Identification Of Mutations Research Articles

Генотип-фенотипическая характеристика детей с семейной средиземноморской лихорадкой (периодической болезнью) в регионе Российской Федерации

Familial Mediterranean fever (FMF) is the most common monogenic autoinflammatory disease (AID) caused by mutations in the MEFV gene. The purpose of this research was to investigate clinical variability and potential genotypic and phenotypic correlations in children with clinically verified FMF and MEFV gene mutations in the City of Moscow, Russia. Materials and methods used: among 188 pediatric patients with suspected monogenic AIDs, MEFV gene mutations were identified in 9 through sequencing. In order to confirm the FMF diagnosis, patients were evaluated according to the modified Tel-Hashomer criteria and the Eurofever/PRINTO classification criteria. Results: clinical picture of FMF was characterized by the presence of periodic attacks of the disease lasting from 1 to 7 days accompanied by fever and increased acute phase reactants (observed in all patients), abdominal pain (in 8 children), peritonitis requiring diagnostic laparotomy (in a single child), chest pain (in 2 patients), pleurisy (in a single child), arthritis (in 7 children) and erysipeloid-like rash (in a single child). The pathogenic mutation M694V was identified in the MEFV gene in 8 out of 9 patients, this mutation was homozygous in 5 patients and heterozygous in 1, M680I mutation was detected on another allele in 2 children (compound heterozygous), and a mutation of unknown significance K695R was detected in a single child. No obvious clinical differences were found between homozygotes and heterozygotes as well as compound heterozygotes. Clinical response was achieved in 5 patients with colchicine monotherapy while canakinumab was prescribed to 4 patients due to ongoing attacks. Conclusion: the diagnosis involving the identification of MEFV gene mutations may allow the assessment of genotype-phenotype correlations in patients with FMF.

Diagnostic and prognostic genomic aberrations in upper tract urothelial carcinoma can be identified in focal barbotage samples.

To investigate whether genetic analysis of focal barbotage samples obtained at ureterorenoscopy (URS) is possible, and to identify genetic aberrations that might add prognostic information. This prospective study included barbotage samples from 42 patients with upper urinary tract urothelial carcinoma (UTUC) confirmed at URS. At URS, focal barbotage specimens were collected for cytology and for gene sequencing. Tumour grades were determined from cytology and/or biopsy, or from radical nephroureterectomy samples. Next-generation sequencing using a 385-gene panel was performed and single nucleotide variants (SNVs), deletions/insertions (indels) and copy number aberrations (CNAs) were identified. Manual filtering of the SNVs/indels was performed to identify possible pathogenic mutations. Of the 42 samples, two failed quality control, therefore, 40 focal barbotage samples were sequenced. We identified known and suspected pathogenic mutations and other genomic aberrations in 36 samples. The most common variants were in TERT (78%), FGFR3 (50%), KMT2D (42%), KDM6A (42%), ARID1A (39%), TP53 (19%) and deletion of 9q (50%). Known pathogenic mutations in FGFR3 were common in grade 1 and 2 tumours, but not present in any grade 3 tumour. No patients with an FGFR3 mutation died during follow-up. TP53 variants or deletions, as well as amplifications of MDM2, were only present in high-grade (HG) tumours or low-grade (LG) tumours in patients who had metastasis/died from urinary tract carcinoma. CNAs were detected in 36/40 barbotage samples, 91% of the HG samples and 69% of the LG samples, including those from all five patients with LG tumours with metastasis or who died from urinary tract cancer. Focal barbotage samples enable identification of gene mutations and other genetic aberrations that may add important prognostic information to histopathology and cytology. Refined prognostication of UTUC patients already at diagnosis can guide treatment decisions and follow-up programmes.

A MALDI-TOF MS-based multiple detection panel of drug resistance-associated multiple single-nucleotide polymorphisms in Candida tropicalis.

