Children with suspected hereditary spastic paraplegia clearly benefit from whole exome analysis.

BackgroundMitochondrial DNA depletion syndrome 13 (MTDPS13) is an autosomal recessive disorder presenting in early infancy with encephalopathy, hypotonia, lactic acidosis, and severe global developmental delay. Patient‐derived cells typically exhibit impaired mitochondrial oxidative phosphorylation and a marked reduction in mitochondrial DNA (mtDNA) copy number.Case ReportWe report the case of a male preterm neonate born at 31 + 3 weeks of gestation following a pregnancy marked by severe polyhydramnios. At birth, his weight was 1400 g. Physical examination revealed dysmorphic features, redundant and lax skin, and generalized muscular hypotonia. Laboratory investigations showed marked lactic acidosis associated with lactic aciduria, ketonuria, and urinary biomarkers indicating activation of preoxidative phosphorylation biochemical pathways to sustain ATP production. Echocardiography demonstrated mild, early‐onset hypertrophic cardiomyopathy.The Exome Analysis Clinical and Biochemical Markers: The exome analysis, performed within the first week of life, highlighted a pathogenic variant in homozygous state of FBXL4 gene (c.1648_1649delGA), which led to the diagnosis of MTDPS13. In this clinical contest, a ketogenic diet (KD) was started with a daily caloric intake of 120 kcal/kg and an initial ketogenic ratio of 1:1. These intakes were administered both with a parenteral nutrition and continuous nasogastric tube feeding and were gradually increased and adapted on a day‐by‐day basis according to lactic acidosis, growth increase, and common metabolic parameters such as glucose, electrolytes, creatinine, and blood urea nitrogen. After 3 days of this treatment approach, a significant reduction in lactate levels and improvement in acid–base balance and growth trend were observed along with clinical and cardiovascular parameters. At discharge from neonatal intensive care unit, the KD was continued at home and during follow‐up. The infant showed stability in the clinical and biochemical markers.ConclusionsThis is the first documented report of the use of a KD in a preterm neonate with this mitochondrial disorder during the early days of life. Prompt genetic confirmation and early initiation of KD may enable a more targeted and effective management of MTDPS within the neonatal intensive care setting.

Introduction . Aortic arch anomalies, especially the “bovine arch”, can cause the development of an ascending aortic aneurysm. There is a high coefficient of heritability of this pathology, however, genetic studies are rare. Since the “bovine arch” is one of the variants of the development of the aortic arch and large vessels during embryogenesis, this pathology may be associated with genes encoding proteins involved in the embryonic development of the cardiovascular system. Aim: To identify rare, clinically significant variants of genes of cardiovascular embryonic development in patients with sporadic ascending aortic aneurysm and a “bovine arch”. Material and Methods . The study included 42 patients with a sporadic form of ascending aortic aneurysm, including 11 patients with a “bovine arch”. Analysis of the clinical exome was performed based on DNA sequencing data using Clinical Exome Solution (Sophia Genetics, Switzerland) and NextSeq 500 genetic sequencer (Illumina, USA). The search for rare, clinically significant variants (minor allele frequency <1%) was carried out in exons and adjacent introns of 120 genes of embryonic development of the cardiovascular system. Validation of identified variants was performed using Sanger sequencing. Results. In patients with aortic aneurysm and “bovine arch”, the following clinically significant variants were identified: the pathogenic variant c.610-2A>G of the CCDC39 gene, which is a single-nucleotide substitution leading to the loss of the acceptor splice site (ΔScore = 0.97 Spliceailookup) and a variant of uncertain clinical significance (VUS) c.2564T>C in the ANKS6 gene, which has high pathogenicity rates on the CADD (Phred = 28.3) and AlphaMissense (0.972) scales. A likely pathogenic variant c.1151T>C of the ACVR2B gene was identified in the group of patients with aortic aneurysm without supraaortic vessels anomaly (AlphaMissense = 0.966). Among the 38 genes whose sequences revealed VUS in both groups of patients, the protein products of 17 (44.7%) are involved in the functioning of cilia and microtubules, and the proteins encoded by the genes MKS1, CCDC40, DNAAF1, ANKS6, CCDC39, DNAH5, DNAAF3 are also responsible for the development of the cardiovascular system. Conclusion . Rare, clinically significant variants in the CCDC39 and ANKS6 genes, which are crucial for primary cilia function, contribute to the development of sporadic ascending aortic aneurysm in combination with a “bull’s arch.” When a normal aortic arch is present, variants in the ACVR2B gene, belonging to the TGF-beta signaling protein superfamily, play an important role.

