Correction: Kucinska et al. The Use of CGH Arrays for Identifying Copy Number Variations in Children with Autism Spectrum Disorder. Brain Sci. 2024, 14, 273.

In the original publication [...].

The Use of CGH Arrays for Identifying Copy Number Variations in Children with Autism Spectrum Disorder.

Autism spectrum disorders (ASDs) encompass a broad group of neurodevelopmental disorders with varied clinical symptoms, all being characterized by deficits in social communication and repetitive behavior. Although the etiology of ASD is heterogeneous, with many genes involved, a crucial role is believed to be played by copy number variants (CNVs). The present study examines the role of copy number variation in the development of isolated ASD, or ASD with additional clinical features, among a group of 180 patients ranging in age from two years and four months to 17 years and nine months. Samples were taken and subjected to array-based comparative genomic hybridization (aCGH), the gold standard in detecting gains or losses in the genome, using a 4 × 180 CytoSure Autism Research Array, with a resolution of around 75 kb. The results indicated the presence of nine pathogenic and six likely pathogenic imbalances, and 20 variants of uncertain significance (VUSs) among the group. Relevant variants were more prevalent in patients with ASD and additional clinical features. Twelve of the detected variants, four of which were probably pathogenic, would not have been identified using the routine 8 × 60 k microarray. These results confirm the value of microarrays in ASD diagnostics and highlight the need for dedicated tools.

Broad phenotypic spectrum of germ line 7p12.1 microdeletions encompassing the IKZF1 gene includes predisposition to acute lymphoblastic leukemia.

Microdeletions of 7p12.1 encompassing the IKZF1 gene locus are rare, with few cases reported. The common phenotype includes intellectual disability, overgrowth, and facial dysmorphism accompanied, albeit rarely, by congenital anomalies. Haploinsufficiency of IKZF1 predisposes individuals to childhood acute lymphoblastic leukemia (ALL). In this study, we comprehensively analyzed the frequency of 7p12.1 deletions among 4581 Polish individuals who underwent chromosomal microarray testing for unexplained developmental delay, intellectual disability, and/or congenital anomalies. Two unrelated individuals (0.04%) with a de novo interstitial 7p12.1 microdeletion encompassing IKZF1 were identified. One developed ALL. Analysis of the incidence and the phenotype of constitutional 7p12.1 microdeletion, which based on the previously annotated patients data in public databases and literature reports, revealed 21 cases including five patients diagnosed with ALL.

Genome-Wide Association Study to Find Modifiers for Tetralogy of Fallot in the 22q11.2 Deletion Syndrome Identifies Variants in the GPR98 Locus on 5q14.3.

BACKGROUND: The 22q11.2 deletion syndrome (22q11.2DS; DiGeorge syndrome/velocardiofacial syndrome) occurs in 1 of 4000 live births, and 60% to 70% of affected individuals have congenital heart disease, ranging from mild to severe. In our cohort of 1472 subjects with 22q11.2DS, a total of 62% (n=906) have congenital heart disease and 36% (n=326) of these have tetralogy of Fallot (TOF), comprising the largest subset of severe congenital heart disease in the cohort. METHODS AND RESULTS: To identify common genetic variants associated with TOF in individuals with 22q11.2DS, we performed a genome-wide association study using Affymetrix 6.0 array and imputed genotype data. In our cohort, TOF was significantly associated with a genotyped single-nucleotide polymorphism (rs12519770, P=2.98×10-8) in an intron of the adhesion GPR98 (G-protein-coupled receptor V1) gene on chromosome 5q14.3. There was also suggestive evidence of association between TOF and several additional single-nucleotide polymorphisms in this region. Some genome-wide significant loci in introns or noncoding regions could affect regulation of genes nearby or at a distance. On the basis of this possibility, we examined existing Hi-C chromatin conformation data to identify genes that might be under shared transcriptional regulation within the region on 5q14.3. There are 6 genes in a topologically associated domain of chromatin with GPR98, including MEF2C (Myocyte-specific enhancer factor 2C). MEF2C is the only gene that is known to affect heart development in mammals and might be of interest with respect to 22q11.2DS. CONCLUSIONS: In conclusion, common variants may contribute to TOF in 22q11.2DS and may function in cardiac outflow tract development.

