Variant Type Research Articles

WDR45 variants as a major cause for a clinically variable intellectual disability syndrome from early infancy in females.

Pathogenic variants of WD repeat domain 45 (WDR45) cause neurodegeneration with brain iron accumulation 5 (NBIA5), which is characterised by progressive neurological regression and brain iron accumulation in adulthood. Early diagnosis of NBIA5 patients is difficult because they often show only a non-specific developmental delay in childhood, but it is essential for lifelong medical management. We investigated 32 females with developmental delays for coding variants of WDR45 using Sanger sequencing. Whole-genome sequencing (WGS) and X chromosome inactivation (XCI) analysis were also performed. We identified two disease-causing variants, one of which was a novel stop-loss variant, c.1051delG p.(Val351CysfsTer60), in a female with severe developmental delay from early infancy with epileptic spasms. The XCI analysis (which we originally developed) suggested a random pattern in white blood cells. WGS did not reveal any other pathogenic variants, including those in two iron transporter genes. Together with our previous findings in the WGS study, WDR45 variants accounted for 12% (6/51) of the females with developmental delay, suggesting that WDR45 is a major gene in females with developmental delay. Pathogenic variants of WDR45 result in various phenotypes that do not necessarily correlate with variant types or XCI skewing patterns.

Micro-capture-C in vessel wall cell types identifies mechanisms underlying coronary artery disease susceptibility loci

Abstract Genetics is estimated to account for 50% of Coronary Artery Disease (CAD) risk. Genome-Wide Association Studies (GWAS) have revealed 100s of genomic loci which are associated with CAD (1). However, moving from GWAS signals to causal genes has proved challenging, slowing progress in developing interventions for CAD and other diseases. The greatest challenge in interpreting GWAS data is that only 10% of variants are in protein-coding regions and 90% are in "non-coding" genomic regions. Many of these non-coding variants are found in regulatory elements such as enhancers. Enhancers are distal regulatory elements that bind transcription factors and regulate genes up to 1 million base pairs away. This is achieved by DNA looping bringing enhancers into physical proximity with target genes. However, it is not possible to predict which gene(s) a given enhancer will regulate based on genomic location alone. We aimed to develop a generalisable workflow to solve CAD GWAS signals accurately and sensitively, by identifying causal enhancer SNPs and linking them mechanistically to output genes in a cell-type specific manner. We combined cell-specific epigenomic mapping with machine learning to prioritise 21,959 SNPs from 861 candidate CAD loci, in endothelial cells (HUVECs) and smooth muscle cells (HCASMCs). Micro-Capture-C (MCC) was used to resolve enhancer-promoter interactions at base-pair resolution (2). MNase footprinting determined differential transcription factor binding at specific enhancer SNPs. In HCASMCs, 20 putative enhancers containing CAD SNPs were found to interact with 32 genes, and in HUVECs 25 enhancers interacted with 48 genes. These genes were enriched for pathways including TGFb signalling, RUNX3 activity, and MAPK6/MAPK4 signalling. To prove causality at specific loci, heterozygous SNPs were identified in the individual primary cell lines. The interaction frequency at these elements was statistically compared between risk and non-risk alleles. For example, at the 9p21.3 locus, an enhancer containing a non-risk T allele was found to interact more strongly with the CDKN2B gene, compared to the risk G allele. Interestingly, this imbalance between allele interaction was potentiated by stimulation with TGFb, a key mediator in atherosclerosis. Furthermore, the transcription factor footprint at the SNP location was altered by the risk allele, indicating the mechanistic cause of the CAD-associated change in CDKN2B expression. We demonstrate a combined computational and experimental approach to identify causal non-coding variants in CAD risk loci, at scale. Among the key outputs of this study is the identification of the risk variant (rs1537373), output gene (CDKN2B), and specific cell type (HCASMC) underlying the 9p21.3 locus association with CAD risk. Using this approach to translate GWAS signals into cell-type specific outputs genes, will lead to a better understanding of the pathogenesis of CAD, and new therapeutic opportunities.

Comprehensive genome analysis and variant detection at scale using DRAGEN.

Research and medical genomics require comprehensive, scalable methods for the discovery of novel disease targets, evolutionary drivers and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size or location. Here we present DRAGEN, which uses multigenome mapping with pangenome references, hardware acceleration and machine learning-based variant detection to provide insights into individual genomes, with ~30 min of computation time from raw reads to variant detection. DRAGEN outperforms current state-of-the-art methods in speed and accuracy across all variant types (single-nucleotide variations, insertions or deletions, short tandem repeats, structural variations and copy number variations) and incorporates specialized methods for analysis of medically relevant genes. We demonstrate the performance of DRAGEN across 3,202 whole-genome sequencing datasets by generating fully genotyped multisample variant call format files and demonstrate its scalability, accuracy and innovation to further advance the integration of comprehensive genomics. Overall, DRAGEN marks a major milestone in sequencing data analysis and will provide insights across various diseases, including Mendelian and rare diseases, with a highly comprehensive and scalable platform.

