Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes.

BACKGROUND: Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect copy number variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). AIMS: Identification of genomic disorders in DD/ID. MATERIALS AND METHODS: We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. RESULTS: We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes. We further identified and discussed 51 cases with likely pathogenic CNVs spanning novel candidate genes, including genes encoding synaptic components and/or proteins involved in corticogenesis. Additionally, we identified two deletions spanning potential Topological Associated Domain (TAD) boundaries probably affecting the regulatory landscape. DISCUSSION AND CONCLUSION: We show how phenotypic and genetic analyses of array-CGH data allow unraveling complex cases, identifying rare disease genes, and revealing unexpected position effects.

A child with macrocephaly: case report of a patient with megalencephalic leukoencephalopathy with subcortical cysts and a compound heterozygosity for two mutations in the MLC1 gene.

Megalencephaly is as a rule accompanied by macrocephaly, an occipitofrontal circumference (OFC) greater than the 98th percentile. Megalencephaly is divided into an anatomic type (developmental) and a metabolic type. Metabolic megalencephaly refers to various storage and degenerative encephalopathies. The differential diagnosis includes Alexander's disease, Canavan's disease, glutaric aciduria type 1, GM1 and GM2 gangliosidosis, merosin-deficient variant of congenital muscular dystrophy and megalencephalic leukoencephalopathy with subcortical cysts (MLC). The distinctive features of this syndrome are enlarged cranial circumference, present at birth or starting in the first year of life, and magnetic resonance imaging (MRI) evidence of diffuse with matter abnormalities with subcortical cysts in the tips of the temporal lobes and in frontoparietal subcortical areas. Mutations in the MLC1 gene have been found as causative of MLC in 60-70 % of affected subjects, without genotype-phenotype correlation. The child we describe presented with progressive macrocephaly not associated with dysmorphic features and large abdominoscrotal hydrocele. At the age of 8 months, encephalic MRI showed anomalies suggestive for MLC and brainstem auditory evoked potentials (BAEP) documented alterations of signal conduction in right tracts. At the time, clinical neurologic examination was normal. Extensive metabolic assays were within normal range. Sequence analysis for MLC1 gene revealed a compound heterozygosity for two mutations in MLC1 gene, inherited from healthy non consanguineous parents.

Auriculo-condylar syndrome or new syndrome?

We describe a girl with peculiar auricular dysmorphism, renal agenesis and supernumerary rib. Some different diagnostic hypotheses are discussed.

[Genomic imprinting and human pathology. 2]. / Imprinting genomico e patologia umana--Parte seconda.

Genetic imprinting does occur in humans. This is manifest at the level of the genome, the individual chromosome or subcromosomal region, and the single locus. Genomic imprinting is manifest in the developmental defects of hydatiform mole, teratoma and triploidy. Chromosomal imprinting effects are revealed when uniparental disomy or deletion occur as costitutional aberration or in tumural tissues. Evidence at the single gene level comes from an increasing number of autosomal dominant genetic diseases. This part of the paper will briefly review the importance of imprinting in the contest of human genetic diseases.

[Genomic imprinting and human pathology. I. General Part]. / Imprinting genomico e patologia umana. I-Parte Generale.

Genetical as well as experimental embryology methods have permitted to uncover a very important feature of mammalian embryonic development: it has been shown that female and male genomic complements are differentially imprinted in such a way that contribution of both a maternally and a paternally derived genome are absolutely necessary for the embryo to complete its normal development. The paternal and maternal genomes are not equivalent and have a complementary role during development in mammals. The differences in activity of each parental genome result from an epigenetic modification of the genome during gametogenesis: the parental imprinting. The recent discovery of several mouse and human genes which are imprinted should permit to address new data of some diseases.

A new syndrome with ocular, skeletal and renal involvement.

A patient with retinitis pigmentosa, hypertension with interstitial nephropathy, short limb dwarfism with Madelung deformity of the forearms and an unclassified type of brachydactyly is described. Such bone dysplasia has never been reported to date either as a single entity or associated with renal and retinal diseases.

Distinctive skeletal dysplasia in Cockayne syndrome.

Cockayne syndrome is a well-known autosomal recessive form of dwarfism with senile-like appearance. Skeletal changes such as flattening of vertebral bodies, ivory epiphyses and thickening of cranial vault, have been observed in some patients with this condition. We describe here a 5.5-year-old girl with the typical clinical signs of Cockayne syndrome and a distinctive form of bone dysplasia with major involvement of the spine.

The Coffin-Siris syndrome in two siblings.

Two sisters with Coffin-Siris syndrome, born to healthy unrelated parents, are reported. The accurate X-ray evaluation of the two patients allows the identification of some new features and a better delineation of the radiological phenotype. Our two cases confirm the proposed autosomal recessive inheritance of the syndrome.

Kniest disease with Pierre Robin syndrome and hydrocephalus.

A 3-month-old male infant with clinical and radiological features of Kniest disease is reported. Additional findings were severe Pierre Robin syndrome and external hydrocephalus. The patient was retarded in mental and motor development. He died at 4 months of age from the complications of tracheostomy. The parents were both normal clinically and radiologically, thus the disease in the child was presumably due to a new mutation. The reported familial cases of Kniest disease suggest autosomal dominant inheritance. The differential diagnosis is discussed in detail.

Interstitial deletion of the short arm of chromosome 7 without craniosynostosis.

Two female infants with apparently identical interstitial deletions at bands p13 to p15 of chromosome 7 are presented. They differ in phenotype. The first infant has failure to thrive, retardation in development, normal head circumference with ridged metopic suture, blepharophimosis, epicanthal folds, mild hypotelorism, small low-set ears, and a bifid right toe. The second infant has a normal weight, length, and head circumference, blepharophimosis, epicanthal folds, widely spaced nipples, enlarged clitoris, and very large hands and feet. The two patients' clinical and karyotypic findings are compared with previous reports of structural abnormalities of the short arm of chromosome 7. Of the three cases in the literature, craniosynostosis was present in the two patients with deletion of band 7p14. Our observations, thus, suggest that deletion of bands 7p13 to 7p15, in contrast to more distal deletions at band 7p2, is not associated with craniosynostosis.

The 49XXXXX syndrome. Report of a case with 48XXXX/49XXXXX mosaicism.

A patient with 48XXXX/49XXXXX mosaicism is presented. Clinical findings include severe growth and developmental retardation, hypertelorism, mongoloid slant of the palpebral fissures, clinodactyly of the fifth fingers, retarded bone age and radio-ulnar synostosis. The findings are similar to those of the cases with a penta-X chromosome complement already described, and are also similar to the signs of the more common 49XXXXY syndrome of males. In both instances the dysmorphic features are less impressive than the mental retardation and the skeletal malformations. This report contributes to a better delineation of the 49XXXXX syndrome. The possible mechanisms of the chromosomal aberration are discussed.