Candida tropicalis is one of the main causes of invasive candidiasis. Rapid identification of antifungal resistance is crucial for selection of an appropriate antifungal to improve patient outcomes. Mutations at specific loci are strongly correlated with resistance to antifungal agents. In this study, we developed a multi-single-nucleotide polymorphism (SNP) panel to accurately identify 36 mutation sites across seven genes of C. tropicalis that are associated with resistance to azoles and/or echinocandins. Ten isolates were selected to test repeatability, and another 20 isolates of C. tropicalis were selected to validate consistency. Intra-assay and inter-assay repeatability of the panel was 100%, with the loci accuracy being 99.44% (716 of 720). Furthermore, 109 isolates were examined for clinical research, and the most commonly detected mutations were G751A and A866T of UPC2, A491T of TAC1, and A395T and C461T of ERG11. The G751A and A866T mutations of UPC2 as well as the A395T and C461T mutations of ERG11 co-existed. The SNP panel enables identification of specific mutations at critical sites of drug-resistant strains to facilitate the rapid selection of appropriate antifungal agents and efficient monitoring of the regional epidemiological trends of resistance of C. tropicalis.IMPORTANCEC. tropicalis infections pose a growing global public health challenge, with mortality rates approaching 40%. C. tropicalis is one of the top four Candida spp. responsible for candidiasis, particularly in the Asia-Pacific region and Latin America, notably affecting patients with neutropenia and malignancies. The azole resistance rate of C. tropicalis ranges from 0% to 30%. Between 2009 and 2018, the China Hospital Invasive Fungal Surveillance Network reported an increase in fluconazole and voriconazole resistance from 5.7% to ~30%. Although resistance to echinocandins and amphotericin B remains low, multi-resistance to echinocandins and azoles has been observed. Current methods for detecting drug resistance are limited by the long turnaround time of antifungal susceptibility testing, low throughput of Sanger sequence to target resistance mutations, complex data analysis, and high costs of second-generation sequencing. We developed and validated a rapid, high-throughput, and cost-effective panel to detect and monitor drug-resistance mutations of C. tropicalis.

Foetal Achondroplasia: Prenatal Diagnosis, Outcome and Perspectives

BackgroundAchondroplasia, due to a specific pathogenic variant in FGFR3, is the most common viable skeletal dysplasia and the diagnosis is mostly done in the prenatal period. Since 2021, the use of Vosoritide, a specific treatment for achondroplasia, validated in phase 3 placebo-controlled trials, has been recommended to significantly increase the height of children and infants. In the light of these new therapeutic prospects, a complete understanding of the pathophysiology of skeletal damages occurring from foetal life is required. ObjectivesTo describe foetal imaging and the antenatal and postnatal management of pregnancies complicated by a diagnosis of foetal achondroplasia. MethodsA retrospective and descriptive study, including all pregnant women with a prenatal diagnosis of achondroplasia, was conducted in the prenatal unit of Necker Hospital (Paris, France) between 2009 to 2022. Maternal and obstetric characteristics and foetal imaging (ultrasound and bone CT) were collected. Pregnancy outcomes, paediatric follow-up in the case of live births, and post-mortem examination (PME) data in the case of termination of pregnancy were reported. In addition, we have prospectively developed a specific research protocol using foetal brain MRI to assess the anatomy of the foramen magnum, following the same approach currently recommended in the postnatal period. Results29 cases of achondroplasia were included. Median gestational age at referral was 31+2 weeks’, about 1 week after the suspected diagnosis on routine ultrasound. Shortening of the femoral length and of all the other long bones, macrocephaly, facial abnormalities, increased metaphyseal-diaphyseal angle and tapering of the proximal femoral bone were the five most prevalent ultrasound signs. Foetal diagnosis was done by the identification of the foetal FGFR3 mutation and/or by CT scans (n=15) where specific abnormalities of the long bones, platyspondyly and abnormal profile have been described in 100% of cases. PME revealed: i) on external examinations (n=7) that all fetuses had very short long bones, moderate platyspondyly, small iliac wings with internal spines, macrocrania, and narrow thorax, ii) on internal examination (n=5) all had severe abnormalities in the growth plate and particularities in the temporal cortex and hippocampal region. One foetal MRI was performed at 33 weeks’ and revealed tight stenosis of the foramen magnum and compression of the spinal cord. Of the live-born infants for whom follow-up was known (n=6), 2/6 (including the case who had a foetal MRI) required neurosurgical intervention in the first few months of life for spinal cord compression due to severe stenosis of the foramen magnum. ConclusionA complete mapping of the skeletal features present in fetuses with achondroplasia is reported here, providing a better understanding of the pathophysiology of this condition. New tools such as foetal MRI, to assess the risk of postnatal severe neurological complications, could help improve the care pathway of the affected neonates.

