Search Results (13)

Background: Intellectual disability (ID) is a heterogeneous condition caused by diverse genetic factors, including single-nucleotide variants (SNVs) and copy number variants (CNVs). Whole-exome sequencing (WES) and clinical exome sequencing (CES) have become essential tools for identifying pathogenic variants; however, their relative diagnostic performance in ID has not been fully characterized. Methods: Children diagnosed with ID or related neurodevelopmental disorders underwent WES or CES. Identified variants were classified according to ACMG/AMP and ClinGen guidelines, with segregation analysis performed when parental samples were available. Diagnostic yields were compared across demographic, prenatal, and phenotypic subgroups. A multidimensional semi-quantitative scoring system encompassing 15 clinical domains (e.g., age at onset, neuro-motor function, seizures, MRI findings, vision, and dysmorphic features) was developed. Z-scores were calculated for each parameter, followed by hierarchical cluster analysis (HCA) and correlation modeling to define genotype–phenotype associations and pathway-level clustering. Results: A broad spectrum of pathogenic and likely pathogenic variants across multiple genes and biological pathways was identified in our study. CNV-associated cases frequently exhibited prenatal anomalies or multisystem phenotypes associated with large chromosomal rearrangements. Monogenic variants and their corresponding phenotypic profiles were identified through clinical exome sequencing (CES) and whole-exome sequencing (WES). Phenotypic HCA based on Z-scores revealed three major biological groups of patients with coherent genotype–phenotype relationships: Group 1, severe multisystem neurodevelopmental disorders dominated by transcriptional and RNA-processing genes (POLR1C, TCF4, HNRNPU, NIPBL, ACTG1); Group 2, intermediate epileptic and metabolic forms associated with ion-channel and excitability-related genes (SCN2A, PAH, IQSEC2, GNPAT); and Group 3, milder or focal neurodevelopmental phenotypes involving myelination and signaling-related genes (NKX6-2, PLP1, PGAP3, SMAD6, ATP1A3). Gene distribution significantly differed among these biological categories (χ² = 54.566, df = 34, p = 0.0141), confirming non-random, biologically consistent grouping. Higher Z-scores correlated with earlier onset and greater neurological severity, underscoring the clinical relevance of the multidimensional analytical framework. Conclusions: This study highlights the genetic complexity and clinical heterogeneity of intellectual disability and demonstrates the superior diagnostic resolution of WES and CES. Integrating multidimensional phenotypic profiling with genomic analysis enhances genotype–phenotype integration and enables data-driven phenotype stratification and pathway-based re-analysis. This combined diagnostic and analytical framework offers a more comprehensive approach to diagnosing monogenic ID and provides a foundation for future predictive and functional studies. Full article

Background: Hypospadias is a common congenital condition in male infants, characterised by incomplete development of the underside of the penile shaft. Genetic factors play a major role in its development. Therefore, studying genetic contributions, especially in familial cases, can enhance our understanding of disease causes and guide targeted interventions. Materials and Methods: Through a structured biobank for hypospadias, we collected blood samples from individuals with familial hypospadias and their relatives. Whole-genome sequencing (WGS) was performed on 27 individuals across seven families to identify potential genetic causes. Bioinformatics analysis, including the GEMINI tool, was used to assess inheritance patterns of single-nucleotide variants (SNVs) within families and identify potential causative SNVs. Results: We identified three likely pathogenic variants in genes not previously associated with hypospadias in EIF2B5, INO80, and ACADVL genes, in three index patients. These variants co-segregated with the condition within the families. Additionally, we detected variants of uncertain significance in hypospadias-related gene families (DNAH12 and LHFP) and in other genes, such as COL6A3, which may cause the phenotype. No potential causative variants were found in two of the seven studied families, indicating the need for further analysis, including the assessment of copy number variants (CNVs). Functional studies will be crucial to establish the role of the identified variants in the development of hypospadias. Conclusions: This study underscores the importance of disease biobanking and genetic analysis in identifying potential underlying causes of congenital conditions, such as hypospadias. The identified variants provide new opportunities for functional research and may enhance our understanding of hypospadias pathophysiology. These findings broaden the genetic landscape of hypospadias and lay the groundwork for functional validation, improved risk assessment, and personalised medicine strategies. Full article