The DNA repair protein RAD18 activates “Y-family” trans-lesion synthesis (TLS) DNA polymerases that are DNA damage-tolerant and potentially error-prone. RAD18 is also frequently overexpressed and pathologically activated in cancer cells. However, the extent to which RAD18 shapes cancer genomes and impacts tumorigenesis is unclear. Therefore, we tested the effect of Rad18 status on chemically induced and oncogene-driven tumorigenesis. In a chemically induced oral carcinogenesis model, acute (2–16 days) 4NQO treatment induces expression of Rad18 and TLS polymerase mRNAs in mouse oral epithelial cells prior to the emergence of oral squamous cell carcinomas (OSCCs). Chronic (8-week) 4NQO treatment leads to the onset of oral tumors that is accelerated in Rad18−/− mice when compared with Rad18+/+ animals. Analysis of OSCC exomes reveals increased levels of G(C)>T(A) transversions in Rad18−/− tumors when compared with Rad18+/+. Therefore, Rad18 promotes error-free bypass of 4NQO-induced DNA lesions and suppresses 4NQO-induced oral carcinogenesis. In a KrasG12D-induced lung carcinogenesis model, Rad18 deficiency did not affect rates or incidence of oncogene-induced lung tumors or mutations. Taken together, we demonstrate that Rad18 has context-specific tumor-suppressive activity. Given the prevalence of 4NQO-like environmental exposures, RAD18 is highly likely to shape human cancer genomes and perhaps influence other aspects of the tumorigenic process.

Exome sequencing reveals rare loss-of-function mutations in FLG and immune genes in patients with multiple food allergies.

Combined exome and RNA-seq analysis in patients with rare non-syndromic inherited brain arteriovenous malformation suggests a novel function for PTPN13 in arterial specification.

Bardet-Biedl syndrome (BBS) is a rare ciliopathic disorder that segregates in an autosomal recessive manner. Genetic studies have so far identified 26 BBS-associated genes worldwide. This study analyzed a multiplex consanguineous Pakistani family with Bardet-Biedl syndrome. Genetic analysis was performed using whole-exome sequencing and Sanger sequencing. Additionally, in silico predictions were performed for functional characterization of the identified mutation. Whole exome analysis of this family identified a novel nonsense mutation [(NM_144596: exon11:c.C1047G: p.(Tyr349*)] in the 11th exon of TTC8 gene. The identified mutation presumably leads to removal of four TPR domains and C-terminus portion. Structural analyses of mutant TTC8 protein showed substantial morphologic and interactional variations, suggesting a defective role of the TTC8 protein in BBSome complex and thus its involvement in disease progression. Identification of novel mutation has expanded the mutational spectrum of TTC8. Moreover, these findings will help in genotype-phenotype association, prenatal diagnosis and genetic counseling of families at risk of BBS syndrome.

