Negative Variant Research Articles

New RPS20 gene variant in colorectal cancer diagnosis: insight from a large series of patients.

Germline pathogenic variants of the RPS20 (ribosomal protein S20) gene are suspected to be involved in the predisposition to familial colorectal cancer (CRC) with no DNA mismatch repair deficiency. RPS20 pathogenic variants are very rare with only five reported cases in the literature. We report in this work the retrospective germline analysis of RPS20 for 1035 consecutive patients with a personal and/or familial history suggestive of hereditary predisposition to CRC. Within this series, a pathogenic variant in known CRC genes was found in 15% of cases and we describe one RPS20 loss-of-function variant (NM_001146227.1:c.115_116del, p.(Leu39Aspfs*33)). This frameshift is the first reported de novo variant in CRC, it was identified in in a female patient diagnosed with rectal cancer at the age of 35, 11 adenomatous polyps in 5 years and breast cancer at the age of 43. RPS20 has an intriguing role in oncogenesis, acting as an oncogene or tumour suppressor depending on the context, and is also involved in Diamond-Blackfan anemia via gain of function or dominant negative variants. This is therefore a complex gene for genetic counselling and, given the rarity of RPS20 pathogenic variants, we emphasise the need to collect data to clarify the phenotypic spectrum of RPS20-associated cancers and thus improve management.

Functional validation of a novel STAT3 'variant of unknown significance' identifies a new case of STAT3 GOF syndrome and reveals broad immune cell defects.

Signal transducer and activator of transcription 3 (STAT3) orchestrates crucial immune responses through its pleiotropic functions as a transcription factor. Patients with germline monoallelic dominant negative or hypermorphic STAT3 variants, who present with immunodeficiency and/or immune dysregulation, have revealed the importance of balanced STAT3 signaling in lymphocyte differentiation and function, and immune homeostasis. Here, we report a novel missense variant of unknown significance in the DNA-binding domain of STAT3 in a patient who experienced hypogammaglobulinemia, lymphadenopathy, hepatosplenomegaly, immune thrombocytopenia, eczema, and enteropathy over a 35-year period. In vitro demonstration of prolonged STAT3 activation due to delayed dephosphorylation, and enhanced transcriptional activity, confirmed this to be a novel pathogenic STAT3 gain-of-function variant. Peripheral blood lymphocytes from this patient, and patients with confirmed STAT3 Gain-of-function Syndrome, were collected to investigate mechanisms of disease pathogenesis. B cell dysregulation was evidenced by a loss of class-switched memory B cells and a significantly expanded CD19hiCD21lo B cell population, likely influenced by a skewed CXCR3+ TFH population. Interestingly, unlike STAT3 dominant negative variants, cytokine secretion by activated peripheral blood STAT3 GOF CD4+ T cells and frequencies of Treg cells were intact, suggesting CD4+ T cell dysregulation likely occurs at sites of disease rather than the periphery. This study provides an in-depth case study in confirming a STAT3 gain-of-function variant and identifies lymphocyte dysregulation in the peripheral blood of patients with STAT3 gain-of-function syndrome. Identifying cellular biomarkers of disease provides a flow cytometric-based screen to guide validation of additional novel STAT3 gain-of-function variants as well as provide insights into putative mechanisms of disease pathogenesis.

Dominant negative ADA2 mutations cause ADA2 deficiency in heterozygous carriers.

Human ADA2 deficiency (DADA2) is an inborn error of immunity with a broad clinical phenotype which encompasses vasculopathy including livedo racemosa and lacunar strokes, as well as hemato-immunological features. Diagnosis is based on the combination of decreased serum ADA2 activity and the identification of biallelic deleterious alleles in the ADA2 gene. DADA2 carriers harbor a single pathogenic variant in ADA2 and are mostly considered healthy and asymptomatic. However, some DADA2 carriers present a phenotype compatible with DADA2. Here, we report ten patients from seven kindreds presenting with a phenotype indicative of DADA2, in whom only a single pathogenic variant (p.G47R, p.G47V, p.R169Q, p.H424N) was identified. To test whether being heterozygote for specific variants could explain the patients' phenotype, we investigated the effect of the ADA2 missense variants p.G47A, p.G47R, p.G47V, p.G47W, p.R169Q, p.E328K, p.T360A, p.N370K, p.H424N and p.Y453C on ADA2 protein expression, secretion and enzymatic activity. Functional studies indicate that they exert a dominant negative effect on ADA2 enzymatic activity, dimerization and/or secretion. At the molecular level, heterozygosity for these variants mimics what is observed in DADA2. We conclude that humans with heterozygous dominant negative missense variants in ADA2 are at risk of DADA2.

