Severe growth retardation, delayed bone age, and facial dysmorphism in two patients with microduplications in 2p16 → p22.

Interstitial duplications of the short arm of chromosome 2 have been rarely described. Here, we report on two unrelated patients with overlapping chromosome 2p16 → p22 de novo microduplications found by SNP-array analysis. The affected individuals were an 8-year-3-month-old boy with a direct duplication of approximately 14.6 Mb harboring 63 genes, and a 12-year-old girl with a direct duplication of around 9.6 Mb harboring 48 genes. Both patients have severe growth retardation, delayed bone age, prominent veins on trunk and extremities, total IGF1 level in the low range, mild developmental delay, and facial dysmorphism such as relative macrocephaly, a broad and prominent forehead, and a large anterior fontanelle. Comparison with patients previously reported in the literature and in the DECIPHER 5.1 and ECARUCA databases indicates a common region of interest of around 1.9 Mb responsible for most of the features. Two candidate genes (EPAS and RHOQ), may be particularly relevant for the marked growth retardation and developmental delay.

Effects of deletion and duplication in a patient with a 46,XX,der(7)t(7;17)(q36;p13)mat karyotype.

Exact breakpoint determination by DNA-array has dramatically improved the analysis of genotype-phenotype correlations in chromosome aberrations. It allows a more exact definition of the most relevant genes and particularly their isolated or combined impact on the phenotype in an unbalanced state. Here, we report on a 21-year-old female with severe growth retardation, severe intellectual disability, hypoplasia of the corpus callosum, unilateral sacral hypoplasia, tethered cord, various minor facial dysmorphisms, and a telomeric deletion of about 4.4 Mb in 7q36.2->qter combined with a telomeric duplication of about 8 Mb in 17pter->p13.1. Fine mapping was achieved with the Illumina® Infinium HumanOmni1-Quad v1.0 BeadChip. Most of the major clinical features correspond to the well-known effects of haploinsufficiency of the MNX1 and SHH genes. In addition, review of the literature suggests an association of the 17p duplication with specific facial dysmorphic features and skeletal anomalies, but also an aggravating effect of the duplication-deletion for severe growth retardation as well as sacral and corpus callosum hypoplasia by one or more genes located on the proximal half of the segmental 17p duplication could be elaborated by comparison with other patients from the literature carrying either the deletion or the duplication found in our patient.

Combined Dup(7)(q22.1q32.2), Inv(7)(q31.31q31.33), and Ins(7;19)(q22.1;p13.2p13.2) in a 12-year-old boy with developmental delay and various dysmorphism.

De novo combined duplications/inversions are very rare chromosomal rearrangements. For chromosome 7 just some dozen cases of duplications of various parts of the long arm have been published. We report on a 12-year-old boy with muscular hypotonia, global developmental delay, short stature, and various facial dysmorphism including frontal bossing, temporal narrowing, slightly down-slanting palpebral fissures, a broad nasal root, a long philtrum, a thin and tented upper lip, a drooping lower lip, micrognathia, prominent ears, a short neck, and a low posterior hairline. Karyotype analysis and molecular investigations revealed a complex de novo chromosomal rearrangement on 7q. FISH analysis with locus specific YACs and BACs and SNP array with the Illumina(®) HumanOmni1-Quad v1.0 BeadChip disclosed a direct duplication in the long arm of chromosome 7 (q22.1→q32.2) and an inversion located at the breakpoint between the two copies of the duplication (q31.31→q31.33). In addition, breakpoint characterization at the molecular level revealed a 386 bp insertion carrying two Alu elements of chromosome 19p13.2 between the two copies of the duplication. By a comparison of the SNP haplotypes of the derivative chromosome of the patient and both parents a two-step formation during spermatogenesis was suggested as the most likely mechanism of formation.

Single nucleotide polymorphism array analysis in men with idiopathic azoospermia or oligoasthenozoospermia syndrome.

OBJECTIVE: To identify copy number variations (CNVs) as a hint toward genes relevant for spermatogenesis and related to male factor infertility. DESIGN: Analysis of genomic DNA with high resolution Illumina SNP arrays (HumanOmni1-Quad Bead Chip). Sanger sequencing of the CLCA4 gene in all patients of the study. Analysis of CLCA4 expression in various human tissue samples. SETTING: University department. PATIENT(S): A total of 39 infertile men with idiopathic infertility ranging from oligoasthenoteratozoospermia to azoospermia. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Copy number variations more than 10 kb. RESULT(S): We detected a heterozygous deletion including exons 4-9 of the CLCA4 gene in one man with cryptozoospermia, as well as a total of 149 CNVs not yet reported in various databases and carrying 200 protein coding genes in the 39 men. CONCLUSION(S): According to our results CLCA4 is apparently expressed in postmeiotic germ cells and somatic cells. We therefore conclude that CLCA4 might be functional during human spermatogenesis after meiosis, most likely as a modifier of CFTR gene expression. CLCA4 can thus be considered as a novel dominant germ line gene potentially causing male factor infertility if functionally disrupted. Our study demonstrates the power of DNA arrays to identify novel CNVs carrying candidate genes causing male factor infertility.

In vitro toxicity of amorphous silica nanoparticles in human colon carcinoma cells.

The use of nanostructured silica (SiO2) particles is no longer restricted to biomedical and (bio-) technological fields but rather finding applications in products of the food industry. Thus, our studies on the toxicological relevance of SiO2 nanoparticles focused on cytotoxic effects, the modulation of the cellular redox status and the impact on DNA integrity in human colon carcinoma cells (HT29). The results indicate that these SiO2 nanoparticles stimulate the proliferation of HT29 cells, depending on the incubation time and the particle size. The cytotoxicity of the investigated SiO2 nanoparticles was found to depend on the concentration, size and on the FCS content of the culture medium. Furthermore, SiO2 seem to interfere with glutathione biosynthesis. The results indicate further that effects of SiO2 NPs are not mediated by oxidative stress but by interference with the MAPK/ERK1/2 as well as the Nrf2/ARE signalling pathways. Additionally, investigations regarding DNA integrity revealed no substantial (oxidative) DNA damage.

Disruption of EXOC6B in a patient with developmental delay, epilepsy, and a de novo balanced t(2;8) translocation.

Most balanced chromosomal aberrations are not associated with a clinical phenotype, however, in some patients they may disrupt gene structure. With the development of various next-generation sequencing techniques, fast and specific analyses of the breakpoint regions of chromosomal rearrangements are possible. Here, we report on a 19-year-old woman with a de novo balanced translocation t(2;8)(p13.2;q22.1) and a severe clinical phenotype including intellectual disability, epilepsy, behavioral features resembling autism, and minor dysmorphic features. By next-generation sequencing, we defined the breakpoints and found disruption of the exocyst complex component 6B (EXOC6B) gene in intron 1 on chromosome 2p13.2 involving two Alu elements with a homology of 81%. No gene was found at the respective breakpoint on chromosome 8. Expression analysis of the EXOC6B in blood lymphocytes and buccal smear revealed reduced expression in the patient in comparison with the control. Our findings in combination with one recently published case and one other patient listed in DECIPHER v5.1 indicate EXOC6B as a gene relevant for intellectual development and electrophysiological stability.