Identification of a novel mutation in PATL2 gene associated with the germinal vesicle arrest of oocytes

The aim of this study was to investigate the genetic factors of a patient with germinal vesicle arrest in oocytes. Clinical data and blood samples were collected from the patient and some were amplified for high-throughput gene and Sanger sequencing. Several molecular and cellular experiments were performed to determine the association between the gene mutation and germinal vesicle arrest. Two mutation sites (c.1282G > T and c.1247C > A) were found in the PATL2 gene. The c.1282G > T mutation is associated with oocyte maturation abnormalities according to previous research, whereas c.1247C > A is a novel mutation of unknown clinical significance. In cell transfection experiments, qRT-PCR, immunofluorescence, and Western blotting revealed that the mRNA and protein levels of the PATL2 gene with the c.1247C > A mutation were reduced. Sanger sequencing suggested that the patient inherited the PATL2 mutations from her parents via a compound heterozygous mode of inheritance. Collectively, this study describes the PATL2-gene c.1247C > A mutation associated with germinal vesicle arrest in oocytes, providing a useful target for genetic and background tests for patients presenting with oocyte maturation abnormalities and/or germinal vesicle arrest following multiple unsuccessful attempts with assisted reproductive technology.

Identification of a Missense Mutation in the FLNC Gene from a Chinese Family with Restrictive Cardiomyopathy [Letter

Identification of a Missense Mutation in the FLNC Gene from a Chinese Family with Restrictive Cardiomyopathy [Letter

Clinical and genetic diversity in Iranian individuals with RAPSN-related congenital myasthenic syndrome.

Congenital myasthenic syndromes (CMSs) are genetic disorders affecting motor function with variable symptoms. RAPSN-related CMS, caused by mutations in the RAPSN gene, leads to muscle weakness. Accurate diagnosis is essential for proper management. This study aims to analyze six Iranian families affected by RAPSN-CMS, focusing on clinical manifestations, genetic variants, treatment response, and outcomes. Clinical assessments, genetic analysis, and whole-exome sequencing were performed on the six families to identify RAPSN gene mutations. The study examined symptoms, disease severity, age of onset, treatment response, and outcomes. Treatment with pyridostigmine and salbutamol was given to assess its effectiveness. Three homozygous known variants in RAPSN gene were identified: c.491G > A in three families, c.264C > A in two families, and c.-210A > G in one family. Clinical assessments showed diversity in symptoms and treatment responses. Pyridostigmine and salbutamol treatment improved symptoms and quality of life. This study highlights the significance of molecular diagnosis for RAPSN-related congenital myasthenic syndromes (CMS) in Iran, marking the first comprehensive genetic analysis in the region. The identification of specific pathogenic variants underscores the unique genetic landscape of local patients. Furthermore, our long-term follow-up revealed variable treatment responses, emphasizing the need for personalized care strategies. The clinical variability among patients with identical mutations necessitates a multidisciplinary approach for effective management. By enhancing genetic awareness and refining follow-up methods, we aim to improve diagnosis accuracy and interventions, fostering better outcomes for affected families in the Iranian population.

Patient-derived glioma organoids real time identification of IDH mutation, 1p/19q-codeletion and CDKN2A/B homozygous deletion with differential ion mobility spectrometry.

Extent of brain tumor resection continues to be one of the central decisions taken during standard of care in glioma patients. Here, we aimed to evaluate the most essential molecular factors, such as IDH (isocitrate dehydrogenase) mutation in gliomas classification with patient-derived glioma organoids (PGOs) using differential mobility spectrometry (DMS). we prospectively recruited 12 glioma patients, 6 IDH-mutated and 6 IDH wild-type tumors, from which PGOs were generated ex-vivo. Altogether, 320 PGOs DMS spectra were analyzed with a classifier algorithm based on linear discriminant analysis (LDA). LDA model classification accuracy (CA) obtained between IDH-mutant and IDH wild-type PGOs was 90% (91% sensitivity and 89% specificity). Furthermore, 1p/19q codeletion classification within IDH mutant PGOs reached 98% CA (93% sensitivity and 99% specificity), while CDKN2A/B homozygous loss status had 86% CA (63% sensitivity 93% specificity). DMS suitability to differentiate IDH-mutated PGOs was thus validated in ex vivo cultured samples, PGOs. Preliminary results regarding 1p/19q codeleted PGOs and CDKN2A/B loss PGOs identification endorse testing in a prospective intraoperative glioma patient cohort. Our results reveal a sample classification set-up that is compatible with real-time intraoperative surgery guidance.