Dominant negative variants in ITPR3 impair T cell Ca2+ dynamics causing combined immunodeficiency.

The importance of calcium (Ca2+) as a second messenger in T cell signaling is exemplified by genetic deficiencies of STIM1 and ORAI1, which abolish store-operated Ca2+ entry (SOCE) resulting in combined immunodeficiency (CID). We report five unrelated patients with de novo missense variants in ITPR3, encoding a subunit of the inositol 1,4,5-trisphosphate receptor (IP3R), which forms a Ca2+ channel in the endoplasmic reticulum (ER) membrane responsible for the release of ER Ca2+ required to trigger SOCE, and for Ca2+ transfer to other organelles. The patients presented with CID, abnormal T cell Ca2+ homeostasis, incompletely penetrant ectodermal dysplasia, and multisystem disease. Their predominant T cell immunodeficiency is characterized by significant T cell lymphopenia, defects in late stages of thymic T cell development, and impaired function of peripheral T cells, including inadequate NF-κB- and NFAT-mediated, proliferative, and metabolic responses to activation. Pathogenicity is not due to haploinsufficiency, rather ITPR3 protein variants interfere with IP3R channel function leading to depletion of ER Ca2+ stores and blunted SOCE in T cells.

Description of a clinical case of stomach adenocarcinoma during pregnancy

The frequency of malignant neoplasms during pregnancy has recently become a usually problem in modern medical practice. On average, 1 in 1,000 women will experience cancer during pregnancy. The most common pregnancy-related cancers include cervical, breast, ovarian, malignant melanoma, malignant lymphomas and leukemia, as well as colon and thyroid cancers. The main factor of late diagnosis and poor treatment results is the non-specificity of the symptoms of the disease in the early stages. The occurrence of difficulty at the diagnostic stage is an underestimation of the indications for conducting a diagnostic search. Signet ring cell carcinoma of the stomach is characterized by an aggressive course, rapid metastasis, and therefore is more often diagnosed in late stages and is a prognostically negative histological variant of stomach cancer. Stomach cancer during pregnancy is estimated to complicate 0.026–0.1 % of all pregnancies In this clinical case, an example of the course of signet ring cell carcinoma of the stomach against the background of pregnancy with dichoric diamniotic twins with increasing protein-energy deficiency is given.

The value of NGS-based multi-gene testing for differentiation of benign from malignant and risk stratification of thyroid nodules.

Fine-needle aspiration (FNA) biopsy is typically used in conjunction with cytopathologic evaluation to differentiate between benign and malignant thyroid nodules. Even so, the cytology results for 20-30% of thyroid nodules are indeterminate. This study sought to evaluate the usefulness of next-generation sequencing (NGS)-based multi-gene panel testing for risk stratification and the differentiation of benign from malignant thyroid nodules. Thyroid nodule samples were obtained from a cohort of 359 patients who underwent FNA. An NGS-based multi-gene panel testing was conducted for these samples, in which single-nucleotide variants (SNVs) and small insertion/deletions (InDels) can be detected in 11 genes and fusion events can be identified in 5 genes. Surgical resection was conducted for 113 patients (113/359), and then histopathology results were obtained. In comparison to cytology alone, the diagnostic sensitivity of NGS combination cytology increased from 0.7245 (95% CI: 0.6289-0.8032) to 0.898 (95% CI: 0.8223-0.9437); the associated AUC was 0.8303 (vs. Cytology AUC: 0.7622, P < 0.001). BRAF V600E was identified in 136 patients, of whom 79 underwent surgery and were diagnosed with papillary thyroid carcinoma (PTC) pathologically. TERT promoter mutations or BRAF/RAS co-mutations with other genes were identified in 5 patients, while 4 patients were diagnosed with malignant thyroid cancer using the pathological method. RAS mutations were identified in 27 patients, while 10 patients underwent surgery, which showed that 3 patients were classified as PTC and 7 cases were benign. In addition, 4 RET fusions, 1 RET activation mutation, and 3 TP53 inactivation mutations were identified in the remaining 8 patients who have not undergone surgery. Negative genetic test results or variants with uncertain significance were identified in 183 patients. Among these patients, 12 malignant thyroid tumors, including 11 PTC and 1 MTC, were diagnosed in 20 patients who received surgery. Thyroid nodules coupled with BRAF V600E, TERT promoter variants, BRAF/RAS co-mutations with other genes, RET fusions, and RET activating mutations were classified as high-risk. Nodules with RAS mutations (NRAS, KRAS, HRAS) and TP53 inactivating mutations were considered to be in the intermediate-risk group, while those with non-pathogenic mutations (negative and variants of uncertain significance) were placed in the low-risk group. When combined with cytopathology, NGS increases the sensitivity of diagnosing benign and malignant thyroid nodules, and the reference is useful for patient risk stratification.