Hereditary papillary renal carcinoma (HPRC) is a rare monogenic hereditary disease in the group of hereditary cancer syndromes. Clinically, HPRC results in the development of multiple papillary renal cell carcinomas of the kidneys in young adults. HPRC is caused by point activating mutations in the MET gene encoding a transmembrane tyrosine kinase receptor. Until now, all detected germline mutations in HPRC patients were missense variants leading to a constitutive activation of the tyrosine kinase domain. We describe, for the first time, unrelated patients with clinical features similar to HPRC and without MET pathogenic missense variants but harboring an extended heterozygous duplication ~101.4 kb in length (chr7:116740252-116841718) in 7q31.2 determined using whole-genome sequencing (WGS). This duplication results in an additional copy of the MET gene fragment, including exons 5-21. The duplicated exons encode most of the receptor domains. According to the American College of Medical Genetics and Genomics (ACMG) criteria, this duplication is classified as variant of uncertain significance (VUS) at present, but it is not excluded that this duplication may represent an activating mutation. Perhaps, further segregation analysis and functional studies will allow us to more accurately resolve the pathogenicity and diagnostic significance of this germline CNV. Full article

Waardenburg syndrome (WS) is a common genetic cause of syndromic hearing loss, accounting for 2–5% of congenital cases. It is characterized by hearing impairment and pigmentation abnormalities in the skin, hair, and eyes. Seven genes are associated with WS: PAX3, MITF, EDNRB, EDN3, SOX10, KITLG, and SNAI2. This study investigates the genetic causes of WS in three familial cases. Whole-exome sequencing (WES) was performed to identify single nucleotide variants (SNVs). Copy number variants (CNVs) were analyzed from the WES raw data and through multiplex ligation-dependent probe amplification (MLPA). The study identified one pathogenic SNV and two novel CNVs, corresponding to type I and type II WS patterns in the three families. The SNV, a nonsense variant (c.1198C>T p.Arg400*), was found in MITF and segregated in the affected father. The two CNVs were a deletion of exon 5 in PAX3 in a family with two affected members and a large novel deletion comprising seven genes, including SOX10, in a family with three affected members. These findings confirmed a WS diagnosis through genetic testing. The study emphasizes the importance of integrating multiple genetic testing approaches for accurate and reliable diagnosis, highlighting their role in improving patient management and providing tailored genetic counseling. Full article

Congenital cataract (CC), the most prevalent cause of childhood blindness and amblyopia, necessitates prompt and precise genetic diagnosis. The objective of this study is to identify the underlying genetic cause in a Swiss patient with isolated CC. Whole exome sequencing (WES) and copy number variation (CNV) analysis were conducted for variant identification in a patient born with a total binocular CC without a family history of CC. Sanger Sequencing was used to confirm the variant and segregation analysis was used to screen the non-affected parents. The first de novo missense mutation at c.391T>C was identified in exon 3 of CRYGC on chromosome 2 causing the substitution of a highly conserved Tryptophan to an Arginine located at p.Trp131Arg. Previous studies exhibit significant changes in the tertiary structure of the crystallin family in the following variant locus, making CRYGC prone to aggregation aggravated by photodamage resulting in cataract. The variant can be classified as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) criteria (PP3 + PM1 + PM2 + PS2; scoring 10 points). The identification of this novel variant expands the existing knowledge on the range of variants found in the CRYGC gene and contributes to a better comprehension of cataract heterogeneity. Full article