Role of next‐generation sequencing in revolutionizing healthcare for cancer management

AbstractNext‐generation sequencing (NGS) has emerged as a transformative technology in oncology, revolutionizing cancer diagnostics and personalized treatment strategies. By providing comprehensive insights into the genetic landscape of tumors, NGS enables the identification of critical somatic and germline mutations, copy number variations (CNVs), and gene fusions. Over the past decade, advancements in NGS platforms have led to greater accuracy, speed, and cost‐effectiveness, making it an integral part of cancer research and clinical diagnostics. Despite its widespread adoption, significant challenges remain, including the need for improved methods to detect minimal residual disease (MRD) and accurately profile tumor heterogeneity. This review explores the evolution of NGS technologies and their pivotal role in cancer biology, from early diagnostics to therapeutic guidance. It delves into the application of NGS in identifying CNVs and gene fusions, monitoring MRD, and the increasing relevance of targeted NGS and spatial genomics. Furthermore, the integration of spatial transcriptomics is highlighted as a frontier in understanding the tumor microenvironment. By addressing these critical aspects, this review provides a comprehensive overview of how NGS is shaping the future of cancer research and treatment, offering a complete overview of potential NGS applications in scientific and clinical oncology.

Identification of mutation of MYOC (c.1099G>A), a pedigree pathogenic gene of juvenile open angle glaucoma (JOAG): A case report

Rationale: The MYOC gene is associated with juvenile open-angle glaucoma (JOAG). This study aims to provide genetic counseling for a Chinese JOAG family by detecting MYOC mutations to identify high-risk individuals for early JOAG intervention. It also supplements the clinical characteristics of glaucoma patients with MYOC gene mutations. Patient concerns: A 43-year-old presented sought medical attention in a local hospital due to a 6-month decline in binocular vision. He was diagnosed as JOAG and underwent glaucoma surgery. The patient also had 11 family members with a history of JOAG. Diagnoses: After sequencing the polymerase chain reaction products of the patient, MYOC c.1099 G > A (p.G367R) mutation was observed. That is consistent with a diagnosis of JOAG. Intervention: Polymerase chain reaction analyses of 9 patients and 42 healthy family members were performed to explore potential mutations associated with familial JOAG. Outcomes: JOAG assisted in diagnosing the III-5 proband. Genetic detection indicated that III-5 was exposed to a novel heterozygous missense mutation of MYOC (c.1099 G > A [p.G367R]). The co-segregation of this gene with the trait observed in the pedigree was verified. All 10 participants exhibiting this mutation had JOAG phenotypes, whereas other participants did not show this mutation. In terms of MYOC mutation c.1099 G > A (p.G367R), this mutation occurred when the 1099th nucleotide in the encoding zone of MYOC changed from G to A. Moreover, the 367th amino acid coded by this base got mutated from glycine to arginine. DNAMAN sequence homology results showed that the G residues of MYOC: 367 were significantly conserved among different species. In addition, 3D protein conformation predicted that these mutations could decrease protein stability. Lessons: MYOC c.1099 G > A was identified as a pathogenic gene of JOAG in this pedigree. The addition of the MYOC mutant spectrum to JOAG in the Chinese population facilitates a complete understanding of the molecular pathogenesis and clinical diagnosis of MYOC.

Practical application of precision oncology in adult onset craniopharyngiomas.

