cri-du-chat syndrome

Constitutional interstitial deletions of 5q are relatively rare and most are poorly characterized cytogenetically. Consequently a definite karyotype-phenotype correlation is difficult to establish. We report on a new case of a girl presenting with an abnormal cry, upslanting palpebral fissures, hypertelorism, anteverted nostrils, microretrognathia, growth retardation, and an adenoid cyst at the base of the tongue. The first suspected diagnosis was cri-du-chat syndrome because of the mewing cry. Standard cytogenetic analyses were interpreted as normal, but FISH studies using the probe of cri-du-chat syndrome with the control probe EGR1 (5q31.2)/D5S23 (Abbott) revealed a 5q31.2 microdeletion which was then confirmed by CGH-array (Abbott). FISH studies using PACs and BACs clones (Rocchi, Italia) enabled us to characterize the breakpoints of the deleted region. Cytogenetic analysis with FISH studies revealed a normal karyotype with normal 5q31 region in both parents. This case is compared with the other cases reported in the literature.

Molecular cytogenetic analysis of a de novo interstitial deletion of 5q23.3q31.2 and its phenotypic consequences

We report a 2(3/12)-year-old boy with a constitutional interstitial deletion of 5q,46,XY,del(5)(q23.3q31.2) de novo. Clinical manifestations in this patient included failure to thrive, psychomotor retardation, mild facial dysmorphic features, and long and slender fingers and toes. The precise location and extent (9.5 Mb) of the deletion was determined by fluorescence in situ hybridization (FISH) using 19 YAC and BAC clones. Comparison of the present patient with six other patients with deletions of chromosomal bands 5q22-5q31 allowed further delineation of a constitutional del5q22q31 syndrome. The main features of this syndrome are psychomotor retardation, failure to thrive, hypotonia, hypoplastic muscles, cleft or high arched palate, low-set and dysplastic ears, flat nasal bridge, downslanting palpebral fissures, hypertelorism, anteverted nostrils, and micro- and/or retrognathia.

Identification of novel target genes of CeTwist and CeE/DA

Twist, a basic helix-loop-helix (bHLH) transcription factor, plays an important role in mesoderm development in many organisms, including C. elegans where CeTwist is required to direct cell fate specifications of a subset of mesodermal cells. Although several target genes of CeTwist have been identified, how this protein accomplishes its function is unclear. In addition, several human genes whose mutations cause different syndromes of craniosynostosis (premature fusion of cranial sutures) have homologues in the CeTwist pathway. Identification of novel target genes of CeTwist will shed more light on the functions of CeTwist in mesoderm development, and the corresponding human homologues will be good candidates for related syndromes with unidentified mutated genes. In our study, both CeTwist and its heterodimeric partner, CeE/DA, were overexpressed from the inducible heat-shock promoter, and potential target genes were detected with Affymetrix oligonucleotide microarrays. Using transcriptional GFP reporters, we found 11 genes were expressed in cells coincident with known CeTwist target gene products. Based on subsequent validation experiments, 9 genes were defined as novel CeTwist and CeE/DA targets. Human homologues of two of these genes might be involved in craniofacial diseases, which further validates C. elegans as a good model organism for providing insights into these disorders.

Phenotypic and molecular characterisation of a de novo 5q deletion that includes the APC gene

We report on a 12-year-old female patient with mild dysmorphic signs, including bilateral epicanthal folds, low-set dysplastic ears, a short nose with anteverted nostrils, conically shaped fingers, generalised increase of subcutaneous fat, multiple fine venous teleangiectasia on her back, mild pectus carinatum, and a general muscular hypotonia. Cytogenetic analysis and fluorescence in situ hybridisation (FISH) studies using region-specific BAC and YAC clones indicated a de novo interstitial deletion of the long arm of chromosome 5, resulting in monosomy 5q21.1-q23.1. Molecular analysis of polymorphic markers helped to narrow down the breakpoints and demonstrated that the derivative chromosome 5 is of paternal origin. By using the same panel of polymorphic markers, a reinvestigation of a similar, already published, 5q deletion case [Raedle et al. (2001) Am J Gastroenterol 96:3016-3020] was performed, allowing a more detailed genotype-phenotype correlation. Phenotypic classification was also carried out. Several known genes, including APC and MCC, were found to map to the common deleted genomic segment. Genetic counselling based on the molecular analysis data was performed for the index family.