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by restrictive interests and/or repetitive behaviors and deficits in social interaction and communication. ASD is a multifactorial disease with a complex polygenic genetic architecture. Its genetic contributing factors are not yet fully understood, especially large structural variations (SVs). In this study, we aimed to assess the contribution of SVs, including copy number variants (CNVs), insertions, deletions, duplications, and mobile element insertions, to ASD and related language impairments in the New Jersey Language and Autism Genetics Study (NJLAGS) cohort. Within the cohort, ~77% of the families contain SVs that followed expected segregation or de novo patterns and passed our filtering criteria. These SVs affected 344 brain-expressed genes and can potentially contribute to the genetic etiology of the disorders. Gene Ontology and protein–protein interaction network analysis suggested several clusters of genes in different functional categories, such as neuronal development and histone modification machinery. Genes and biological processes identified in this study contribute to the understanding of ASD and related neurodevelopment disorders. Full article

Copy number variations regions (CNVRs) can be classified either as segregating, when found in both parents, and offspring, or non-segregating. A total of 65 segregating and 31 non-segregating CNVRs identified in at least 10 individuals within a dense pedigree of the Gochu Asturcelta pig breed was subjected to enrichment and functional annotation analyses to ascertain their functional independence and importance. Enrichment analyses allowed us to annotate 1018 and 351 candidate genes within the bounds of the segregating and non-segregating CNVRs, respectively. The information retrieved suggested that the candidate genes spanned by segregating and non-segregating CNVRs were functionally independent. Functional annotation analyses allowed us to identify nine different significantly enriched functional annotation clusters (ACs) in segregating CNVR candidate genes mainly involved in immunity and regulation of the cell cycle. Up to five significantly enriched ACs, mainly involved in reproduction and meat quality, were identified in non-segregating CNVRs. The current analysis fits with previous reports suggesting that segregating CNVRs would explain performance at the population level, whereas non-segregating CNVRs could explain between-individuals differences in performance. Full article

Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome. Full article

Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language. Full article

Lower urinary tract obstruction (LUTO) is, in most cases, caused by anatomical blockage of the bladder outlet. The most common form are posterior urethral valves (PUVs), a male-limited phenotype. Here, we surveyed the genome of 155 LUTO patients to identify disease-causing CNVs. Raw intensity data were collected for CNVs detected in LUTO patients and 4.392 healthy controls using CNVPartition, QuantiSNP and PennCNV. Overlapping CNVs between patients and controls were discarded. Additional filtering implicated CNV frequency in the database of genomic variants, gene content and final visual inspection detecting 37 ultra-rare CNVs. After, prioritization qPCR analysis confirmed 3 microduplications, all detected in PUV patients. One microduplication (5q23.2) occurred de novo in the two remaining microduplications found on chromosome 1p36.21 and 10q23.31. Parental DNA was not available for segregation analysis. All three duplications comprised 11 coding genes: four human specific lncRNA and one microRNA. Three coding genes (FBLIM1, SLC16A12, SNCAIP) and the microRNA MIR107 have previously been shown to be expressed in the developing urinary tract of mouse embryos. We propose that duplications, rare or de novo, contribute to PUV formation, a male-limited phenotype. Full article

Maternal uniparental disomy of chromosome 7 is present in 5–10% of patients with Silver-Russell syndrome (SRS), and duplication of 7p including GRB10 (Growth Factor Receptor-Bound Protein 10), an imprinted gene that affects pre-and postnatal growth retardation, has been associated with the SRS phenotype. Here, we report on a 17 year old girl referred to array-CGH analysis for short stature, psychomotor delay, and relative macrocephaly. Array-CGH analysis showed two copy number variants (CNVs): a ~12.7 Mb gain in 7p13-p11.2, involving GRB10 and an ~9 Mb loss in 7q11.21-q11.23. FISH experiments performed on the proband’s mother showed a chromosome 7 pericentric inversion that might have mediated the complex rearrangement harbored by the daughter. Indeed, we found that segmental duplications, of which chromosome 7 is highly enriched, mapped at the breakpoints of both the mother’s inversion and the daughter’s CNVs. We postulate that pairing of highly homologous sequences might have perturbed the correct meiotic chromosome segregation, leading to unbalanced outcomes and acting as the putative meiotic mechanism that was causative of the proband’s rearrangement. Comparison of the girl’s phenotype to those of patients with similar CNVs supports the presence of 7p in a locus associated with features of SRS syndrome. Full article