Restored Collagen VI Microfilaments Network in the Extracellular Matrix of CRISPR-Edited Ullrich Congenital Muscular Dystrophy Fibroblasts.

Collagen VI is an essential component of the extracellular matrix (ECM) composed by α1, α2 and α3 chains and encoded by COL6A1, COL6A2 and COL6A3 genes. Dominant negative pathogenic variants in COL6A genes result in defects in collagen VI protein and are implicated in the pathogenesis of muscular diseases, including Ullrich congenital muscular dystrophy (UCMD). Here, we designed a CRISPR genome editing strategy to tackle a dominant heterozygous deletion c.824_838del in exon 9 of the COL6A1 gene, causing a lack of secreted collagen VI in a patient's dermal fibroblasts. The evaluation of efficiency and specificity of gene editing in treating patient's fibroblasts revealed the 32% efficiency of editing the mutated allele but negligible editing of the wild-type allele. CRISPR-treated UCMD skin fibroblasts rescued the secretion of collagen VI in the ECM, which restored the ultrastructure of the collagen VI microfibril network. By using normal melanocytes as surrogates of muscle cells, we found that collagen VI secreted by the corrected patient's skin fibroblasts recovered the anchorage to the cell surface, pointing to a functional improvement of the protein properties. These results support the application of the CRISPR editing approach to knock out COL6A1 mutated alleles and rescue the UCMD phenotype in patient-derived fibroblasts.

Deep estimation of the intensity and timing of natural selection from ancient genomes.

Leveraging past allele frequencies has proven to be key for identifying the impact of natural selection across time. However, this approach suffers from imprecise estimations of the intensity (s) and timing (T) of selection, particularly when ancient samples are scarce in specific epochs. Here, we aimed to bypass the computation of allele frequencies across arbitrarily defined past epochs and refine the estimations of selection parameters by implementing convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time. Using computer simulations, we first show that genotype-based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and the number of available ancient genotypes. When applying this method to empirical data from modern and ancient Europeans, we replicated the reported increased number of selection events in post-Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC-based estimations of s and T for a set of positively and negatively selected variants, including iconic cases of positive selection and experimentally validated disease-risk variants. Our CNN predictions support a history of recent positive and negative selection targeting variants associated with host defence against pathogens, aligning with previous work that highlights the significant impact of infectious diseases, such as tuberculosis, in Europe. These findings collectively demonstrate that detecting the footprints of natural selection on ancient genomes is crucial for unravelling the history of severe human diseases.

Targeting heterozygous dominant negative variant of KCNA2 using Gapmer ASO for the treatment of drug-resistant epilepsy

A missense mutation c.1220C>G of KCN2A gene was recently identified in an infant with epilepsy. KCNA2 encodes Kv1.2 subunits that form voltage-gated potassium channels (VGKC) via tetrameric assembly. The mutation results in amino acid change P407R at the highly conserved PVP motif. Functional characterization revealed that mutant Kv1.2_P407R subunits formed loss-of-function channels and suppressed both Kv1.2 and Kv1.1 channel activities. Hetero-tetrameric assembly of the Kv1.2_P407R subunits with other neuronal voltage-gated potassium channels of Shaker subfamily could lead to general deficit of repolarising potassium current and potentially underlie the enhanced seizure susceptibility. Indeed, expression of human Kv1.2_P407R in early postnatal rat cortical neurons or genetically engineered hESC-derived neurons disclosed broadening of action potential duration and early afterdepolarization (EAD), associating with reduced potassium current. We hypothesize that Gapmer antisense oligonucleotides (ASO) targeted to c.1220C>G mutation will selectively degrade the mutant mRNA while allowing the remaining WT subunits to form functional channels. As a proof of principle, delivery of Gapmer packaged in lipid nanoparticle into cortical neurons selectively suppressed Kv1.2_P407R over the WT protein expression, reversing the broadening of action potential duration, abrogating the EAD and leading to overall increase in potassium current.