Associations between genotype, phenotype and behaviours measured by the Rett syndrome behaviour questionnaire in Rett syndrome

IntroductionRett syndrome (RTT) is a rare neurodevelopmental disorder with developmental impairments, comorbidities, and abnormal behaviours such as hand stereotypies and emotional features. The Rett Syndrome Behaviour Questionnaire (RSBQ) was developed to describe the behavioural and emotional features of RTT. Little is known how RSBQ scores are associated with genetic and clinical characteristics in RTT. This study investigated relationships between genotype, age, walking, hand function, sleep, and RSBQ total and subscale scores in RTT.MethodsThis is a cross-sectional analysis of data collected in the Australian Rett Syndrome Database and the International Rett Syndrome Phenotype Database. Parent caregivers completed the RSBQ and Sleep Disturbance Scale for Children [subscales for disorders of initiating and maintaining sleep (DIMS), disorders of excessive somnolence (DOES)], and provided information on age, variant type, functional abilities (mobility, hand function), seizure frequency and gastrointestinal problems. Associations between the RSBQ scores and the independent variables were modelled using linear regression.ResultsData were available for 365 individuals with RTT [median (range) age 17.8 (2.9–51.9) years, 2 males]. Compared to adults, 2- to 12-year-old children had higher mean Total, Night-time Behaviour and Fear/Anxiety scores. Compared to individuals with a C-terminal deletion, individuals with the p.Arg255* variant had higher mean Total and Night-time Behaviours scores, whereas the p.Arg294* variant had higher mean Mood scores. Individuals with intermediate mobility and hand function abilities had a higher mean Total score. Total RSBQ and subscale scores were similar across categories for seizures, constipation, and reflux, but were higher with abnormal DIMS and abnormal DOES scores.ConclusionExcept for associations with sleep, the RSBQ measures the behavioural phenotype rather than clinical severity in RTT, as traditionally conceptualised in terms of functional abilities and comorbidities. When designing clinical trials, the RSBQ needs to be complemented by other outcome measures to assess specific core functions and associated comorbidities in RTT.

Genetic analysis of preaxial polydactyly: identification of novel variants and the role of ZRS duplications in a Chinese cohort of 102 cases.

Preaxial polydactyly (PPD) is a congenital limb malformation, previously reported to be caused primarily by variants in the ZRS and upstream preZRS regions. This study investigated genetic variations associated with PPD, focusing on point variants and copy number variations (CNVs) in the ZRS and preZRS regions. Comprehensive genetic analyses were conducted on 102 patients with PPD, including detailed clinical examinations and Sanger sequencing of the ZRS and preZRS regions. Additionally, real-time quantitative PCR (qPCR) was used to detect CNVs in the ZRS region. The evolutionary conservation and population frequencies of identified variants were also evaluated. Six point variants were identified, among which four are likely pathogenic novel variants: 93G > T (g.156584477G > T), 106G > A (g.156584464G > A), 278G > A (g.156584292G > A), and 409A > C (g.156585378A > C). Additionally, qPCR analysis revealed that 66.67% of patients exhibited ZRS duplications. Notably, these duplications were also present in cases with newly identified potential pathogenic point variants. These findings suggest the possible interaction of point variants in ZRS and preZRS through a common pathogenic mechanism, leading jointly to PPD. The findings expand the variant spectrum associated with non-syndromic polydactyly and highlight that, despite different classifications, anterior polydactyly caused by variants in ZRS and nearby regions may share common pathogenic mechanisms. The incorporation of various variant types in genetic screening can effectively enhance the rate of pathogenic variant detection and contribute to the cost-effectiveness of genetic testing for limb developmental defects, thereby promoting healthy births.