Primary bilateral macronodular adrenal hyperplasia (PBMAH) is a rare cause of Cushing's syndrome. The study aimed to characterize changes in steroidogenesis in PBMAH through immunohistochemistry (IHC), transcriptomics and exome analysis with detailed clinical data assessment. Our cohort included 22 PBMAH patients who underwent adrenalectomy, and we investigated IHCs for five key steroidogenic enzymes (CYP11B1, CYP11B2, CYP17A1, HSD3B2 and CYB5A), covering the adrenocortical hormone secretion pathways. Unsupervised clustering of IHC staining identified three clusters: Cluster 1 exhibited low CYP11B1 and CYP17A1 expression, elevated HSD3B2 expression, smaller tumors, and included ARMC5 mutants. Cluster 2 showed higher enzyme staining for CYP11B1, CYP17A1 and CYB5A and included KDM1A mutants and female-only cases. Cluster 3 was characterized by slightly increased CYP11B2 staining and comprised of wild-type samples lacking ARMC5 and KDM1A variants. Exome sequencing identified steroidogenic pathway germline variants across the three clusters. Importantly, in Cluster 1, a higher burden of predicted damaging variants across various steroidogenic genes were found potentially leading to reduced enzyme staining through altered functions of the variant. However, this distinctive variant pattern was less evident in Cluster 2 and Cluster 3. Transcriptomics identified no differences between the clusters in terms of gene expression, hinting the influence of possible epigenetic factors on IHC. In summary, our study identified distinct groups in PBMAH based on their IHC staining patterns and highlights the importance for integrated molecular profiling for comprehensive characterization of heterogeneity in PBMAH.

Colorectal cancer (CRC) lung metastases exhibit high recurrence rates after resection, underscoring the need for improved therapeutic strategies. This study aimed to characterize the tumor microenvironment (TME) of CRC lung metastases and identify the factors associated with recurrence. Fifteen CRC patients who underwent lung metastasectomy were enrolled. Multiplex immunohistochemistry (IHC), whole exome sequencing, transcriptome profiling, and single-cell RNA sequencing (scRNA-seq) were conducted on matched tumor, adjacent and distant normal lung tissues. Immune cell populations and gene expression profiles were analyzed and correlated with clinical recurrence outcomes. Exome and transcriptome analyses revealed frequent TP53, KRAS, and APC mutations. Most tumors corresponded to consensus molecular subtypes 2 and 4, characterized by immune-depleted and fibrotic features. Tumors showed downregulation of effector T and NK cell signatures. IHC revealed reduced density and increased distance of CD8+ T cells and macrophages from the epithelial cells. scRNA-seq demonstrated increased regulatory T cells and decreased NK and effector T cells in tumor. Tumor-associated macrophages (TAMs), particularly SPP1 (osteopontin)-expressing subsets, were markedly enriched in tumor and correlated with suppressed effector T cella activity. High SPP1 expression was associated with early recurrence and poor overall survival. Patients with recurrence had higher proportion of PD-1+ CD8+ T cells in adjacent normal tissues. Immunosuppressive features including enrichment of SPP1+ TAMs and depletion of effector T and NK cells contribute to recurrence after CRC lung metastasectomy. Therapeutic strategies targeting both TAMs and T cells may enhance clinical outcomes in this patient population.