A national education program for rapid genomics in pediatric acute care: Building workforce confidence, competence, and capability

PurposeTo develop and evaluate a scalable national program to build confidence, competence and capability in the use of rapid genomic testing (rGT) in the acute pediatric setting. MethodsWe used theory-informed approaches to design a modular, adaptive program of blended learning aimed at diverse professional groups involved in acute pediatric care. The program comprised 4 online learning modules and an online workshop and was centered on case-based learning. We evaluated the program using the Kirkpatrick 4-level model of training evaluation and report our findings using the Reporting Item Standards for Education and its Evaluation (RISE2) guidelines for genomics education and evaluation. ResultsTwo hundred and two participants engaged with at least 1 component of the program. Participants self-reported increased confidence in using rGT, (P < .001), and quiz responses objectively demonstrated increased competence (eg, correct responses to a question on pretest counseling increased from 30% to 64%; P < .001). Additionally, their capability in applying genomic principles to simulated clinical cases increased (P < .001), as did their desire to take on more responsibility for performing rGT. The clinical interpretation of more complex test results (such as negative results or variants of uncertain significance) appeared to be more challenging, indicating a need for targeted education in this area. ConclusionThe program format was effective in delivering multidisciplinary and wide-scale genomics education in the acute care context. The modular approach we have developed now lends itself to application in other medical specialties or areas of health care.

Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index

MotivationAlignment of reads to a reference genome sequence is one of the key steps in the analysis of human whole-genome sequencing data obtained through Next-generation sequencing (NGS) technologies. The quality of the subsequent steps of the analysis, such as the results of clinical interpretation of genetic variants or the results of a genome-wide association study, depends on the correct identification of the position of the read as a result of its alignment. The amount of human NGS whole-genome sequencing data is constantly growing. There are a number of human genome sequencing projects worldwide that have resulted in the creation of large-scale databases of genetic variants of sequenced human genomes. Such information about known genetic variants can be used to improve the quality of alignment at the read alignment stage when analysing sequencing data obtained for a new individual, for example, by creating a genomic graph. While existing methods for aligning reads to a linear reference genome have high alignment speed, methods for aligning reads to a genomic graph have greater accuracy in variable regions of the genome. The development of a read alignment method that takes into account known genetic variants in the linear reference sequence index allows combining the advantages of both sets of methods.ResultsIn this paper, we present the minimap2_index_modifier tool, which enables the construction of a modified index of a reference genome using known single nucleotide variants and insertions/deletions (indels) specific to a given human population. The use of the modified minimap2 index improves variant calling quality without modifying the bioinformatics pipeline and without significant additional computational overhead. Using the PrecisionFDA Truth Challenge V2 benchmark data (for HG002 short-read data aligned to the GRCh38 linear reference (GCA_000001405.15) with parameters k = 27 and w = 14) it was demonstrated that the number of false negative genetic variants decreased by more than 9500, and the number of false positives decreased by more than 7000 when modifying the index with genetic variants from the Human Pangenome Reference Consortium.

Low-loss vanadium dioxide-enabled mmWave tunable reflective electromagnetic surface with complementary unit cells for wave manipulation

This study presents a novel implementation of vanadium dioxide (VO2) phase change material in an electromagnetic (EM) surface with beam steering capabilities. For the first time, we present the design, fabrication, and measurement of a globally actuated, VO2-based beamforming reflective EM surface. We propose a design featuring complementary unit cells that enable beam steering with a single excitation, marking a pioneering use of low-loss VO2 in creating a complementary EM surface for the mmWave band. The unit cells incorporating VO2 exhibit low-loss characteristics, with −0.92 and −1.9 dB in the hot state and −0.49 and −0.25 dB in the cold state, respectively. We incorporate both positive and negative phase variants alongside two temperature-independent phase unit cells. The complementary design enables us to utilize two beam operating states, effectively exploiting the otherwise unused cold state. We experimentally demonstrated beamforming at ±5° and ±10° from the broadside. In the case of ±10°, the measured gains at 35 GHz in the cold and hot states were 19.4 and 20.3 dB, respectively, which aligned well with the simulated gains of 20.9 and 21.5 dB. Manipulation of the electromagnetic wave direction with a single excitation has the potential for imaging, sensing, and communication applications. The complementary unit cell design methodology can be further adapted for mmWave beamforming, absorbing, and cloaking reconfigurable EM surfaces. Furthermore, the use of VO2 can be extended up to sub-THz frequencies due to the wideband, low-loss characteristics compared with conventional reconfigurable devices, such as PIN diodes or MEMS switches.

Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA

Implementation of whole genome sequencing (WGS) for patient care is hindered by limited Mycobacterium tuberculosis (Mtb) in clinical specimens and slow Mtb growth. We evaluated droplet multiple displacement amplification (dMDA) for amplification of minute amounts of Mtb DNA to enable WGS as an alternative to other Mtb enrichment methods. Purified genomic Mtb-DNA (0.1, 0.5, 1, and 5 pg) was encapsulated and amplified using the Samplix Xdrop-instrument and sequenced alongside a control sample using standard Illumina protocols followed by MAGMA-analysis. The control and 5 pg input dMDA samples underwent nanopore sequencing followed by Nanoseq and TB-profiler analysis. dMDA generated 105-2400 ng DNA from the 0.1-5 pg input DNA, respectively. Followed by Illumina WGS, dMDA raised mean sequencing depth from 7 × for 0.1 pg input DNA to ≥ 60 × for 5 pg input and the control sample. Bioinformatic analysis revealed a high number of false positive and false negative variants when amplifying ≤ 0.5 pg input DNA. Nanopore sequencing of the 5 pg dMDA sample presented excellent coverage depth, breadth, and accurate strain characterization, albeit elevated false positive and false negative variants compared to Illumina-sequenced dMDA sample with identical Mtb DNA input. dMDA coupled with Illumina WGS for samples with ≥ 5 pg purified Mtb DNA, equating to approximately 1000 copies of the Mtb genome, offers precision for drug resistance, phylogeny, and transmission insights.

SERPINE-1 gene polymorphism in patients with cardiovascular diseases

Currently, the issues of recurrent course of cardiovascular diseases are given great importance. Today, there is a search for more and more new factors and causes, including genetic ones, that contribute to the increase in the incidence of circulatory system diseases. The study of polymorphic variants of hemostasis system genes made it possible to study the molecular mechanisms underlying the causes of cardiovascular complications. Polymorphism of theSERPINE-1gene, encoding plasminogen activator inhibitor-1, is associated with the occurrence of cardiovascular diseases. This literature review examines the influence ofSERPINE-1gene polymorphism and the concentration of the plasminogen activator inhibitor-1 it encodes on the development and severity of circulatory system diseases; as well as the role of plasminogen activator inhibitor-1 as one of the indicators reflecting the antifibrinolytic potential of the blood. Taking into account the opinion of most authors, we can conclude that the polymorphism of theSERPINE-1gene and its homozygous variant 4G/4G, due to which the synthesis of plasminogen activator inhibitor-1 is increased, is an unfavorable predictor of many pathological processes. However, most of the data have been obtained on the association of theSERPINE-1gene polymorphism with cardiovascular diseases, where, according to most authors, the 4G/4G genotype is a prognostically negative variant. However, a number of researchers believe that the heterozygous 5G/4G variant is likely associated with the occurrence of cerebral ischemia. The inconsistency of the data obtained, ofcourse, requires further study of the characteristics of theSERPINE-1gene polymorphism in various pathological conditions, which is an important prerequisite for understanding the mechanisms of a number of diseases. To prepare the review, a literature search method in PubMed databases for the period 2013–2023 was used.

Functional analysis of cell lines derived from SMAD3-related Loeys-Dietz syndrome patients provides insights into genotype-phenotype relation.