Dinucleotide composition representation -based deep learning to predict scoliosis-associated Fibrillin-1 genotypes

IntroductionScoliosis is a pathological spine structure deformation, predominantly classified as “idiopathic” due to its unknown etiology. However, it has been suggested that scoliosis may be linked to polygenic backgrounds. It is crucial to identify potential Adolescent Idiopathic Scoliosis (AIS)-related genetic backgrounds before scoliosis onset.MethodsThe present study was designed to intelligently parse, decompose and predict AIS-related variants in ClinVar database. Possible AIS-related variant records downloaded from ClinVar were parsed for various labels, decomposed for Dinucleotide Compositional Representation (DCR) and other traits, screened for high-risk genes with statistical analysis, and then learned intelligently with deep learning to predict high-risk AIS genotypes.ResultsResults demonstrated that the present framework is composed of all technical sections of data parsing, scoliosis genotyping, genome encoding, machine learning (ML)/deep learning (DL) and scoliosis genotype predicting. 58,000 scoliosis-related records were automatically parsed and statistically analyzed for high-risk genes and genotypes, such as FBN1, LAMA2 and SPG11. All variant genes were decomposed for DCR and other traits. Unsupervised ML indicated marked inter-group separation and intra-group clustering of the DCR of FBN1, LAMA2 or SPG11 for the five types of variants (Pathogenic, Pathogeniclikely, Benign, Benignlikely and Uncertain). A FBN1 DCR-based Convolutional Neural Network (CNN) was trained for Pathogenic and Benign/ Benignlikely variants performed accurately on validation data and predicted 179 high-risk scoliosis variants. The trained predictor was interpretable for the similar distribution of variant types and variant locations within 2D structure units in the predicted 3D structure of FBN1.DiscussionIn summary, scoliosis risk is predictable by deep learning based on genomic decomposed features of DCR. DCR-based classifier has predicted more scoliosis risk FBN1 variants in ClinVar database. DCR-based models would be promising for genotype-to-phenotype prediction for more disease types.

Molecular epidemiological characteristics, variant spectrum and genotype-phenotype correlation of glucose-6-phosphate dehydrogenase deficiency in China: A population-based multicenter study using newborn screening.

Newborn screening (NBS) for glucose-6-phosphate dehydrogenase (G6PD) deficiency by biochemical tests is being used worldwide, however, the outcomes arising from combined genetic and biochemical tests have not been evaluated. This research aimed to evaluate the outcomes of application of combined genetic and biochemical NBS for G6PD deficiency and to investigate the molecular epidemiological characteristics, variant spectrum, and genotype-phenotype correlation of G6PD deficiency in China. A population-based cohort of 29,601 newborns were prospectively recruited from eight NBS centers in China between February 21 and December 30, 2021. Biochemical and genetic NBS was conducted simultaneously. The overall prevalence of G6PD deficiency was 1.12% (1.86% for male, and 0.33% for female; 1.94% for South China and 0.08% for North China). Genetic NBS identified 10 male patients undetected by biochemical NBS. The overall positive predictive values (PPVs) of biochemical and genetic NBS were 79.95% and 47.57%, respectively. A total of 15 variants were identified, with the six most common variants being c.1388G > A, c.1376G > T, c.95A > G, c.871G > A, c.1024C > T and c.392G > T (94.2%). The activity of G6PD was correlated with the type and WHO classification of variants. This study highlighted that combined screening could enhance the efficiency of current NBS for diagnosing G6PD deficiency. The prevalence, variant spectrum and allele frequency of G6PD deficiency vary across different regions. Our data provide valuable references for clinical practice and optimization of future screening strategies for G6PD deficiency.

A single immunization of Borreliella burgdorferi-infected mice with Vanguard crLyme elicits robust antibody responses to diverse strains and variants of outer surface protein C.

Lyme disease, caused by Borreliella burgdorferi and related species, is a growing health threat to companion animals across North America and Europe. Vaccination is an important preventive tool used widely in dogs living in, or near, endemic regions. In this report, we assessed anti-outer surface protein (Osp) A and anti-OspC antibody responses in B. burgdorferi-infected and -naïve mice (C3H/HeN) after immunization with a murine-optimized single dose of the Lyme disease subunit vaccine, Vanguard crLyme. crLyme is comprised of OspA and an OspC chimeritope-based immunogen designated as CH14. Mice that were infected and immunized developed higher levels of anti-OspC antibodies (Abs) than those infected only or that received one vaccine dose. The anti-OspC Abs that developed in the infected/immunized mice bound to all OspC variants tested (n = 22), whereas OspC Abs in serum from infected mice bound predominantly to the OspC variant (type A) produced by the infecting B. burgdorferi strain. Consistent with the absence of OspA expression in infected mammals, none of the infected mice developed Abs to OspA and did not develop anti-OspA Abs after single dose immunization. Lastly, serum from infected/immunized mice displayed significantly higher and broader killing activity than serum from non-immunized infected mice. The results of this study demonstrate that a single vaccination of actively infected mice results in strong anti-OspC Ab responses. This study contributes to our understanding of Ab responses to vaccination in actively infected mammals.