Abstract Pancreatic neuroendocrine tumors (panNETs) undergo high-grade (HG) transformation often, with the liver being a common site for metastasis​. Surgical resection being considered as long-term outcomes for selected patients. However, recurrence and grade transformation remain potential significant challenges, with recurrence rates approaching 50–95%.1,2 Despite extensive whole exome analysis and construction of phylogenetic trees, we were unable to identify either a consistent genetic driver or any specific patterns of tumor transformation.2 We are also concerned that some of our treatments may inadvertently contribute to grade transformation. To assess the treatment effects, we performed pre- and post- trans arterial embolization bulk-transcriptome analysis, which revealed cell population shifts in panNETs that may be linked to grade transformation.4To explore cellular shifts within the liver tumor microenvironment during panNET progression, we performed single-cell RNA sequencing. The resulting data was processed using Seurat.v5. The clusters of panNET cells, fibroblasts, hepatocytes, and immune cells were annotated by known markers. Additionally, we distinguished malignant cells from a reference of immune cells, fibroblasts, and hepatocytes by InferCNV. To understand the tumor progression, we performed trajectory analysis using monocle3. Differential metabolic activity between the panNETs grades were assessed using the scMetabolism package. Cell-cell communication and related ligand-receptor pairs were inferred using CellChatDB. Our results revealed distinct transcriptional trajectories, with pseudotime analysis demonstrating a trajectory of tumor evolution from low-grade (LG) to HG states. HG tumors were enriched for proliferative and aggressive subclusters compared to LG cells. Metabolic profiling further highlighted grade-specific adaptations, with HG tumors showing enhanced oxidative phosphorylation and TCA cycle across tumor cells, whereas LG tumors displayed relatively lower metabolic activity. Notably, immune cells were found metabolically active in LG via glycolysis. Conversely, HG panNETs exhibit glucose depletion in immune cells and less active microenvironment. The CellChat analysis revealed distinct cellular communication patterns in panNET grade. For instance, in HG tumors, signaling was primarily mediated between fibroblasts and panNET cells, with Glu-(SLC1A2+GLS)-GRM7 as the dominant ligand–receptor pair. In LG tumors, major interactions occurred among immune cells, hepatocytes, and panNET cells, with Glu-(SLC1A3+GLS)-GRIK2 representing the highest contributor. The results suggest that metabolic rewiring, altered intercellular signaling, and transcriptional plasticity underlie progression from LG to HG disease. Reference: 1. Spolverato etal J Gastrointest Surg. 2017, 21(12):2039-2047 2. Mayo etal Ann Surg Onc. 2011, 18(13):3657-65. 3. Singh et al. Early ... Margie and Robert E. Peterson Neuroendocrine Tumor Research Symposium. 2023. 4. Singh et al. Post... Margie and Robert E. Peterson Neuroendocrine Tumor Research Symposium.2023 Citation Format: Himanshu N. Singh, Chenyang Zhan, Jessica C. Puzzuoli, Elias-Ramzey Karnoub, Jungeui Hong, Nitya Raj, Olca Basturk, Zeynep Tarcan, Christine A. Iacobuzio, Etay Ziv. Metabolic rewiring and cellular crosstalk may drive grade transformation in pancreatic neuroendocrine tumors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Cancer Evolution: The Dynamics of Progression and Persistence; 2025 Dec 4-6; Albuquerque, NM. Philadelphia (PA): AACR; Cancer Res 2025;85(23_Suppl):Abstract nr B025.

The DNA repair protein RAD18 activates ‘Y-family’ Trans-Lesion Synthesis (TLS) DNA polymerases that are DNA damage-tolerant and potentially error-prone. RAD18 is also frequently overexpressed and pathologically activated in cancer cells. However, the extent to which RAD18 shapes cancer genomes and impacts tumorigenesis is unclear. Therefore, we tested the effect of Rad18 status on chemically-induced and oncogene-driven tumorigenesis. In a chemically-induced oral carcinogenesis model, acute (2–16 days) 4NQO-treatment induces expression of Rad18 and TLS polymerase mRNAs in mouse oral epithelial cells prior to emergence of oral squamous cell carcinomas (OSCCs). Chronic (8 week) 4NQO-treatment leads to onset of oral tumors that is accelerated in Rad18−/− mice when compared with Rad18+/+ animals. Analysis of OSCC exomes reveals increased levels of G(C)>T(A) transversions in Rad18−/− tumors when compared with Rad18+/+. Therefore, Rad18 promotes error-free bypass of 4NQO-induced DNA lesions and suppresses 4NQO-induced oral carcinogenesis. In a KrasG12D-induced lung carcinogenesis model, Rad18-deficiency did not affect rates or incidence of oncogene-induced lung tumors or mutations. Taken together, we demonstrate that Rad18 has context-specific tumor-suppressive activity. Given the prevalence of 4NQO-like environmental exposures, RAD18 is highly likely to shape human cancer genomes and perhaps influence other aspects of the tumorigenic process.

Piloting an Interpretive External Quality Assurance Model for Genomic Testing for Childhood Syndromes and Intellectual Disability.