Histone Modifier Genes Alter Conotruncal Heart Phenotypes in 22q11.2 Deletion Syndrome.

We performed whole exome sequence (WES) to identify genetic modifiers on 184 individuals with 22q11.2 deletion syndrome (22q11DS), of whom 89 case subjects had severe congenital heart disease (CHD) and 95 control subjects had normal hearts. Three genes including JMJD1C (jumonji domain containing 1C), RREB1 (Ras responsive element binding protein 1), and SEC24C (SEC24 family member C) had rare (MAF < 0.001) predicted deleterious single-nucleotide variations (rdSNVs) in seven case subjects and no control subjects (p = 0.005; Fisher exact and permutation tests). Because JMJD1C and RREB1 are involved in chromatin modification, we investigated other histone modification genes. Eighteen case subjects (20%) had rdSNVs in four genes (JMJD1C, RREB1, MINA, KDM7A) all involved in demethylation of histones (H3K9, H3K27). Overall, rdSNVs were enriched in histone modifier genes that activate transcription (Fisher exact p = 0.0004, permutations, p = 0.0003, OR = 5.16); however, rdSNVs in control subjects were not enriched. This implicates histone modification genes as influencing risk for CHD in presence of the deletion.

Human sperm aneuploidy after exposure to polycyclic aromatic hydrocarbons.

The purpose of this cross-sectional study was to investigate whether environmental exposure to polycyclic aromatic hydrocarbons (PAHs) was associated with sperm aneuploidy. A sample of 181 men who attended an infertility clinic for diagnostic purposes and who had a normal semen concentration of 20-300×106 spermatozoa mL-1 or slight oligozoospermia (semen concentration of 15-20×106 spermatozoa mL-1;

The association between environmental exposure to pyrethroids and sperm aneuploidy.

The aim of the present study is to determine whether the environmental exposure to pyrethroids was associated with males sperm chromosome disomy. The study population consisted of 195 men who attended the infertility clinic for diagnostic purposes and who had normal semen concentration of 20-300×10(6) mL(-1) or slight oligozoospermia (semen concentration of 15-20×10(6) mL(-1)) (WHO, 1999). Participants were interviewed and provided a semen sample. The pyrethroids metabolites: 3-phenoxybenzoic acid (3PBA), cis-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid (CDCCA), trans-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid (TDCCA) and cis-2,2-dibromovinyl-2,2-dimethylcyclopropane-1-carboxylic acid (DBCA) were analysed in the urine using a validated gas chromatography ion-tap mass spectrometry method. Sperm aneuploidy was assessed using multicolor FISH (DNA probes specific for chromosomes X, Y, 18, 13, 21). Our results showed that CDCCA >50th percentile was associated with disomy of chromosome 18 (p=0.05) whereas the level of TDCCA in urine >50th percentile was related to XY disomy (p=0.04) and disomy of chromosome 21 (p=0.05). Urinary 3PBA level ⩽50 and >50 percentile was related to disomy of sex chromosomes: XY disomy (p=0.05 and p=0.02 respectively), Y disomy (p=0.04 and 0.02 respectively), disomy of chromosome 21 (p=0.04 and p=0.04 respectively) and total disomy (p=0.03 and p=0.04 respectively). Additionally disomy of chromosome 18 was positively associated with urinary level of 3PBA >50 percentile (p=0.03). The results reported here are found that pyrethroids may be a sperm aneugens. These findings may be of concern due to increased pyrethroid use and prevalent human exposure.

Lifestyle factors and sperm aneuploidy.