Integrating D4Z4 methylation analysis into clinical practice: improvement of FSHD molecular diagnosis through distinct thresholds for 4qA/4qA and 4qA/4qB patients

BackgroundFacioscapulohumeral dystrophy (FSHD) is a myopathy characterized by the loss of repressive epigenetic features affecting the D4Z4 locus (4q35). The assessment of DNA methylation at two regions (DUX4-PAS and DR1) of D4Z4 locus proved to be an effective method to detect epigenetic signatures compatible with FSHD. The present study aims at validating the employment of this method into clinical practice and improving the protocol by refining the classification thresholds of 4qA/4qA patients. To this purpose, 218 subjects with clinical suspicion of FSHD collected in 2022–2023 were analyzed. Each participant underwent in parallel the traditional FSHD molecular testing (D4Z4 sizing) and the proposed methylation assay. The results provided by both analyses were compared to evaluate the concordance and calculate the performance metrics of the methylation test.ResultsAmong the 218 subjects, the 4q variant type distribution was 54% 4qA/4qA, 43% 4qA/4qB and 3% 4qB/4qB. The methylation analysis was performed only on carriers of at least one 4qA allele. After refining the classification threshold, the test reached the following performance metrics: sensitivity = 0.90, specificity = 1.00 and accuracy = 0.93. These results confirmed the effectiveness of the methylation assay in identifying patients with genetic signature compatible with FSHD1 and FSHD2 based on their DUX4-PAS and DR1 profile, respectively. The methylation data were also evaluated with respect to the clinical information.ConclusionsThe study confirmed the ability of the method to accurately identify methylation profiles compatible with FSHD genetic signatures considering the 4q genotype. Moreover, the test allows the detection of hypomethylated profiles in asymptomatic patients, suggesting its potential application in identifying preclinical conditions in patients with positive family history and FSHD genetic signatures. Furthermore, the present work emphasizes the importance of interpreting methylation profiles considering the patients’ clinical data.

Clinical characteristics and genetic analysis of mental retardation disorder with TRIO gene variant

Objective: To summarize the clinical and genetic characteristics of mental retardation disorder (MRD) with TRIO gene variant in children. Methods: Case series study. The data of 9 children with TRIO gene variants were collected retrospectively from August 2019 to March 2024 in Department of Neurology, Beijing Children's Hospital, Capital Medical University and Department of Pediatrics, the Third Affiliated Hospital of Zhengzhou University. The data included gender, age, intellectual and motor development, appearance, seizures, neuroimaging and genetic results. The clinical features and genotype-phenotype correlations were summarized. Results: Of the 9 children, 6 boys and 3 girls, 4 MRD63 children presented with moderate to severe developmental delays accompanied by macrocephaly; 5 MRD44 children had mild to moderate developmental delays with microcephaly. A total of 5 children had dysmorphic facial features (flat occiput, thick eyebrows, unibrow, large ears, short fingers, pale skin, yellow hair, and strabismus), 2 children experienced seizures (1 child with myoclonic seizure and 1 with absence seizure), 4 children had feeding difficulties, 1 child had congenital cataracts, 1 child had congenital heart disease, 1 child had recurrent infections, and 1 child had tiger-striped changes in the fundus examination. TRIO gene variants carried by the 9 children were all de novo, involving 8 variant sites, including 7 missense variants and 1 frameshift variant, c.3232C>T/p.R1078W (2 cases), c.3920A>G/p.Y1307C, c.4112A>T/p.H1371L, c.4283G>T/p.R1428L, c.4394A>G/p.N1465S, c.6041T>C/p.I2014T, c.6821G>A/p.R2274H, c.7027delC/p.Q2343Sfs*70. Among them, 2 sites are located in the Spectrin domain, 4 sites are in the GEFD1 domain, 2 sites are in the GEFD2 domain, and 1 site (frameshift variant) is in the PH2-SH3 domain. The individual with frameshift variant exhibit absence seizures, mild developmental delay, and the mildest phenotype. The child with myoclonic seizures was treated with valproic acid and levetiracetam for seizure control, while the child with absence epilepsy was treated with valproic acid and lamotrigine for seizure control. All 9 children underwent regular rehabilitation exercises, making slow progress. Conclusions: TRIO gene related MRD is characterized by varying degrees of developmental delay, and often accompanied by macrocephaly or microcephaly, dysmorphic facial features, and with or without seizures. The main variant types are missense variants, which are mostly concentrated in the Spectran domain and GEFD domain. p. R1078W may be a relative hotspot variant. The phenotype caused by the frameshift variant is relatively milder.

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer.