Craniopharyngiomas (CPs) are benign and rare tumors found in adults. Their location close to vital neurovascular structures makes traditional treatment modalities (surgery and radiation) challenging and potentially fraught with morbidity. The 2021 WHO classification has divided what was previously considered two subtypes of craniopharyngioma into separate entities. Identification of specific molecular driver mutations in each type- BRAF V600E in papillary craniopharyngiomas (PCP) and CTNNB1 in adamantinomatous craniopharyngiomas (ACP) has resulted in a paradigm shift in the management of adult CPs. In this study, we describe our experience in treating PCPs with targeted therapy and highlight nuances in management accounting for current evidence. This review also explores the current scope and application of precision oncology in adult CPs including the experience with ongoing trials and prospects for future research. The high prevalence of targetable mutation in cases of PCP and the efficacy of BRAF inhibitors alone or in combination with MEK inhibitors has improved the disease control in these patients. In the current scenario, while surgery is warranted to obtain histopathological diagnosis, radical resection and its associated risks can be avoided. In case of ACPs, dysregulation of multiple pathways has been implicated. This has prompted the use of a variety of targeted therapies with inconsistent outcomes. The results of ongoing and future trials may define its role in management. Precision oncology is a promising addition to the treatment armamentarium of adult CPs.

Bmpr1aa modulates the severity of the skeletal phenotype in an fkbp10-deficient Bruck syndrome zebrafish model.

Rare monogenic disorders often exhibit significant phenotypic variability among individuals sharing identical genetic mutations. Bruck syndrome (BS), a prime example, is characterized by bone fragility and congenital contractures, although with a pronounced variability among family members. BS arises from recessive biallelic mutations in FKBP10 or PLOD2. FKBP65, the protein encoded by FKBP10, collaborates with the LH2 enzyme (PLOD2) in type I collagen telopeptide lysine hydroxylation, crucial for collagen cross-linking. To identify potential modifier genes and to investigate the mechanistic role of FKBP10 in BS pathogenesis, we established an fkbp10a knockout zebrafish model. Mass-spectrometry analysis in fkbp10a-/- mutants revealed a generally decreased type I collagen lysyl hydroxylation, paralleled by a wide skeletal variability similar to human patients. Ultrastructural examination of the skeleton in severely affected mutants showed enlarged type I collagen fibrils and disturbed elastin layers. Whole-exome sequencing of 7 mildly and 7 severely affected mutant zebrafish siblings, followed by SNP-based linkage analysis, indicated a linked region on chromosome 13, which segregates with phenotypic severity. Transcriptome analysis identified six differentially expressed genes (DEGs) between mildly and severely affected mutants. The convergence of genes within the linked region and DEGs highlighted bmpr1aa as a potential modifier gene, as its reduced expression correlates with increased skeletal severity. In summary, our study provides deeper insights into the role of FKBP10 in BS pathogenesis. Additionally, we identified a pivotal gene that influences phenotypic severity in a zebrafish model of BS. These findings hold promise for novel treatments in the field of bone diseases.

Identification of biallelic intronic EPM2A mutations in a Lafora disease kindred.

Lafora disease (LD) is a severe autosomal recessive disease, which usually presents as seizure and myoclonus, followed by behavioral changes, dysarthria, intellectual decline, and finally progressed to dementia and a vegetative state. The main cause of LD is the loss-of-function mutations in EPM2A and NHLRC1 that encode laforin and malin, respectively. Targeted genetic testing is the gold standard to confirm the diagnosis of LD. To describe the pathogenic role of biallelic EPM2A intronic mutations carried by patients in a family diagnosed as LD. Here, we present clinical findings in a patient presenting with epileptic seizures and Lafora bodies in muscle biopsy. Long-read DNA and RNA sequencing were performed to identify the causative mutation. Western blot and qPCR confirmed the pathogenic role of biallelic EPM2A intronic mutations. Genetic testing identified two intronic mutations in EPM2A which caused aberrant mRNA splicing. c.301+1 G > A in EPM2A caused aberrant splicing at donor site and resulted in intron retention in transcript NM_005670.4, while c.476+14860 C > A caused aberrant splicing in transcript NM_001368129.2 and NM_001368132.1. Our findings expand the spectrum of variants in LD disease, additionally providing evidence linking non-coding regulatory regions mutations to LD disease.