BackgroundWhile numerous genomic loci have been identified for dementia, the contribution of protein‐coding variants and the genetic correlations between dementia and neuropsychiatric traits have yet to be determined.MethodHere, we conducted a large‐scale whole‐exome‐sequencing study to interrogate the impact of protein‐coding variants on dementia and other 68 neuropsychiatric traits (containing 45 neuropsychiatric diseases and 23 cognition and mental health measures) in 350,770 adults from the UK Biobank. Pairwise estimation of genetic correlations between dementia and neuropsychiatric traits at coding‐variant level were then conducted using burden heritability regression analysis. Finally, a comprehensive multi‐omics analysis was performed to investigate whether alterations in brain structures, blood proteins and inflammation potentially contribute to the gene‐phenotype linkages.ResultTwenty novel genes were associated with neuropsychiatric diseases through coding variants, among which 14 genes had impacts on the longitudinal risks of diseases. Specially, gene‐based analysis identified seven genes for dementia, among which four (ADAMTSL5, P4HB, PSMD7, and LMTK3) were novel. Thirty novel genes were associated with cognition and mental health measures, with SYNGAP1 showing pleiotropic effects across cognitive function domains. Burden heritability regression highlighted shared genetic associations among dementia and stroke, neurodegenerative diseases and some mental disorders. Moreover, we found significant genetic correlations within neurodegenerative and psychiatric disorders at whole‐exome level, but not between neurological and psychiatric disorders. The multi‐omics analysis revealed that 29 identified genes were consistently correlated with the right medial orbitofrontal cortex, implicating its potential role in neuropsychiatric conditions.ConclusionOur findings characterized a compendium of protein‐coding variants for future research on the biology and therapeutics of neuropsychiatric phenotypes including dementia.

FAM20B encodes glycosaminoglycan xylosylkinase, a key enzyme in proteoglycan biosynthesis. Biallelic pathogenic variants have only recently been linked to skeletal dysplasia. We report two pregnancies from one couple, resulting in three fetuses (twin sibs and younger sib) with severe skeletal anomalies. Prenatal findings included enlarged nuchal translucency, short bowed and dislocated limbs, intrauterine growth restriction, and multiple malformations. Intra-uterine fetal death occurred in Probands 1 and 2, and neonatal death of Proband 3. Postnatally, all three probands showed limb shortening with joint (sub)luxations and contractures, and craniofacial dysmorphisms. SNP-array and exome analysis revealed compound heterozygosity for two novel FAM20B variants: a paternal ~8 kb deletion encompassing the terminal exon and a maternal missense variant (p.Arg290Cys) at an evolutionary conserved position. The same amino acid residue was previously affected in a child with a milder phenotype. In silico modeling supports a destabilizing effect of the missense change on protein structure, especially due to the loss of a salt bridge essential for catalytic function. This report describes the prenatal phenotype of FAM20B-related dysplasia and can help establish the phenotypic spectrum of the disorder. It further supports the essential role of FAM20B in early skeletal development.

Hypogonadotropic hypogonadism (HH) with severe ataxia, impotence and dementia has been reported in a handful of patients carrying RNF216 gene variants. However, the underlying molecular mechanism explaining this complex phenotype remains unclear to date. RNF216 encodes a 'RING-between-RING'(RBR)-class E3 ubiquitin ligase. Among the targets of RNF216 is Beclin-1, a pivotal regulator of autophagy, particularly within the central nervous system. 1) To assess the prevalence of RN216 mutations in a large cohort of patients with HH. 2) To examine the impact on autophagy of identified RNF216 pathogenic variants. Exome analysis in a monocentric cohort of patients with HH. In vitro functional analysis of RNF216 variants in the regulation of autophagy and cell viability. Among 1,476 patients, we identified a unique NM_207111.4:c.2056C>T:p.(Arg686*) RNF216 variant in the homozygous state in one family with two affected patients presenting with HH associated with late-onset ataxia and dementia. We observed that in cells expressing this RNF216 variant, the regulation of autophagy was disrupted, indicating a loss-of-function effect. We demonstrated that inhibiting RNF216 expression decreased cell viability. Z-VAD, a pan-caspase inhibitor, did not protect cells from death, whereas 3-MA, an autophagy inhibitor, prevented cell death. Interestingly, we found that other RNF216 variants reported to be associated with this form of HH had a similar functional impact on autophagy. Our results suggest that alteration of RNF216 function leads to cell death through an autophagy-mediated mechanism which contributes to combined HH and ataxia and dementia in affected patients.