As a major type of structural variants, tandem duplication plays a critical role in tumorigenesis by increasing oncogene dosage. Recent work has revealed that noncoding enhancers are also affected by duplications leading to the activation of oncogenes that are inside or outside of the duplicated regions. However, the prevalence of enhancer duplication and the identity of their target genes remains largely unknown in the cancer genome. Here, by analyzing whole-genome sequencing data in a non-gene-centric manner, we identify 881 duplication hotspots in 13 major cancer types, most of which do not contain protein-coding genes. We show that the hotspots are enriched with distal enhancer elements and are highly lineage-specific. We develop a HiChIP-based methodology that navigates enhancer-promoter contact maps to prioritize the target genes for the duplication hotspots harboring enhancer elements. The methodology identifies many novel enhancer duplication events activating oncogenes such as ESR1, FOXA1, GATA3, GATA6, TP63, and VEGFA, as well as potentially novel oncogenes such as GRHL2, IRF2BP2, and CREB3L1 In particular, we identify a duplication hotspot on Chromosome 10p15 harboring a cluster of enhancers, which skips over two genes, through a long-range chromatin interaction, to activate an oncogenic isoform of the NET1 gene to promote migration of gastric cancer cells. Focusing on tandem duplications, our study substantially extends the catalog of noncoding driver alterations in multiple cancer types, revealing attractive targets for functional characterization and therapeutic intervention.

Novel homozygous ESAM variants in two families with perinatal strokes showing variable neuroradiologic and clinical findings.

Biallelic loss of function variants in ESAM (endothelial cell adhesion molecule) have recently been reported in 14 individuals (9 families) presenting with prenatal intracranial hemorrhage. Here, we describe four patients from two unrelated families in whom three of them presented with variable onset encephalopathy and seizures while one only displayed profound delay without seizures. Brain MRI showed variable onset intracranial hemorrhage that evolved to hydrocephalus in 3 patients, whereas hemosiderin deposits, white matter volume loss, and porencephalic cysts were noted in one patient. Unlike the majority of described cases, the youngest brother of the first family did not show microcephaly and failure to thrive. Exome sequencing identified two novel homozygous ESAM variants. A splice variant (c.731-2A>G) was identified in one family which was confirmed by investigating the patient's mRNA to result in exon skipping and early protein truncation. In addition, a missense variant (c.561G>C; p.Trp187Cys) was identified in the other family, which is the first disease causing missense variant to be described in patients with ESAM deficient phenotype. In addition, a maternally inherited pathogenic MC4R variant (c.811T>C; p.Cys271 Arg) was also identified in the youngest brother of the first family. Variants in the MC4R gene are associated with a non-syndromic form of obesity that could explain the unusual macrocephaly and obesity. Our work establishes ESAM as a tight junction gene that can present with variable neuroradiological and clinical phenotypes when mutated. Moreover, it refines the phenotype of this ultrarare syndrome and extends the number and type of variants described to date.

Genotype‐phenotype associations in individuals with Diamond Blackfan anaemia

AbstractIntroductionDiamond Blackfan anaemia (DBA) is a rare disorder characterized by failure of red blood cell production, congenital abnormalities and cancer predisposition, primarily caused by pathogenic germline variants in genes encoding ribosomal proteins.MethodsWe conducted a genotype‐phenotype and outcome study of 121 patients with DBA spanning the 20‐year history of the National Cancer Institute's Inherited Bone Marrow Failure Syndromes study. Patient phenotypes were compared by large versus small ribosomal protein genes, across genes with >5 cases (RPS19, RPS29, RPS26 and RPL35A) and by type of pathogenic variants (hypomorphic versus null, large deletions versus others).ResultsA pathogenic germline variant was identified in 71% of patients (n = 86/121) from 54 families. After adjusting for multiple testing, we found that patients with RPS29 variants were least likely to need treatment for anaemia while those with large ribosomal protein subunit variants had a higher proportion of intellectual disability and gastrointestinal abnormalities compared with small ribosomal protein subunit variants (p < 3.5 × 10−4). There were no statistically significant differences in overall survival or cancer incidence among patients with large or small ribosomal subunit genes.ConclusionThis detailed genotype‐phenotype study of DBA improves our understanding of the role of germline genetics in the clinical manifestations that may help guide the management of people with DBA.

