BACKGROUND: Neurodevelopmental disorders (NDDs) and/or associated multiple congenital abnormalities (MCAs) represent a genetically heterogeneous group of conditions with an adverse prognosis for the quality of intellectual and social abilities and common daily functioning. The rapid development of exome sequencing (ES) techniques, together with trio-based analysis, nowadays leads to up to 50% diagnostic yield. Therefore, it is considered as the state-of-the-art approach in these diagnoses. RESULTS: In our study, we present the results of ES in a cohort of 85 families with 90 children with severe NDDs and MCAs. The interconnection of the in-house bioinformatic pipeline and a unique algorithm for variant prioritization resulted in a diagnostic yield of up to 48.9% (44/90), including rare and novel causative variants (41/90) and intragenic copy-number variations (CNVs) (3/90). Of the total number of 47 causative variants, 53.2% (25/47) were novel, highlighting the clinical benefit of ES for unexplained NDDs. Moreover, trio-based ES was verified as a reliable tool for the detection of rare CNVs, ranging from intragenic exon deletions (GRIN2A, ZC4H2 genes) to a 6-Mb duplication. The functional analysis using PANTHER Gene Ontology confirmed the involvement of genes with causative variants in a wide spectrum of developmental processes and molecular pathways, which form essential structural and functional components of the central nervous system. CONCLUSION: Taken together, we present one of the first ES studies of this scale from the central European region. Based on the high diagnostic yield for paediatric NDDs in this study, 48.9%, we confirm trio-based ES as an effective and reliable first-tier diagnostic test in the genetic evaluation of children with NDDs.
Rhabdomyosarcomas (RMS) constitute a heterogeneous spectrum of tumors with respect to clinical behavior and tumor morphology. The paternal uniparental disomy (pUPD) of 11p15.5 is a molecular change described mainly in embryonal RMS. In addition to LOH, UPD, the MLPA technique (ME030kit) also determines copy number variants and methylation of H19 and KCNQ1OT1 genes, which have not been systematically investigated in RMS. All 127 RMS tumors were divided by histology and PAX status into four groups, pleomorphic histology (n = 2); alveolar RMS PAX fusion-positive (PAX+; n = 39); embryonal RMS (n = 70) and fusion-negative RMS with alveolar pattern (PAX-RMS-AP; n = 16). The following changes were detected; negative (n = 21), pUPD (n = 75), gain of paternal allele (n = 9), loss of maternal allele (n = 9), hypermethylation of H19 (n = 6), hypomethylation of KCNQ1OT1 (n = 6), and deletion of CDKN1C (n = 1). We have shown no difference in the frequency of pUPD 11p15.5 in all groups. Thus, we have proven that changes in the 11p15.5 are not only specific to the embryonal RMS (ERMS), but are often also present in alveolar RMS (ARMS). We have found changes that have not yet been described in RMS. We also demonstrated new potential diagnostic markers for ERMS (paternal duplication and UPD of whole chromosome 11) and for ARMS PAX+ (hypomethylation KCNQ1OT1).
Inflammatory rhabdomyoblastic tumor (IRMT) is a rare, recently described skeletal muscle neoplasm of uncertain malignant potential. We report an unusual tumor in the right arm of a 5-year-old boy, which is the first case of a pediatric IRMT. Immunohistochemically, most cells in the tumor were positive for CD163 and CD68 staining. The neoplastic cells themselves showed a skeletal muscle phenotype with a diffuse expression of desmin and a focal expression of myoD1. Mitotic activity was low (1/10 HPF), and no necrosis was observed.