Pathogenic (P)/likely pathogenic (LP) SMAD3 variants cause Loeys-Dietz syndrome type 3 (LDS3), which is characterized by arterial aneurysms, dissections and tortuosity throughout the vascular system combined with osteoarthritis. Investigate the impact of P/LP SMAD3 variants with functional tests on patient-derived fibroblasts and vascular smooth muscle cells (VSMCs), to optimize interpretation of SMAD3 variants. A retrospective analysis on clinical data from individuals with a P/LP SMAD3 variant and functional analyses on SMAD3 patient-derived VSMCs and SMAD3 patient-derived fibroblasts, differentiated into myofibroblasts. Individuals with dominant negative (DN) SMAD3 variant in the MH2 domain exhibited more major events (66.7% vs. 44.0%, P= 0.054), occurring at a younger age compared to those with haploinsufficient (HI) variants. The age at first major event was 35.0years [IQR 29.0-47.0] in individuals with DN variants in MH2, compared to 46.0years [IQR 40.0-54.0] in those with HI variants (P = 0.065). Fibroblasts carrying DN SMAD3 variants displayed reduced differentiation potential, contrasting with increased differentiation potential in HI SMAD3 variant fibroblasts. HI SMAD3 variant VSMCs showed elevated SMA expression and altered expression of alternative MYH11 isoforms. DN SMAD3 variant myofibroblasts demonstrated reduced extracellular matrix formation compared to control cell lines. Distinguishing between P/LP HI and DN SMAD3 variants can be achieved by assessing differentiation potential, and SMA and MYH11 expression. The differences between DN and HI SMAD3 variant fibroblasts and VSMCs potentially contribute to the differences in disease manifestation. Notably, myofibroblast differentiation seems a suitable alternative in vitro test system compared to VSMCs.

Assessment of the visibility of unprotected road users in pedestrian crossing

The article presents selected results of research on improving pedestrian traffic safety. Based on annually-updated accident statistics made available by the police, as well as the new pedestrian traffic regulations in force, detailed work was undertaken to assess the level of visibility of pedestrians by drivers in pedestrian crossing areas. The research was carried out by analyzing several characteristic cases of pedestrian crossings occurring in Poland, in which there was only dedicated lighting for crossings, only street lighting, and a variant of coexistence of both of the above lighting solutions. Illuminance measurements were made in the horizontal and vertical planes of pedestrian crossings, and the results were confronted with the relevant guidelines. The next step involved a complementary measurement of the luminance distribution of the vertical plane containing the pedestrian and a portion of the sub- and super-horizontal background. Visibility pedestrians was considered in positive and negative contrast variants, and was then related to the obtained results of the illumination distribution. The analysis of the results of the study indicated the possibility of limited visibility of pedestrians at the crossings despite the satisfactory results obtained from measurements of the illuminance distribution within the crossings.

Altered neurological and neurobehavioral phenotypes in a mouse model of the recurrent KCNB1-p.R306C voltage-sensor variant

Pathogenic variants in KCNB1 are associated with a neurodevelopmental disorder spectrum that includes global developmental delays, cognitive impairment, abnormal electroencephalogram (EEG) patterns, and epilepsy with variable age of onset and severity. Additionally, there are prominent behavioral disturbances, including hyperactivity, aggression, and features of autism spectrum disorder. The most frequently identified recurrent variant is KCNB1-p.R306C, a missense variant located within the S4 voltage-sensing transmembrane domain. Individuals with the R306C variant exhibit mild to severe developmental delays, behavioral disorders, and a diverse spectrum of seizures. Previous in vitro characterization of R306C described altered sensitivity and cooperativity of the voltage sensor and impaired capacity for repetitive firing of neurons. Existing Kcnb1 mouse models include dominant negative missense variants, as well as knockout and frameshifts alleles. While all models recapitulate key features of KCNB1 encephalopathy, mice with dominant negative alleles were more severely affected. In contrast to existing loss-of-function and dominant-negative variants, KCNB1-p.R306C does not affect channel expression, but rather affects voltage-sensing. Thus, modeling R306C in mice provides a novel opportunity to explore impacts of a voltage-sensing mutation in Kcnb1. Using CRISPR/Cas9 genome editing, we generated the Kcnb1R306C mouse model and characterized the molecular and phenotypic effects. Consistent with the in vitro studies, neurons from Kcnb1R306C mice showed altered excitability. Heterozygous and homozygous R306C mice exhibited hyperactivity, altered susceptibility to chemoconvulsant-induced seizures, and frequent, long runs of slow spike wave discharges on EEG, reminiscent of the slow spike and wave activity characteristic of Lennox Gastaut syndrome. This novel model of channel dysfunction in Kcnb1 provides an additional, valuable tool to study KCNB1 encephalopathies. Furthermore, this allelic series of Kcnb1 mouse models will provide a unique platform to evaluate targeted therapies.