Comprehensive Analysis of Complex Copy Number Variations in the Plasmodium falciparum Genome via Long-Read Sequencing: Implications for Antimalarial Resistance and Broad Genomic Insights

Abstract Introduction/Objective The genome of Plasmodium falciparum, characterized by a high AT content and a propensity for copy number variations (CNVs), presents a model for understanding how genomes adapt to stress. Our research focused on the prevalence and distribution of CNVs highlights long-read sequencing as a tool for detecting complex structural variants in other models. Methods/Case Report P. falciparum parasites were cultured and treated with DSM1 and aphidicolin that induce replication stress. Long-read sequencing was conducted using the Oxford Nanopore Technology Minion, with an emphasis on an optimizing DNA extraction method for preserving intact chromosomes. Visualization of CNVs, including tandem and inverted duplications, was achieved through a custom R Shiny application that allowed both quantitative and qualitative assessments. Results (if a Case Study enter NA) Long read sequencing identified an enrichment of multiple CNV types in treated samples, with a significant enrichment of inverted duplications as well as other types of structural variants. Aphidicolin and DSM1-treated samples demonstrated significant accumulation of these variations compared to controls (2.0 and 5.6-fold, respectively with a p value of < 0.0001 in both treatment groups). These occurred mainly in core genomic regions that do not contain variable gene copies. An increase in the number of inverted duplications may be related to stress response to the treatment and may be a potential adaptive mechanism of the parasite. Our manual single-read visualization technique made it possible to visualize the structure of various CNV types, which provides unique insight on CNVs as they arise in single genomes. Conclusion We hypothesize that inverted duplications represent stalled replication forks, and we are currently assessing their frequency in replicating and non-replicating cells. This study highlights the role of long-read sequencing in detecting complex genomic structures in P. falciparum, which may influence the parasite’s resistance to drug treatment. These findings not only advance our understanding of malaria pathology but also aid our comprehension of how cancer cells might react to drug-induced stress and the mechanisms behind CNV formation in neoplastic cells.

Understanding renal tubular acidosis

Renal tubular acidosis is a group of disorders characterised by metabolic acidosis, hyperchloraemia, normal anion gap, and potassium imbalance. Genetic mutations, drugs or acquired disorders disrupt the function of various transport proteins and enzymes in the renal tubules, causing diminished bicarbonate reabsorption or inability to excrete hydrogen ions, leading to proximal (type 2) and distal (type 1) renal tubular acidosis, respectively. These conditions are typically associated with hypokalaemia, which, if severe, can cause muscle paralysis and dangerous cardiac arrhythmias. A rare mixed variant (type 3), including features of both type 1 and type 2 renal tubular acidosis, has also been described. On the other hand, aldosterone deficiency or resistance leads to the hyperkalaemic form of renal tubular acidosis (type 4). If untreated, renal tubular acidosis can lead to long-term severe complications such as growth retardation, osteoporosis, rickets, osteomalacia, and renal calculi. Moreover, renal tubular acidosis might be the initial presentation of a more severe underlying pathology, such as autoimmune disease or plasma cell dyscrasias. A better understanding of the condition can help physicians diagnose and treat it early and prevent adverse outcomes.

Cohen syndrome: Can early-onset recurrent infections and hypotonia provide early diagnosis and intervention for intellectual disability?

Cohen syndrome is a rare disease associated with neurodevelopmental disorders, especially intellectual disability (ID), neutropenia and recurrent infections are consistently reported in cases. Neutropenia is an important part of the syndrome, as well as ID. Homozygous variants in the VPS13B gene, located on chromosome 8q22 and containing 62 exons, have been found to cause Cohen syndrome. Cohen syndrome is commonly diagnosed when dysmorphological findings and developmental delay become more apparent. However, the identification of some findings with increasing age has caused the diagnosis of Cohen syndrome to be delayed. Cases diagnosed with ID were evaluated using whole-exome sequencing/clinical exome sequencing method. Family segregation analysis was performed using Sanger sequencing. We presented the clinical and genetic findings of three cases diagnosed with Cohen syndrome and their parents in detail. In this study, we presented the occurrence of symptoms in different age groups, and the prognosis of three cases carrying the VPS13B gene variants, including three different variant types: missense, frameshift and nonsense. Although our cases had different variant types, they shared important similarities on the onset period and prognosis of the symptoms. All cases presented hypotonia, difficulties in swallowing, recurrent respiratory tract infections, neutropenia, delay in motor development, ID and hyperactivity. Our cases did not have a diagnosis of autism spectrum disorder. All cases had increased willingness to engage in social communication. We emphasize the importance of early-onset recurrent infections and hypotonia for early diagnosis and preventive genetic counselling in Cohen syndrome.

