A novel missense mutation in the NSDHL gene identified in a Lithuanian family by targeted next-generation sequencing causes CK syndrome.

The NSDHL gene encodes 3ß-hydroxysteroid dehydrogenase involved in one of the later steps of the cholesterol biosynthetic pathway. Mutations in this gene can cause CHILD syndrome (OMIM 308050) and CK syndrome (OMIM 300831). CHILD syndrome is an X-linked dominant, male lethal disorder caused by mutations in the NSDHL gene that result in the loss of the function of the NSDHL protein. CK syndrome is an allelic X-linked recessive disorder. So far, 13 patients with CK syndrome from two families have been reported on. We present a new five-generation family with affected males manifesting clinical features of CK syndrome. Next generation sequencing was targeted to a custom panel of 542 genes with known or putative implication on intellectual disability. Missense mutation p.Gly152Asp was identified in the NSDHL gene in the DNA sample of the affected male. Mutation carrier status was confirmed for all the obligate carriers in the family. The clinical features of the affected males in the family manifested as weak fetal movements, severe intellectual disability, seizures, spasticity, atrophy of optic discs, microcephaly, plagiocephaly, skeletal abnormalities, and minor facial anomalies, including a high nasal bridge, strabismus, and micrognathia. A highly significant preferential transmission of the mutation was observed in this and previous families segregating CK syndrome. Our report expands the clinical spectrum of this syndrome to include weak fetal movements, spasticity, and plagiocephaly, and transmission ratio distortion. The various findings in these patients increase our understanding of the diversity of the clinical presentation of cholesterol biosynthesis disorders.

A new single gene deletion on 2q34: ERBB4 is associated with intellectual disability.

We report on a 15-year-old patient with hyperactivity, intellectual disability and severe speech developmental delay. An array CGH analysis revealed de novo 2q34 deletion, 958 kb in size, involving a single protein coding gene ERBB4 (position 212,505,294-213,463,152; NCBI build 36). The ERBB4 gene is important in numerous neurobiological processes in both the developing and the adult brain. The NRG1-ERBB4 signaling pathway has been recently implicated in the pathophysiology of schizophrenia and epilepsy. Many risk haplotypes were identified in several studies across different populations. The severe clinical consequences in our patient demonstrate that the haploinsufficiency of ERBB4 is crucial for intellectual and cognitive function. These observations are compatible with previously reported results.

Relevance of nasal potential difference in diagnosis of cystic fibrosis among children.

OBJECTIVE. The aim of this study was to estimate the significance of nasal potential difference (NPD) in the diagnosis of cystic fibrosis (CF) in children with clinical symptoms suggestive of the disease, positive sweat test results, and/or genetically confirmed diagnosis. MATERIAL AND METHODS. NPD measurements according to the modifications by Alton were performed in 50 children with clinical CF symptoms supported by positive sweat test results, 50 children with other obstructive lung diseases, and 50 healthy children. A subgroup of 17 children with the diagnosis confirmed by 2 identified mutations in the CF transmembrane regulatory gene was analyzed individually. RESULTS. The mean NPD value recorded in 50 children with clinical symptoms of CF supported by positive sweat test results and/or genetic analysis was -28.0 mV [SD, 10.2]. The mean NPD value in the subgroup of children with 2 identified mutations in the CF gene (n=17) was more negative than in the subgroup of children with unrecognized mutations (n=33) (-37.1 mV [SD, 7.0] vs. -23.4 mV [SD, 8.3], P<0.001). The mean NPD value in patients with other obstructive lung diseases and healthy children was significantly more positive than in the group of CF children with positive sweat test results and/or identified mutations (-18.1 mV [SD, 3.6] and -15.5 mV [SD, 4.3] vs. -28.0 mV [SD, 10.2], P<0.001). The NPD cut point value for the genetically confirmed diagnosis of CF was -35.0 mV (sensitivity, 93.9%; specificity, 88.2%), while in general, the NPD prognostic value was -24.0 mV (sensitivity, 58.0%; specificity, 98.0%). CONCLUSIONS. The NPD measurement is a valuable tool for the diagnosis of CF in children, but further studies are necessary to establish NPD values related to the CF genotype and to reduce the intrasubject variability of this test.