The genetic heterogeneity observed in acute myeloid leukemia (AML) contributes to a wide range of clinical presentations and prognoses. We conducted a retrospective study to investigate genetic abnormalities, clinical characteristics, and survival of AML patients. Targeted exome analysis of 25 genes using a QIAact Myeloid DNA UMI Panel with the GeneReader NGS was performed. De novo AML (dAML) and secondary AML (sAML) were observed in 163 and 56 patients, respectively. ASXL1, SRSF2, and RUNX1 mutations were significantly observed in sAML patients. Among dAML patients, mutant IDH1, ASXL1, TP53, and TET2 were associated with low WBC count (< 4 × 109/L), and mutations of FLT3-ITD and NPM1 were associated with high WBC count (> 100 × 109/L). In dAML group, KIT and FLT3-TKD mutations were commonly found in favorable cytogenetic risk, RAS and SF3B1 mutations were significantly observed in the abnormal chromosome 3 group, whereas IDH1, IDH2, RUNX1, and SRSF2 mutations were significantly observed in trisomy group. Mutant TP53 was seen significantly in AML patients with complex and monosomy karyotypes. ASXL1, IDH1, IDH2, TP53, and SRSF2 mutations were independent factors associated with poor OS through univariate analysis. Nevertheless, multivariate analysis showed IDH1 (HR = 2.699; 95% CI: 1.331-5.473), TP53 (HR = 2.200; 95% CI: 1.409-3.435) and ASXL1 (HR = 1.592; 95% CI: 1.040-2.436) mutations were significantly associated with short OS in AML patients. In contrast, RUNX1 (HR = 3.667; 95% CI: 1.213-11.084) and DNMT3A (HR = 2.094; 95% CI: 1.080-4.081) mutations were significantly associated with poor DFS on multivariate analysis. The complexity of AML was influenced by various cytogenetic and molecular abnormalities, which contributed to patients' heterogeneous presentation and survival outcomes. In addition to the previous data, IDH1, IDH2, and DNMT3A mutations might have affected survival outcomes in AML patients in our retrospective cohort. However, further studies with larger sample sizes are needed to validate these observations.

Abstract BACKGROUND Pediatric and adult brain tumors, including glioblastoma, astrocytoma, ependymoma, and medulloblastoma, are associated with poor prognosis and limited treatment options. Standard of care (SOC) therapies such as surgery, radiation, and chemotherapy often fail to control tumor progression and are associated with severe toxicity. The lack of personalized therapeutic approaches underscores the urgent need for clinically relevant human models that reflect tumor heterogeneity and enable testing of novel therapies, including immunotherapies. METHODS We analyzed a panel of ten low-passage patient-derived brain tumor (PBT) lines and matched patient-derived xenograft (PDX) models from surgical specimens. Tumors were characterized using single-cell and bulk RNA sequencing, DNA exome analysis, multiparameter flow cytometry, and immunohistochemistry. Freshly dispersed tumor (FDT) samples and derived PBT lines were compared to assess fidelity in maintaining key molecular and cellular features. RESULTS FDT-matched PBT lines were successfully established in approximately 70% of cases and preserved patient-specific mutations (IDH1, MGMT, p53, PTEN) and expression profiles of key therapeutic targets including IL13Rα2, EGFR, HER2, WNT1, JAK1/2, and NOTCH1-4. Correlation analysis demonstrated significant similarity between FDT and PBT profiles (R = 0.31, p = 0.018). Notably, PBTs and PDX models retained heterogeneous and non-clonal populations, enabling the identification of therapy-resistant subclones under in vitro selection pressures. These features support their use in evaluating used for the optimization of immunotherapy and other therapies for patients with brain tumors. CONCLUSION We report the generation of clinically relevant PBT and PDX models that recapitulate the molecular and histopathological features of primary brain tumors. These models provide a powerful platform for dissecting therapeutic response and resistance, and for advancing precision medicine approaches. Our work lays the foundation for optimizing immunotherapy and next-generation treatments for both pediatric and adult brain tumor patients.