The evaluation of SARS-CoV-2 mutations at the early stage of the pandemic in Istanbul population

BackgroundDetermination of SARS-CoV-2 variant is significant to prevent the spreads of COVID-19 disease.MethodsWe aimed to evaluate the variants of SARS-CoV-2 rate in positive patients in Kanuni Sultan Suleyman Training and Research Hospital (KSS-TRH), Istanbul, Türkiye between 1st January and 30th November 2021 by using RT-PCR method.ResultsHerein, 825,169 patients were evaluated (male:58.53% and female:41.47%) whether COVID-19 positive or not [( +):21.3% and (−):78.7%] and 175,367 patient was described as positive (53.2%-female and 46.8%-male) by RT-PCR. COVID-19 positive rate is observed highest in the 6–15- and 66–75-year age range. The frequencies were obtained as SARS-CoV-2 positive (without mutation of B.1.1.7 [B.1.1.7 (U.K), E484K, L452R, B.1.351 (S. Africa/Brazil) spike mutations] as 66.1% (n: 115,899), B.1.1.7 Variant as 23.2% (n:40,686), Delta mutation (L452R) variant as 9.8% (n:17,182), B.1.351 variant as 0.8% (n:1370) and E484K as 0.1% (n: 230). In April 2021, general SARS-CoV-2 and B.1.1.7 variant were dominantly observed. Up to July 2021, B.1.617.2 (Delta variant/ Indian variant) and E484K has been not observed. B.1.351 variant of SARS-CoV-2 has been started in February 2021 at the rarest ratio and March 2021 is the top point. September 2021 is the pick point of E484K. African/Brazil variant of SARS-CoV-2 has been started in February 2021 at the rarest ratio and March 2021 is the top point. September 2021 is the pick point of E484K. When the gender type is compared within the variants, women were found to be more prevalent in all varieties.ConclusionsThe meaning of these mutations is very important to understand the transmission capacity of the COVID-19 disease, pandemic episode, and diagnosis of the virus with mutation types. Understanding the variant type is important for monitoring herd immunity and the spread of the disease.

12497 Stage 1 Results Of The Phase 2 Daybreak Trial Assessing Setmelanotide In Patients With Early-onset, Severe Obesity And Hyperphagia Who Carried A Confirmed Variant Related To The Melanocortin-4 Receptor Pathway

Abstract Disclosure: G. Ortiz: Speaker; Self; Rhythm Pharmaceuticals, Inc. S.B. Ten: Advisory Board Member; Self; Rhythm Pharmaceuticals, Inc. Speaker; Self; Rhythm Pharmaceuticals, Inc. W. Herring: Advisory Board Member; Self; Rhythm Pharmaceuticals, Inc, Novo Nordisk. O. Pinhas-Hamiel: None. E.A. Oral: Consulting Fee; Self; Rhythm Pharmaceuticals, Inc., Akcea Therapeutics, Ionis Pharmaceuticals Inc., Morphic Medical, Fractyl Laboratories, Regeneron Pharmaceuticals, Amryt Pharmaceuticals (now Chiesi), Third Rock Ventures, Rejuvenate Bio, NIDDK. Other; Self; Has patents for use of metreleptin in lipodystrophy and recombinant leptin or analogues in NASH. N. Rosano: Consulting Fee; Self; Novo Nordisk. Speaker; Self; Rhythm Pharmaceuticals, Inc. D. Koren: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. H. Lee: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. J. Garrison: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. O. Ohayon: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. P. Sleiman: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. M. Wabitsch: Consulting Fee; Self; Rhythm Pharmaceuticals, Inc.. Speaker; Self; Rhythm Pharmaceuticals, Inc.. Other; Self; Rhythm Pharmaceuticals, Inc. E. van den Akker: Speaker; Self; Federatie Medisch Specialisten, Stichting Kwaliteitsgelden Medisch Specialisten, Medialane TV, Pfizer, Inc.. Other; Self; Nederlandse Hartstichting/ZonMW, Stichting Erasmus Trustfonds, Rhythm Pharmaceuticals, Inc. J. Argente: Advisory Board Member; Self; Rhythm Pharmaceuticals, Inc. Speaker; Self; Rhythm Pharmaceuticals, Inc.. I. Farooqi: None. Background: DAYBREAK (NCT04963231) was designed to evaluate setmelanotide in individuals who carried a confirmed variant in ≥1 of 31 genes with strong or very strong relevance to the melanocortin-4 receptor (MC4R) pathway, which regulates energy balance and satiety. Methods: DAYBREAK is a 2-stage, double-blind, placebo-controlled trial conducted at 37 sites across 8 countries. Individuals aged 6 to 65 years with body mass index (BMI) ≥40 kg/m2 (aged ≥18 years) or ≥97th percentile (aged ≥6 to <18 years) and hyperphagia who carried variants classified as uncertain significance (VUS), likely pathogenic, or pathogenic according to the American College of Medical Genetics (ACMG) criteria in ≥1 of the 31 genes were eligible. Individuals with ≥5% BMI reduction from baseline (ie, responders) at the end of the 16-week, open-label run-in period (Stage 1) were eligible to enter a 24-week, double-blind, randomized, placebo-controlled period (Stage 2). The primary endpoint of Stage 1 was the proportion of responders per gene cohort at the end of the Stage. Results: A total of 164 individuals were enrolled; 100 patients who completed Stage 1 and 12 who discontinued treatment within a prespecified 2 weeks before the end of Stage 1 were included in the completers analysis. Participants were divided into 15 gene cohorts; of 7 cohorts with ≥5 patients, 6 (SEMA3[A-G], PLXNA[1-4], PHIP, TBX3, MAGEL2, and SIM1) showed potential setmelanotide efficacy (KSR2 did not). Response rates across cohorts (range, 25.0%-56.3%), intracohort response magnitudes (percent BMI change from baseline to Week 16; range, −6.4% to −4.0%), and intracohort variant types varied. While response rate was highest in the PHIP cohort (56.3% of the full cohort and 69.2% of completers), ≥1 patient per cohort achieved ≥10% BMI reduction. Because ∼80% of VUS are eventually reclassified to benign or likely benign, the inclusion of VUS may have contributed to response variability. An ad hoc analysis showed an increased response rate with updated versus starting ACMG variant classification. Overall, 49 responders across 6 gene cohorts were randomized into Stage 2. Setmelanotide was well tolerated with no new safety concerns. Conclusions: DAYBREAK Stage 1 identified 6 additional genes or gene families in the MC4R pathway that respond to setmelanotide. Response was associated with predicted variant pathogenicity, allowing for further refinement of patient selection. Stage 2 results will further elucidate Stage 1 findings. Presentation: 6/3/2024