Clinical and molecular characterization of a second case of 7p22.1 microduplication.

The use of high-resolution microarray technology for investigation of patients with intellectual disability and/or congenital anomalies provided the unique possibility to identify new microdeletion/microduplication syndromes and discover the dosage sensitive genes, which are implicated in the manifestation of various genetic conditions. Microduplication of the 7p22.1 region, 1.7 Mb in size, has very recently been reported, representing the smallest interstitional 7p duplication, associated with specific facial features and speech delay. We report on a patient with an even smaller 7p22.1 de novo microduplication, 1 Mb in size, detected in a 14.5-year-old patient with mild intellectual disability and similar facial dysmorphism, including macrocephaly, ocular hypertelorism, low-set ears, and other features. There are 15 RefSeq genes included in this duplication. ACTB gene is a strong candidate gene for the alteration of craniofacial development. Further cases with similar duplications will contribute to the delineation of a potential new microduplication syndrome of 7p22.1.

De novo 5q35.5 duplication with clinical presentation of Sotos syndrome.

We report on a girl with developmental delay and a de novo 264 kb interstitial duplication in the region of Sotos syndrome at 5q35.3 in the immediate vicinity of critical NSD1 gene, but manifesting the phenotype, of overgrowth both prenatal stage and postnatal, macrocephaly, developmental delay, and resembling that of Sotos syndrome, rather than the recently reported syndrome of reciprocal duplication. The duplication is located right downstream from the NSD1 gene, a region which appears critical for the expression of the gene as regulatory elements might be disrupted or the expression of a not amplified critical gene might be otherwise affected by the duplicated region. Thus,in the process of evaluating identified CNVs attention should be drawn to the possible influence of chromosomal rearrangement on distant genes, which could add additional diversity to genomic disorders. Our case demonstrates that evaluation of the size of chromosomal alteration and gene content are not sufficient for assessment of CNV's pathogenicity and the context of adjacent genes should be considered.

R368X mutation in MID1 among recurrent mutations in patients with X-linked Opitz G/BBB syndrome.

Opitz G/BBB syndrome is a genetically heterogeneous condition, with both autosomal dominant and X-linked forms. The MID1 gene is associated with X-linked Opitz G/BBB syndrome. Most mutations identified are unique, which makes it difficult to assess possible genotype/phenotype correlations. We report on a familial c.1102C>T (p.R368X) mutation in the MID1 gene, previously reported by Cox et al. (Hum Mol Genet 9:2553-2562, 2000), and document it as a recurrent mutation causing Opitz G/BBB syndrome. This mutation may result in various midline defects, including cleft lip/palate, laryngeal cleft, hypertelorism, Dandy-Walker malformation, ventricular septal defect and hypospadias in male patients, with intrafamilial variability. Seven other mutations (c.712G>T, c.829C>T, c.1108A>G, c.1444_1447dupAACA, c.1483C>T, c.1798dupC and entire gene deletions) have been previously reported as recurrent mutations. The presented family with the c.1102C>T mutation provides additional information about the clinical consequences of the nonsense mutation causing premature truncation of the protein at the level of the COS domain.

Considering specific clinical features as evidence of pathogenic copy number variants.

Since the introduction of high-resolution microarray technologies, it has become apparent that structural chromosomal rearrangements can lead to a wide variety of clinical manifestations, including developmental delay/intellectual disability (DD/ID). It has been shown previously that the diagnostic yield of genome-wide array-based identification of submicroscopic alterations in patients with ID varies widely and depends on the patient selection criteria. More attempts have recently been made to define the phenotypic clues of pathogenic copy number variants (CNVs). The aim of this study was to investigate a well-phenotyped cohort of patients with DD/ID and determine whether certain clinical features may serve as indicators for pathogenic CNVs. A retrospective analysis was conducted for patients with DD/ID (n = 211) who were tested using genome-wide chromosomal microarray technologies and a review of the clinical data was performed. Pathogenic CNVs were detected in 29 patients. In comparison with individuals who had normal molecular karyotyping results (n = 182), malformations of the musculoskeletal system; congenital malformations of the CNS (particularly hydrocephalus and congenital malformations of the corpus callosum); minor anomalies of the eye, face, and neck subgroup (particularly downward-slanting palpebral fissures, minor anomalies of the ear, and micrognathia); brachydactyly; and umbilical hernia were more common in patients with chromosomal alterations. A multivariate logistic regression analysis allowed the identification of three independent pathogenic CNV predictors: congenital malformations of the corpus callosum, minor anomalies of the ear, and brachydactyly. Insights into the chromosomal phenotype may help to increase the diagnostic yield of microarray technologies and sharpen the distinction between chromosomal alterations and other conditions.

