Mechanism and genotype-phenotype correlation of two proximal 6q deletions characterized using mBAND, FISH, array CGH, and DNA sequencing.

Proximal 6q deletions have a milder phenotype than middle and distal 6q deletions. We describe 2 patients with non-overlapping deletions of about 15 and 19 Mb, respectively, which subdivide the proximal 6q region into 2 parts. The aberrations were identified using karyotyping and analysed using mBAND and array CGH. The unaffected mother of the first patient carried a mosaic karyotype with the deletion in all metaphases analysed and a small supernumerary marker formed by the deleted material in about 77% of cells. Her chromosome 6 centromeric signal was split between the deleted chromosome and the marker, suggesting that this deletion arose through the centromere fission mechanism. In this family the location of the proximal breakpoint in the centromere prevented cloning of the deletion junction, but the junction of the more distal deletion in the second patient was cloned and sequenced. This analysis showed that the latter aberration was most likely caused by non-homologous end joining. The second patient also had a remarkably more severe phenotype which could indicate a partial overlap of his deletion with the middle 6q interval. The phenotypes of both patients could be partly correlated with the gene content of their deletions and with phenotypes of other published patients.

[Application of SNP array method in prenatal diagnosis]. / Aplikace metody SNP array v prenatální diagnostice.

OBJECTIVES: SNP array (array method using Single Nucleotide Polymorphisms) enables to detect cytogenetically undetectable submicroscopic alterations (microdeletions, microduplications), which could be also causative for ultrasonographic anomalies of fetus. This article describes the principle, advantages, disadvantages and application possibilities of the SNP array method in prenatal diagnosis. The ten month experience with SNP array use in prenatal diagnosis is presented. DESIGN: Prospective study. SETTINGS: Gennet, Prague. MATERIAL AND METHODS: During the period from April 2010 to January 2011 we performed 110 SNP array analyses of fetal DNA: 14 chorionic villi samples (CVS), 88 amniotic fluid samples (AMC), 1 cord blood sample and 7 miscarriage samples. Laboratory tests were carried out on DNA from both cultured and uncultured fetal cells. Examinations were performed in fetuses with sonographic abnormal findings having normal karyotype. In addition 14 fetal cytogenetic abnormalities were solved. SNP array analysis was performed using Illumina InfiniumHD HumanCytoSNP-12 chip. All data were analysed by Illumina KaryoStudio and GenomeStudio software. RESULTS: SNP array analysis was performed in 108 fetuses (only 2 examination failures, 1.8%). In total, we detected CNV (copy number variation) in 29 samples (29/108 = 27%). 15% (16/108) of fetuses with abnormal ultrasound findings were found to carry clinically relevant CNV. Probably benign CNVs were found in 8 samples (8/108 = 7%) and in additional 5 CNVs parental samples have not been analysed yet. Excluding karyotypically abnormal cases clinically relevant CNVs were found in 10% of fetuses (9/94). In all cases with de novo chromosomal aberration the clinical relevancy was clarified (imbalances in 50%). CONCLUSION: Our data suggest that SNP array analysis is a relevant and useful technique in prenatal diagnosis.

Double heterozygosity with mutations involving both the GJB2 and GJB6 genes is a possible, but very rare, cause of congenital deafness in the Czech population.

Mutations in the GJB2 gene are the most common cause of prelingual, autosomal recessive, sensorineural hearing loss worldwide. Nevertheless, 10% to 50% of patients with prelingual nonsyndromic deafness only carry one mutation in the GJB2 gene. Recently a large 342 kb deletion named Delta(GJB6-D13S1830) involving the GJB6 gene was reported in Spanish and French deafness patients, either in a homozygous state or in combination with a monoallelic GJB2 mutation. No data have been reported about the frequency of this mutation in central Europe. Thirteen Czech patients with prelingual nonsyndromic sensorineural deafness carrying only one pathogenic mutation in the GJB2 gene were tested for the presence of the Delta(GJB6-D13S1830) mutation. One patient with a GJB2 mutation (313del14) also carried the Delta(GJB6-D13S1830). This is the first reported Czech case, and probably also the first central European case, of prelingual deafness due to mutations involving both the GJB2 and GJB6 genes. In addition, the Delta(GJB6-D13S1830) was not detected in 600 control chromosomes from Czech individuals with normal hearing. We show that in the Czech Republic the Delta(GJB6-D13S1830) is not the second most common causal factor in deafness patients heterozygous for a single GJB2 mutation, and that Delta(GJB6-D13S1830) is very rare in central Europe compared to reports from Spain, France and Israel.

Spectrum and frequencies of mutations in the GJB2 (Cx26) gene among 156 Czech patients with pre-lingual deafness.