Identification of heterozygous mutations of ABCC8 gene responsible for maturity-onset diabetes of the young with exome sequencing

Abstract Background Although the MODY12 subtype, caused by ABCC8 mutations, is rare, it is highly sensitive to sulfonylureas. The identification of ABCC8 mutations in patients clinically diagnosed with MODY has the ability to contribute to the precise management of diabetes. Methods Genetic analysis of two families with MODY were conducted using whole-exome sequencing (WES) and Sanger sequencing. The spatial structures of the mutant proteins were constructed using MODELLER and PyMOL software to provide further evidence of pathogenicity. Results The heterozygous missense mutations V357I and R1393H in ABCC8 were found in probands of two unrelated MODY pedigrees, which co-segregated with the hyperglycemic phenotypes in these two pedigrees. Detection of the V357I mutation enabled the proband of family A to successfully transfer from insulin to sulfonylurea (SU). After 3 months of follow-up for the SU trial, the HbA1c level of proband A improved from 12.4% at the initial diagnosis to 7.20%. Proband B was treated with insulin because of pregnancy and poor islet function. In silico analysis indicated that the R1393H mutation resulted in a longer hydrogen bond distance to L1389 and cleavage of carbon-hydrogen bonds to V1395, A1390, and L1389. Conclusions We have described two pathogenic missense mutations in ABCC8 in Chinese families with MODY. Our findings support the heterogeneity in the clinical features of MODY12 caused by ABCC8 mutations.

Analysis of BRCA1 Exon 2 Mutations in FFPE Tissues of Bangladeshi Bangali Females with Breast Cancer

Background: Among all breast cancers, 5 to 10% are hereditary and related to mutation of BRCA1 and BRCA2 gene. To date, extensive researches have been carried out for detection of mutations in the exon2 of BRCA1 gene. Genetic study on these two genes from formalin-fixed paraffin-embedded tissue in Bangladeshi population has not been reported so far. Objective: To identify mutation in exon2 of BRCA1 gene from formalin-fixed paraffin-embedded tissue of adult Bangladeshi Bangali female patients with breast cancer. Methods: The research was cross-sectional descriptive type of study. The study was conducted on Adult Bangladeshi Bangali female patients with breast cancer aged more than 18 years. A questionnaire was developed to record information on socio-demographic and reproductive characteristics. The data was analyzed by SPSS (Statistical package for the social sciences) version 23.0. The whole sequence of exon2 of chromosome 17 was amplified by short range PCR using the Gotaq master mix and primer sequence. The amplicons were confirmed by 2% agarose gel electrophoresis and sequencing was done by Sanger sequencer. Data analysis was performed using Chromas® software version 2.33 and Mega 7 software. The quary sequences were compared with the NCBI database. Results: Average age of the breast cancer patients was 45.46 (± 11.52) and the mean age at menarche was 12.46 (± 0.646). In this study, new mutations along with known mutations were found in exon2 of BRCA1 gene of eight adult female breast cancer patients. The mutations are insertions (C>A, C>T, T>A, G>T, G>C, T>C, A>T, C>G), deletion (C_) and single nucleotide substitution (T-C, G-A, T-G, C-G, T-A, G-C, C-A) in types. Conclusions: The aim of the research was to identify mutation in exon2 of BRCA1 gene. Eight patients have mutation in their DNA sequence revealed from formalin-fixed paraffin-embedded tissue. Further studies are required to evaluate whether these mutation contribute to breast cancer or not. Identification of known mutation along with new mutation with this small sample size emphasizes the importance of exploration the genetic makeup of Bangladeshi population to develop a database for proper screening and genetic counseling of the disease.

TREATMENT OPTIONS FOR RECURRENT MALIGNANT DIFFUSE ASTROCYTOMA (WHO GRADE IV)