MDS without clonal marker: When depth outperforms breadth

Abstract Description Autoimmune disease in human is caused by breakdown of tolerance such that the immune system attacks self cells and tissues, leading to damage and injuries. We aim to compare genomic risk factors among patients with JDM and childhood onset cSLE. Genomic DNA from 51 JDM and 43 cSLE patients recruited at our study site were subjected to WES, using sequences in GnomAD for comparison. Analyses of WES data were performed by 2 × 2 Fisher’s exact test. We also compared patient’s clinical and microarray gene expression data. Top deleterious sequence variants identified among patients with JDM and cSLE were present in the complement, coagulation and platelet activation pathways. JDM patients have more mutations among genes related to platelet activation and complement regulation. Compared with healthy controls, patients with JDM have higher platelet counts (p = 3x10-12) but less platelet activation. cSLE have more variants engaged in activations of complement, coagulation and platelets. The Ser192Tyr of tyrosinase TYR was prevalent among JDM (patients: 41% vs controls: 25%). Arg402Gln is another variant of TYR that is prevalent among cSLE (patients: 32.6% vs controls: 17.6%). Both TYR variants are related to UV damage on the skin. For gene expression, both diseases are induced by IFN-α, although more severe in SLE. Among down-regulated genes, patients with cSLE feature genes engaged in gene expression, while patients with JDM have dysregulated genes in chemokine receptors and T cells. Funding Sources Supported by grants from the CureJM Foundation and NIAMS-NIH grant R01AR073311. Topic Categories Immune Mechanisms of Human Disease (HUM)

Abstract Background and Aims Monogenic kidney stone diseases are reported to be present in up to 15% of patients attending specialised metabolic kidney stone clinics. This is relevant as many of these disorders are actionable, guiding personalised treatment to reduce future stone formation. This study evaluated the medical and family history of patients who had already received a genetic test, to look for pre-existing factors that may suggest the presence of a genetic disorder related to kidney stones. The aim was to ascertain which clinical factors, in patients attending a metabolic kidney stone clinic, are most likely to predict a positive genetic diagnosis. Hence, certain categories of stone forming patients can be prioritised for future genetic testing. Method We analysed all patients attending the Royal Free Hospital's metabolic stone clinic from September 2022 to September 2024 who had genetic testing either with next generation sequencing or whole genome sequencing with a focused exome analysis using the nephrolithiasis and nephrocalcinosis gene panel (R256) provided by the NHS Genomic Medicine Service. Patients had been tested over this time period on the basis of either clinical suspicion of a specific diagnosis, or because clinical and biochemical analysis had not yielded a diagnosis. We therefore retrospectively analysed this cohort against clinical criteria known to be associated with underlying genetic diagnoses in stone forming patients. 35 patients were tested during the selected period. Patients with a confirmed genetic mutation (“positive,” n = 6) and the remainder with no mutation found (“negative,” n = 29), were compared using a t-test to look for differences between the two groups in certain relevant parameters. These were age at the time of the test, sex, family history of kidney stones, age at the time of first stone, presence of nephrocalcinosis, rate of recurrence of kidney stones, and eGFR at the time of the test. In addition, an arbitrarily weighted scoring system, based on widely accepted risk factors for monogenic stone disease (Fig. 1), was used to generate a cumulative score for each patient. Results We found three parameters that were significantly different between the “positive” genetic test group compared to the “negative” group. These factors were: first episode of stone at age &amp;lt;18 y.o. (P = 0.0107), presence of nephrocalcinosis (P = 0.0040) and having a higher cumulative score (P = 0.0073). 6 out of 35 patients received a positive genetic diagnosis: two cases of Bartter syndrome, and one case each of cystinuria, primary hyperoxaluria type 1, primary hyperoxaluria type 3, and hereditary hypophosphataemic rickets with hypercalciuria. Conclusion Although based on a small and highly selected sample of patients, this study highlights that genetic testing is more likely to yield a positive outcome in patients who form stones at young age and/or have nephrocalcinosis. A composite score, which combines and weights multiple parameters, may also be a clinically useful method of prioritising those patients who should receive the R256 genomic medicine test. This is important because determining the sensitivity of genetic screening in all stone formers would require the entire cohort to be tested, which is neither practical nor cost effective. Meanwhile, our data support the idea that clinicians should enquire about age of first stone in all stone formers.