- MeSH
- lidé MeSH
- nádorové biomarkery metabolismus MeSH
- nádory * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
Pathogenic variants affecting the BLM gene are responsible for the manifestation of extremely rare cancer‐predisposing Bloom syndrome. The present study reports on a case of an infant with a congenital hypotrophy, short stature and abnormal facial appearance. Initially she was examined using a routine molecular diagnostic algorithm, including the cytogenetic analysis of her karyotype, microarray analysis and methylation‐specific MLPA, however, she remained undiagnosed on a molecular level. Therefore, she and her parents were enrolled in the project of trio‐based exome sequencing (ES) using Human Core Exome kit. She was revealed as a carrier of an extremely rare combination of causative sequence variants altering the BLM gene (NM_000057.4), c.1642C>T and c.2207_2212delinsTAGATTC in the compound heterozygosity, resulting in a diagnosis of Bloom syndrome. Simultaneously, a mosaic loss of heterozygosity of chromosome 11p was detected and then confirmed as a borderline imprinting center 1 hypermethylation on chromosome 11p15. The diagnosis of Bloom syndrome and mosaic copy‐number neutral loss of heterozygosity of chromosome 11p increases a lifetime risk to develop any types of malignancy. This case demonstrates the trio‐based ES as a complex approach for the molecular diagnostics of rare pediatric diseases.
- MeSH
- Bloomův syndrom * diagnóza genetika patologie MeSH
- dítě MeSH
- heterozygot MeSH
- kojenec MeSH
- lidé MeSH
- lidský chromozom Y MeSH
- mozaicismus MeSH
- sekvenování exomu MeSH
- Check Tag
- dítě MeSH
- kojenec MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
Pathogenic sequence variant in the GNAI1 gene were recently introduced as a cause of novel syndrome with a manifestation of variable developmental delay and autistic features. In our study, we report a case of monozygotic twins with severe intellectual disability and motor delay and developmental dysphasia. Both probands and their parents were examined using multi-step molecular diagnostic algorithm including whole-exome sequencing (WES), resulting in the identification of a novel, de novo pathogenic sequence variant in the GNAI1 gene, NM_002069.6:c.815 A>G, p.(Asp272Gly) in probands. Using WES we also verified the microarray findings of a familial 8q24.23q24.3 duplication and heterozygous 5q13.2 deletion, not associated with clinical symptoms in probands. Our results confirmed the role of the GNAI1 gene in the pathogenesis of syndromic neurodevelopmental disorders. They support trio- or quatro-based WES as a suitable molecular diagnostics method for the simultaneous detection of clinically relevant sequence variants and CNVs in individuals with neurodevelopmental disorders and rare diseases.
- Publikační typ
- tisková chyba MeSH
Nová WHO klasifikace nádorů CNS se do značné míry opírá o molekulární diagnostiku, bez které již nelze některé jednotky prakticky diagnostikovat. Snažíme se ukázat racionální přístup k diagnostice nádorů CNS, který se opírá o konvenční molekulární metody jako je RT-PCR, Sangerovo sekvenování, MLPA, rozšířené o sekvenování nové generace (NGS) a metylační SNP array.
The new WHO classification of CNS tumors is largely based on molecular diagnostic. Without molecular methods some entities can no longer be diagnosed. We are trying to show a rational approach to the CNS tumors diagnostics, which is based on conventional molecular methods such as RT-PCR, Sanger sequencing, MLPA, extended by the next generation sequencing (NGS) and methylation SNP array.
- MeSH
- gliom diagnóza MeSH
- lidé MeSH
- nádory centrálního nervového systému * diagnóza MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- předškolní dítě MeSH
- sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Check Tag
- lidé MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- kazuistiky MeSH
Gliomas are the most common central nervous tumors in children and adolescents. However, spinal cord low-grade gliomas (sLGGs) are rare, with scarce information on tumor genomics and epigenomics. To define the molecular landscape of sLGGs, we integrated clinical data, histology, and multi-level genetic and epigenetic analyses on a consecutive cohort of 26 pediatric patients. Driver molecular alteration was found in 92% of patients (24/26). A novel variant of KIAA1549:BRAF fusion (ex10:ex9) was identified using RNA-seq in four cases. Importantly, only one-third of oncogenic drivers could be revealed using standard diagnostic methods, and two-thirds of pediatric patients with sLGGs required extensive molecular examination. The majority (23/24) of detected alterations were potentially druggable targets. Four patients in our cohort received targeted therapy with MEK or NTRK inhibitors. Three of those exhibited clinical improvement (two with trametinib, one with larotrectinib), and two patients achieved partial response. Methylation profiling was implemented to further refine the diagnosis and revealed intertumoral heterogeneity in sLGGs. Although 55% of tumors clustered with pilocytic astrocytoma, other rare entities were identified in this patient population. In particular, diffuse leptomeningeal glioneuronal tumors (n = 3) and high-grade astrocytoma with piloid features (n = 1) and pleomorphic xanthoastrocytoma (n = 1) were present. A proportion of tumors (14%) had no match with the current version of the classifier. Complex molecular genetic sLGGs characterization was invaluable to refine diagnosis, which has proven to be essential in such a rare tumor entity. Moreover, identifying a high proportion of drugable targets in sLGGs opened an opportunity for new treatment modalities.