Objectives We present the case of a 37-year-old female who underwent partial resection in 2018 for a diffuse fibrillary astrocytoma (WHO II) that invaded almost the entire right cerebral hemisphere. The patient followed conventional radiotherapy and chemotherapy. She presents after 6 years of regularly follow-ups with left hemiparesis, intracranial hypertension syndrome and tumor recurrence on MRI. The patient underwent another surgical intervention and the new histopathological diagnosis was diffuse astrocytoma grade IV. Therapeutic options for these patients are limited considering the fact that a gross total resection or a conventional re-irradiation could impact the quality of life. Therefore, exploring new therapeutic methods, such as targeted molecular therapy like EGFR antagonists or proteasome inhibitors, or proton therapy, should be considered. Material and Methods We conducted extensive research in two public medical databases for information related to the molecular pathways and management of primary and recurrent malignant astrocytoma and relevant articles were selected. Subsequently, we correlated this information with our direct experience in our case and discussed the observed results. Results Treatment modalities for these patients include reintervention, re-irradiation and second line chemotherapeutics. In relapsing cases the goal of reintervention is both to alleviate symptoms and obtain tumoral tissue for immunohistochemical analysis for identification of the new mutations. Conventional re-irradiation for large lesions carries high risks of producing both short-term and long-term side effects, impacting the quality of life. Alternatively, proton therapy minimizes the risk of adverse events due to Bragg peak reducing the irradiation of the surrounding tissue. Conclusions Genetic characterization of these lesions can facilitate targeted molecular therapy and help in establishing the prognosis. Re-irradiation of malignant astrocytomas with proton therapy is an effective treatment measure allowing for comparable tumor control to conventional radiotherapy.

Use of 3' Rapid Amplification of cDNA Ends (3' RACE)-Based Targeted RNA Sequencing for Profiling of Druggable Genetic Alterations in Urothelial Carcinomas.

Targeted treatment of advanced or metastatic urothelial carcinomas (UCs) requires the identification of druggable mutations. This study describes the development of a 3' Rapid Amplification of cDNA Ends (3' RACE)-based targeted RNA sequencing panel which accounts for the status of all genes relevant to UC treatment, namely, FGFR1-4, KRAS, NRAS, BRAF, ERBB2 (HER2), CD274 (PD-L1) and PIK3CA. FGFR2/3-activating point mutations or fusions were found in 54/233 (23.2%) tumors. FGFR3 rearrangements were identified in 11 patients, with eight of them being undetectable by commonly used PCR kits. In addition, one tumor contained a high-copy FGFR2 gene amplification accompanied by strong overexpression of the gene. Mutations in RAS/RAF genes were present in 30/233 (12.9%) UCs and were mutually exclusive with alterations affecting FGFR2/3 genes. On the contrary, activating events in the HER2 oncogene (point mutations and overexpression), as well as PIK3CA mutations, which were relatively common, occurred with similar frequencies in RAS/RAF- or FGFR2/3-positive vs. negative samples. High PD-L1 mRNA expression was associated with advanced disease stage and was not observed in tumors with increased HER2 mRNA expression or in UCs with evidence for FGFR2/3 activation. Three of the studied carcinomas had high-level microsatellite instability (MSI). Overall, more than half of the UCs had potentially druggable genetic alterations. The proposed NGS panel permits comprehensive and cost-efficient analysis of UC-specific molecular targets and may be considered in clinical routine.

Abstract 4138690: A Case of Hypertrophic Cardimyopathy: Digenic Variants of Uncertain Significance Mutations in MHY7 and RYR2 Genes

Introduction: Hypertrophic Cardiomyopathy (HCM) is primarily a disease caused by mutations in single genes, but around 5% of HCM patients, exhibit 2 (digenic) or more (oligogenic) causal mutations in the same gene or in different genes. We present a case of familial HCM with variants of uncertain significance (VUS) mutations in the MYH7 and RYR2 genes, highlighting the complexity of genetic inheritance and its implications on disease severity. Case presentation: A 40-year-old male presented with a history of hypertension, HCM, and two prior myocardial infarctions. He had syncope, non-sustained ventricular tachycardia, and a family history of sudden cardiac death (SCD) in his maternal grandfather. A dual-chamber ICD was placed for primary prevention of SCD because of his high-risk profile. Echocardiography demonstrated normal LV size and function with moderate asymmetric septal hypertrophy. Cardiac MRI indicated diffuse asymmetric hypertrophy and a 10.9% LV myocardial scar burden. Left heart catheterization revealed normal coronary arteries with LVOT gradient up to 60 mmHg, consistent with HCM. Genetic testing revealed VUS in the MYH7 (c.1305G>A, p.Met435Ile) and RYR2 (c.10528C>A, p.Arg3510Ser) genes (Figure 1). Further family genetic testing confirmed these VUS mutations in multiple relatives (Figure 2). Discussion: The identification of VUS mutations in MYH7 and RYR2 genes in multiple family members highlights the complexity of genetic inheritance in HCM. These findings underscore the challenges in clinical interpretation and risk stratification, as the co-occurrence of mutations in different genes may have synergistic effects on disease severity and phenotype expression. Comprehensive genetic evaluation, including family studies, is crucial for understanding the clinical significance of these mutations and guiding personalized management strategies. Further research is needed to elucidate the impact of VUS mutations on the clinical outcomes of HCM patients.