Dynamic behaviors of sandwich panels with 3D-printed gradient auxetic cores subjected to blast load

This study experimentally and numerically investigated the blast resistance of sandwich panels composed of steel face sheets and 3D-printed gradient auxetic chiral core. Five gradient strategies were utilized in the design of auxetic core, including uniform gradient, positive gradient, negative gradient, center positive gradient and center negative gradient. Varying blast loadings were applied by adjusting the masses of explosive charges. The deformation/failure modes of sandwich panels were obtained in the experiments, in terms of the face sheets and gradient auxetic core. The effects of impulse and gradient type of auxetic core on dynamic responses of specimens were examined. In addition, the numerical simulation was employed to clarify the deformation process of sandwich panel, and to analyze the deformation mode of auxetic cores under sufficient compression. It was shown that higher impulse was associated with increased plastic deformation in the face sheet and more serious shear and tensile tearing within the auxetic core. The auxetic cores of varying gradient types displayed distinct compress deformation behaviors. Among them, the negative gradient variant exhibited the least permanent deflection, and the superior negative Poisson's ratio effect, indicating enhanced blast resistance. This work not only contributes to a strategy for designing gradient auxetic cores with enhanced blast resistance, but also provides valuable insights into experimentally understanding the response of complex auxetic configurations under blast loads.

Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases.

Inherited retinal diseases (IRDs) are a group of rare genetic eye conditions that cause blindness. Despite progress in identifying genes associated with IRDs, improvements are necessary for classifying rare autosomal dominant (AD) disorders. AD diseases are highly heterogenous, with causal variants being restricted to specific amino acid changes within certain protein domains, making AD conditions difficult to classify. Here, we aim to determine the top-performing in-silico tools for predicting the pathogenicity of AD IRD variants. We annotated variants from ClinVar and benchmarked 39 variant classifier tools on IRD genes, split by inheritance pattern. Using area-under-the-curve (AUC) analysis, we determined the top-performing tools and defined thresholds for variant pathogenicity. Top-performing tools were assessed using genome sequencing on a cohort of participants with IRDs of unknown etiology. MutScore achieved the highest accuracy within AD genes, yielding an AUC of 0.969. When filtering for AD gain-of-function and dominant negative variants, BayesDel had the highest accuracy with an AUC of 0.997. Five participants with variants in NR2E3, RHO, GUCA1A, and GUCY2D were confirmed to have dominantly inherited disease based on pedigree, phenotype, and segregation analysis. We identified two uncharacterized variants in GUCA1A (c.428T>A, p.Ile143Thr) and RHO (c.631C>G, p.His211Asp) in three participants. Our findings support using a multi-classifier approach comprised of new missense classifier tools to identify pathogenic variants in participants with AD IRDs. Our results provide a foundation for improved genetic diagnosis for people with IRDs.

Significance Associated with Phenotype Score Aids in Variant Prioritization for Exome Sequencing Analysis

Several in silico annotation-based methods have been developed to prioritize variants in exome sequencing analysis. This study introduces a novel metric, the Significance Associated with Phenotypes (SAP) score, which generates a statistical score by comparing an individual's observed phenotypes against existing gene-phenotype associations. To evaluate the SAP score, a retrospective analysis was performed on 219 exomes. Among them, 82 family-based and 35 singleton exomes had at least one disease-causing variant explaining the patient’s clinical features. SAP scores were calculated, and the rank of the disease-causing variant was compared to a known method, Exomiser. Using the SAP score, the known causative variant was ranked in the top 10 retained variants for 94% (77/82) of the family-based exomes and in the first place for 73% of these cases. For singleton exomes, the SAP score analysis ranked the known pathogenic variants within the top 10 for 80% (28/35) of the cases. The SAP score, which is independent of detected variants, demonstrates comparable performance to Exomiser, which considers both phenotype and variant-level evidence simultaneously. Among 102 cases with negative results or variants of uncertain significance, SAP score analysis revealed two cases with a potential new diagnosis based on rank. The SAP score, a phenotypic quantitative metric, can be utilized in conjunction with standard variant filtration and annotation to enhance variant prioritization in exome analysis.