Different environmental and lifestyle factors may interfere with the normal disjunction of sister chromatids/chromosomes during meiosis and may cause aneuploidy. The aim of the study was to examine the association between lifestyle factors and sperm aneuploidy. The study population consisted of 212 healthy men under 45 years of age attending an infertility clinic for diagnostic purposes and who had a normal semen concentration of 20-300×106mL or slight oligozoospermia (semen concentration of 15-20×106/mL). All participants were interviewed and provided a semen sample. Sperm aneuploidy was assessed using multicolor FISH (DNA probes specific for chromosomes X, Y, 18, 13, 21). Results from the study suggest that lifestyle factors are related to sperm aneuploidy. A positive relationship was found between coffee drinking everyday and the lack of chromosome X or Y, as well as coffee drinking 1-6 times per week and additional chromosome 18. Wearing boxer shorts decrease the copy number changes in the whole chromosome 18, the number of additional chromosome 18 and the lack of chromosome 13. Additionally, obesity (BMI 30-40 kg/m²) was positively associated with additional chromosome 21 after being adjusted for potential confounders. These findings demonstrate that changing the men's lifestyle habits may contribute to reduction of the incidence of sperm aneuploidy. It is necessary that men continue to follow sensible health advice concerning excess weight, coffee drinking and wearing tight fitting underwear. As this is the first such study to examine different lifestyle factors and sperm aneuploidy, the results need to be confirmed on larger population.

Human urinary phthalate metabolites level and main semen parameters, sperm chromatin structure, sperm aneuploidy and reproductive hormones.

The aim of the study was to assess the association of phthalate metabolites levels in urine with semen parameters (sperm concentration, motility, morphology, CASA parameters), sperm chromatin structure, sperm aneuploidy and reproductive hormones. The study population consisted of 269 men who were attending an infertility clinic and had normal semen concentration (20-300mln/ml) or slight oligozoospermia (15-20mln/ml). Participants were interviewed and provided a semen sample. The phthalate metabolites were analysed in the urine using a procedure based on the LC-MS/MS method. Urinary phthalate metabolites levels were significantly associated with a decrease in sperm motility (5OH MEHP, MEHP, MINP), CASA parameters (MBP), testosterone level (MEHP) and an increase sperm DNA damage (MBP) and sperm aneuploidy (MBzP, MBP, MEHP, MEP). In view of the importance of human reproductive health and the widespread usage of phthalates, it is important to further investigate these correlations.

Large deletion in the KAL1 gene in two related patients with hypogonadotropic hypogonadism: diagnostic usefulness of cytogenetic and molecular methods.

BACKGROUND: Kallmann syndrome type 1 (KS1) is a heterogeneous disorder where hypogonadotropic hypogonadism (HH) associated with an impaired sense of smell is observed. The aim of this study was to investigate the usefulness of the multiplex ligation-dependent probe amplification (MLPA) technique for differential diagnosis in comparison with molecular cytogenetics - fluorescence in situ hybridisation (FISH) or traditional PCR analysis and propose a diagnostic approach for patients with KS. MATERIAL AND METHODS: Karyotype and PCR analysis in two related patients and other family members were performed, followed by MLPA dosage sensitive analysis. RESULTS: In the proband and his maternal uncle, the PCR allowed the detection of a large deletion within the KAL1 gene, from exon 4 to 14 (c.469-?_6314+?del). The deletion was also diagnosed in three female carriers in the presented family. These results were proved by the MLPA technique. Moreover, we traced the presence of the region located downstream and upstream to the KAL1 gene on Xq22.32. However, FISH analysis failed to reveal any deletion in the critical region for KS. Simultaneously, we report difficulties connected with the PCR technique based on the primers for KAL1 amplification presented in the literature. We designed primers that are specific to the X chromosome and bypass pseudogene KALY amplification. CONCLUSIONS: FISH analysis is a convenient screening technique, but in the presented family it failed to detect the deletion. Therefore, in the face of a distinctive manifestation of KS, a subsequent molecular assay should be introduced. The MLPA is a useful technique for differential diagnosis in patients with HH combined with smell impairment.