Familial distal monosomy 5p15.3-pter with trisomy 12q24.2-qter resulting in neurodevelopmental delay and dysmorphic features.

Developmental delay and brain anomalies leading to significant morbidity and mortality are frequently caused by chromosomal rearrangements. We report on a familial unbalanced translocation resulting in distal monosomy 5p15.3-pter with trisomy 12q24.2-qter in 2 half siblings with cerebral dysgenesis, severe intellectual disability, dysmorphic features, progressive weakness, and atrophy of muscles.

A single gene deletion on 4q28.3: PCDH18--a new candidate gene for intellectual disability?

We report a boy with severe developmental delay, seizures, microcephaly, hypoplastic corpus callosum, internal hydrocephalus and dysmorphic features (narrow forehead, round face, deep-set eyes, blue sclerae, large and prominent ears, nose with anteverted nares, thin upper lip, small and wide-spaced teeth, hyperextensibility of the elbows, wrists, and fingers, fingertip pads, broad hallux, sacral dimple), carrying a 1.53 Mb interstitial deletion at 4q28.3. The deletion was detected by Agilent 105K oligo-array genome hybridization and involves the genomic region between 137,417,338 and 138,947,282 base pairs on chromosome 4 (NCBI build 36). The alteration was inherited from a healthy mother and contains a single gene, PCDH18 which encodes a cadherin-related neuronal receptor thought to play a role in the establishment and function of cell-cell connections in the brain. Thus, haploinsufficiency of this gene may contribute to altered brain development and associated malformations. We found that this deletion is a private inherited copy number variation that is associated with specific clinical findings in our patient and propose the PCDH18 gene as a possible candidate gene for intellectual disability.

Genetic structure of Europeans: a view from the North-East.

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (lambda) (ranging from 1.00 to 4.21), fixation index (F(st)) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

Validation of PAH genotype-based predictions of metabolic phenylalanine hydroxylase deficiency phenotype: investigation of PKU/MHP patients from Lithuania.

BACKGROUND: Phenylalanine hydroxylase (PheOH) deficiency is inherited as an autosomal recessive trait. The associated hyperphenylalaninemia phenotype is highly variable, primarily due to great allelic heterogeneity in the PAH locus. The goal of our study was to assess the relationship between individual PAH locus mutations and biochemical and metabolic phenotypes in phenylketonuria (PKU) and mild hyperphenylalaninemia (MHP) patients. MATERIAL/METHODS: In this study, a total of 184 independent PAH chromosomes (92 unrelated patients with PKU and MHP residing in Lithuania) were investigated. All 13 exons of the PAH gene of all PKU probands tested were scanned for DNA sequence alterations by denaturing gradient gel electrophoresis (DGGE); mutations were identified by direct fluorescent automated sequencing or by restriction enzyme digestion analysis of the relevant exons. PAH genotype-based prediction of metabolic PhOH deficiency phenotype in PKU/MHP patients form Lithuania was estimated by the assigned value (AV) and functional hemizygosity methods. RESULTS: Our data provide evidence that a simple genotype-phenotype correlation does exist in most patients with PheOH deficiency: we observed a perfect match between the expected and observed phenotypes in 96% of the cases investigated. CONCLUSIONS: The results obtained confirm that methods of functional hemizygosity and AV sum are applicable for the estimation of the genotype-phenotype correlation in the investigated group of PKU/MHP patients.