Mutations in the gene gap junction beta 2 (GJB2), the gene for the connexin 26, are the most common cause of pre-lingual deafness worldwide. The mutation 35delG within GJB2 is prevalent in Europe. To date, there are no data about GJB2 mutation spectrum and frequencies from the Czech population. We investigated and report here the spectrum and frequencies of mutations in the GJB2 gene among 156 unrelated, congenital deafness Czech patients. Allele-specific polymerase chain reaction, together with fluorescent fragment analysis, were used for the detection of the 35delG mutation. The entire coding region of the GJB2 was directly sequenced in all patients who were not homozygous for the 35delG. No pathogenic mutation was detected in 51.9% of patients. At least one pathogenic mutation was found in 48.1% of patients, and both pathogenic mutations were detected in 37.8% of patients. Single mutations in a heterozygous state were detected in 10.3% of patients. The mutation 35delG accounts for 82.8% of detected disease mutations, Trp24stop accounts for 9.7% of pathogenic alleles and was found in patients with gypsy heritage. Mutation 313del14 accounts for 3.7% of pathogenic alleles. The frequency of 35delG heterozygotes in the Czech Republic is 1 : 29.6. Testing for only the three most common mutations would detect over 96% of all pathogenic alleles in the Czech Republic.

Retinal detachment in an infant with the ring chromosome 13 syndrome.

PURPOSE: To inform about retinal detachment in an infant with the ring chromosome 13 as a possible new feature of this syndrome. The finding is able to imitate retinoblastoma, which is closely connected to the deletion of 13q14. METHODS: We report on a girl with many congenital anomalies including hypoplasia of both optic discs and chorioretinal coloboma of the right eye. Chromosomal analysis revealed karyotype 46 XX with a ring chromosome 13. The patient was examined again at 15 months of age, where leukocoria was disclosed in the left eye, emerging from a retrolental greyish-white mass. Even though neither sonography nor CT showed a typical picture for retinoblastoma, this tumor could not be ruled out. Enucleation of the left eye was performed. The globe was then investigated histopathologically. RESULTS: No tumor was found in the removed eye. Microscopic examination showed a detached retina with reactive gliosis and neovascularisation. CONCLUSIONS: The possibility of retinal detachment should be included into differential diagnoses in infants with ring 13 chromosome in cases with a non-specific intraocular mass. The assessment of chromosomal breakpoints in children with this aberration would enable clinicians to determine the real risk of retinoblastoma.

DNA diagnosis and clinical manifestations of autosomal dominant polycystic kidney disease.

At least 2 genes, detectable by DNA methods, encode autosomal dominant polycystic kidney disease (ADPKD), which remains the most frequent and serious hereditary renal disease. PKD1 gene, localized on chromosome 16, responds for the clinical course in the majority of ADPKD patients, whereas PKD2 gene, localized on chromosome 4, is responsible for less than 10-15% of cases, with presumed milder phenotypic manifestations. To start the clinical and genetic correlation in patients with different genotypes (PKD1 vs. PKD2) in the Czech population, a pilot group of 88 patients with ADPKD was analysed. Families with PKD1 (n = 44) represented 95.6% and families with PKD2 (n = 2) 4.4% of all families investigated (n = 46). Our clinical analysis, yet based only on a limited number of PKD2 subjects, does not definitely support the concept of a milder phenotype and prognosis in PKD2 versus PKD1 patients, in terms of mean age of diagnosis (29 vs. 29 years), mean age at onset of arterial hypertension (33 vs. 33 years), more favourable renal function or ultrasound findings.

Genetic and physical mapping of the Treacher Collins syndrome locus: refinement of the localization to chromosome 5q32-33.2.

Treacher Collins syndrome (TCOF1) is an autosomal dominant disorder of craniofacial development, the locus for which has been chromosomally localized to 5q31-34. We have isolated four hypervariable microsatellite markers (heterozygosity values range from 0.70 to 0.89) which have been mapped to distal 5q. Fifteen unrelated TCOF1 families have been analyzed for linkage to these markers. There is strong evidence demonstrating linkage to all of these markers; the strongest support for positive linkage being provided by the marker IG52, with a maximum pairwise lod score of 9.77 at a recombination fraction of 0.055. Analysis of recombinant individuals, physical mapping by fluorescence in situ hybridization and genetic linkage analysis demonstrated that the TCOF1 locus was flanked proximally by the loci 2C7 and 2D10, and distally by the loci IG26 and IG52 with a maximum lod score of 14.4, as assessed by multipoint linkage analysis. The refinement of the localization of the TCOF1 locus to 5q32-33.2, with flanking markers, represents an important step towards the identification of the mutated gene itself.

[Personal experience with genetic study of the hearing-impaired]. / Nase zkusenosti s genetickým vysetrením sluchove postizených.

In 1988-1990 the authors examined on account of impaired hearing in the family 78 families, which were divided into two groups. The first group comprises 48 families of actively invited pupils from schools with children with impaired hearing in Prague, the second group comprises 30 families examined in the framework of common counselling and consultation services. On the first group a genetic aetiology of the disorder was revealed in 75% and in the second group in 73.3% of the cases. An autosomal recessive type of heredity was proved unequivocally in 31.3% in group 1 and in 20.0% in group 2. An autosomal dominant type of heredity was found in 6.25% in group 1 and in 6.7% in group 2. X-linked deafness was proved only in group 1 in 4.2% and sporadic syndromes only in group 2 in 13.3%. In 33.3% in both groups it was not possible to differentiate the type of heredity (most frequently the child and both parents were affected). In the first group three genetic syndromes were detected and in group 2 seven genetic syndromes. As the percentage of genetically conditioned hearing disorders in both groups is relatively high, the authors consider active screening of deaf children more useful so far.