Structural aberrations involving more than two breakpoints on two or more chromosomes are known as complex chromosomal rearrangements (CCRs). They can reduce fertility through gametogenesis arrest developed due to disrupted chromosomal pairing in the pachytene stage. We present a familial case of two infertile brothers (with azoospermia and cryptozoospermia) and their mother, carriers of an exceptional type of CCR involving chromosomes 1 and 7 and three breakpoints. The aim was to identify whether meiotic disruption was caused by CCR and/or genomic mutations. Additionally, we performed a literature survey for male CCR carriers with reproductive failures. The characterization of the CCR chromosomes and potential genomic aberrations was performed using: G-banding using trypsin and Giemsa staining (GTG banding), fluorescent in situ hybridization (FISH) (including multicolor FISH (mFISH) and bacterial artificial chromosome (BAC)-FISH), and genome-wide array comparative genomic hybridization (aCGH). The CCR description was established as: der(1)(1qter->1q42.3::1p21->1q42.3::7p14.3->7pter), der(7)(1pter->1p2 1::7p14.3->7qter). aCGH revealed three rare genes variants: ASMT, GARNL3, and SESTD1, which were ruled out due to unlikely biological functions. The aCGH analysis of three breakpoint CCR regions did not reveal copy number variations (CNVs) with biologically plausible genes. Synaptonemal complex evaluation (brother-1; spermatocytes II/oligobiopsy; the silver staining technique) showed incomplete conjugation of the chromosomes. Associations between CCR and the sex chromosomes (by FISH) were not found. A meiotic segregation pattern (brother-2; ejaculated spermatozoa; FISH) revealed 29.21% genetically normal/balanced spermatozoa. The aCGH analysis could not detect smaller intergenic CNVs of few kb or smaller (indels of single exons or few nucleotides). Since chromosomal aberrations frequently do not affect the phenotype of the carrier, in contrast to the negative influence on spermatogenesis, there is an obvious need for genomic sequencing to investigate the point mutations that may be responsible for the differences between the azoospermic and cryptozoospermic phenotypes observed in a family. Progeny from the same parents provide a unique opportunity to discover a novel genomic background of male infertility. Full article

We report a genomic and phenotypic delineation for two chromosome regions with candidate genes for syndromic intellectual disability at 12q12 and Xp22.31, segregating independently in one family with four affected members. Fine mapping of three affected members, along with six unreported small informative CNVs, narrowed down the candidate chromosomal interval to one gene LRRK2 at 12q12. Expression studies revealed high levels of LRRK2 transcripts in the whole human brain, cerebral cortex and hippocampus. RT-qPCR assays revealed that LRRK2 transcripts were dramatically reduced in our microdeletion patient DGDP289A compared to his healthy grandfather with no deletion. The decreased expression of LRRK2 may affect protein–protein interactions between LRRK2 and its binding partners, of which eight have previously been linked to intellectual disability. These findings corroborate with a role for LRRK2 in cognitive development, and, thus, we propose that intellectual disability and autism, displayed in the 12q12 microdeletions, are likely caused by LRRK2. Using another affected member, DGDP289B, with a microdeletion at Xp22.31, in this family, we performed the genomic and clinical delineation with six published and nine unreported cases. We propose HDHD1 and PNPLA4 for X-linked intellectual disability in this region, since their high transcript levels in the human brain substantiate their role in intellectual functioning. Full article