- MeSH
- astrocytom * genetika MeSH
- dítě MeSH
- genomika MeSH
- gliom * genetika patologie MeSH
- lidé MeSH
- mitogenem aktivované proteinkinasy kinas MeSH
- mladiství MeSH
- nádory míchy * genetika MeSH
- nádory mozku * genetika MeSH
- protoonkogenní proteiny B-raf genetika MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mladiství MeSH
- Publikační typ
- časopisecké články MeSH
The aim of this study was to monitor the effect of Bifidobacterium bifidum (BB) and the combination of Lactobacillus sporogenes, Enterococcus faecium, and Bifidobacterium bifidum (LEB) on the health status and weight gain of calves, and the utilisation of nitrogenous substances. The experiment was performed in the period from April 2020 to September 2020. A total of 90 Holstein heifers, which were one to 56 days old, were used as experimental animals. Differences in live weight gain were significant if we compared the LEB vs. BB group and the LEB vs. C, the control group (86.23 ± 5.49 kg vs. 84.72 ± 6.22 kg, p < 0.05; 86.23 ± 5.49 kg vs. 82.86 ± 5.35 kg, p < 0.01). Considering the live weight gain, group BB was heavier than group C only (84.72 ± 6.22 kg vs. 82.86 ± 5.35 kg, p < 0.05). An effect on reducing the incidence and duration of diarrheal diseases was not demonstrated in this study (p = 0.1957). The administration of feed additives had no statistically significant effect on the amount of N excreted in the feces. The values of hematological and biochemical parameters were unaffected except for the first sampling of urea. Other blood parameters were not affected by the addition of probiotic feed additives. The bacterial populations in the feces 5 days and 56 days after birth were not affected by the inclusion of feed additives.
- Publikační typ
- časopisecké články MeSH
Heritability studies on sport-related traits accepted that endurance, speed, power, and strength abilities include an active genetic predisposition to elite soccer participation. This study evaluates the influence of selected genetic variants on performance in speed, power, and strength laboratory tests on a group of elite soccer players, including their playing position. A ninety-nine male elite soccer players were compared to controls (n = 107) and tested for quadriceps and hamstrings isokinetic strength at speed 60°/s, 180°/s, and 300°/s, jump performance, and genotypes of ACTN3 (R577X, rs1815739), ACE (I/D, rs1799752), NOS3 (Glu298Asp, rs1799983), AMPD1 (34C/T, rs17602729), UCP2 (Ala55Val, rs660339), BDKRB2 (+9/-9, rs5810761) and IL1RN (VNTR 86-bp). The ACTN3 XX homozygotes in defenders had lower quadriceps and hamstring isokinetic strength in all tested speeds than ACTN3 RX and RR genotypes (p < 0.05). The ACTN3 RR homozygotes in defenders had higher quadriceps strength in all tested velocities than the RX heterozygotes (p < 0.05). We also found other associations between playing-position in soccer and increased strength of lower limbs for AMPD1 CC and NOS3 Glu/Glu genotypes, and IL1RN*2 allele carriers. Total genetic score regression explained 26% of the variance in jump performance and isokinetic strength. The ACTN3 R allele, NOS3 Glu/Glu genotypes, and IL1RN*2 allele pre-disposed the attackers and defenders playing position in elite soccer, where those positions have higher strength and power measures than midfielders. Midfielders have lower strength and power conditions than other playing positions without relation to strength and power genes.
- Publikační typ
- časopisecké články MeSH