A-045 Analytical and Clinical Evaluation of A1c Test by HPLC - Lifotronic™ H100Plus Analyzer - in a Brazilian Clinical Laboratory

Abstract Background Over the years, the measurement of Glycated Hemoglobin (A1c) has solidified as an important risk marker for pre-diabetic patients and for the diagnosis and control of diabetic patients. The High-Performance Liquid Chromatography (CLAE) method has been adopted in prospective studies such as the DDCT, and international certification by the NGSP is available. In this study, analytical performance metrics including imprecision, correlation, linearity, carryover, and detection of hemoglobin variants were evaluated for the Lifotronic® H100 Plus analyzer from China. Methods The results were evaluated following CLSI guidelines on samples within stability, collected according to standardized procedures. For the comparative method, 40 patient samples ranging from 4 to 15.4% were analyzed, and two concentrations of internal quality control material were used for intra-assay (5 repetitions per day) and inter-assay (over five days) imprecision testing. Linearity was assessed using samples at two concentrations, one low (4.5%) and another high (17.2%). For carryover evaluation, low (4.98%), intermediate (9.97%), and high (14.96%) concentrations were assayed in an interleaved manner. Hemoglobin variants found in the studied population were determined using the same method employed in correlation tests (HbS, HbF, HbC, HbE, and HbD). Results The method comparison study revealed a Total Error for decision levels of 5.6%: 2.23% and 6.5%: 1.70%, which were lower than the maximum allowable Total Error of 3.3% (EFLM - EuBIVAS). The difference plot showed that 95% of the results fell within acceptable limits. Positive bias was observed in 7 out of 40 tested samples, predominantly in samples with concentrations above 6,5%, although the medical team assessed it as having no clinical impact. For intra-assay imprecision, the obtained result was 0.86%, and for inter-assay imprecision, it was 0.87%, both deemed acceptable according to the 3.0 % specification proposed by the supplier for the two tested levels.Linearity tests were approved for concentrations proposed by the manufacturer between 3 and 18%, and no carryover was found between samples. All hemoglobin variants previously detected in the comparative method were also identified in the test method without exception, although the specific type of Hb variant was not identified. Conclusions The Lifotronic™ H100Plus analyzer demonstrated approved analytical performance with some notable observations: positive bias was observed in samples with concentrations above 6,5%, though it was not considered clinically relevant, the throughput of 58 tests per hour could be a limitation for laboratories with high testing volumes and the analyzer detected the presence of Hb variants, although it did not identify their specific types.

ADPKD Progression by Variant Type and Molecular Domain: An Evaluation of Time-Series Disease Trajectories among HALT Participants

ADPKD Progression by Variant Type and Molecular Domain: An Evaluation of Time-Series Disease Trajectories among HALT Participants