CNSC-12. IMMUNOLOGICALLY TARGETING U1 MUTANT SHH MEDULLOBLASTOMA

Abstract OBJECTIVES Medulloblastoma (MB) is the most common malignant pediatric brain tumor representing a significant burden of morbidity and mortality in the US. MB is comprised of four subgroups: Wnt, Shh, Group 3, and Group 4. Shh tumors represent 25% of cases and subdivides into Shh-beta and Shh-gamma, Shh-alpha, and Shh-delta. Half of Shh MB carry an identical somatic point mutation in a non-coding small nuclear RNA (snRNA) called U1 (r.3A>G) which is found in 97% of Shh-d tumors, and in most Shh-alpha tumors with TP53 mutations. Current therapies for patients with TP53 and U1 mutant Shh-alpha MB observe rare survivors, and adult Shh-delta patients continue to experience significant morbidity and mortality calling for urgent prioritization of these tumors for targeted therapy. METHODS Cryptic exons were identified in both Shh-delta U1 snRNA mutant samples and Shh-delta U1 wildtype (WT) samples using CryEx pipeline. In-house scripts were utilized for selecting for cryptic exons that are uniquely expressed in Shh-delta U1 snRNA mutant compared to wildtype (WT) samples. RESULTS Analyzing 180 Shh MB RNA-seq samples, we identified 23% Shh-alpha, no Shh-beta, 97% of Shh-delta and 3% Shh-gamma harbored the U1 mutation. The splicing landscape was then interrogated comparing Shh-delta U1 snRNA mutant samples to WT samples. Expressed exons were filtered to exclude known exons to identify novel or cryptic exons. To select for Shh-delta U1 snRNA mutant induced cryptic exons, CryEx arising from introns, not identified in Shh-delta U1 WT and included >10% of their inclusion rates measured by percent spliced in (PSI) in Shh-delta U1 snRNA mutant samples were filtered. Of the middle CryEx, we identified 43,188 that were U1 mutant induced. Further filtering for cell surface Middle CryEx, three of the 75 middle CryEx overlapped. CONCLUSION The PTCH1 neoantigen formed from the CryEx insertion translates a protein that is unique to the tumor cells (i.e., not in normal tissue) was identified as a juxtamembrane for therapeutic drug discovery.

Segregation of Trans Mutations in the CDH23 Gene in an Emirati Family with Sensorineural Hearing Loss.

Hearing loss (HL) is a significant global health concern, affecting approximately 1 in every 1000 newborns, with over half of these cases attributed to genetic factors. This study focuses on identifying the genetic basis of autosomal recessive non-syndromic hearing loss (ARNSHL) in a consanguineous Emirati family. Clinical exome sequencing (CES) was performed on affected members of the family, followed by Sanger sequencing to validate the findings. Specific primers were used for PCR amplification of target CDH23 exons. Mutations were analyzed using various computational tools to assess their pathogenicity. We identified two heterozygous mutations in the CDH23 gene: a novel nonsense variant (c.264G>A, p.Trp88Ter) and a missense variant (c.5168G>A, p.Arg1723His). Both mutations were found in trans configuration, suggesting a compound heterozygous state contributing to the phenotype. In silico analysis predicted a significant impact on protein function, potentially leading to the observed ARNSHL. This study emphasizes the complexity of genetic factors in hearing loss, particularly in highly consanguineous populations. The identification of both nonsense and missense mutations in the CDH23 gene enhances understanding of its role in hearing loss and provides essential insights for genetic counseling and future therapeutic strategies.