Isolation and Screening of Zn (Zn) Solubilizing Rhizosphere Bacteria from Different Vegetations for Their Ability to Improve Growth, Zn Uptake, and Expression of Zn Transporter Genes in Tomato.

Zinc-solubilizing bacteria (ZSB) can convert insoluble zinc to an accessible form and increase Zn bioavailability in soil, which helps mitigate Zn deficiency in crops. In this study, different bacterial strains were screened for different Zn solubilization and plant growth promotion traits. Two bacterial strains, Acinetobacter pittii DJ55 and Stenotrophomonas maltophilia DJ24, were tested for their Zn-solubilizing potential on plate media, and both showed variable levels of Zn solubilization. The results showed that the bacterial strains applied to the plants in the pot experiment caused improvements in growth parameters compared to control conditions. DJ55, when applied with an insoluble source, enhanced plant height, leaf number, and leaf area compared to DJ24 and control conditions, while the maximum fruit weight was noticed in plants treated with ZnSO4. An increase in chlorophyll contents was noted in plants treated with ZnSO4, while maximum carotenoid contents were observed in plants treated with DJ55 + ZnO when compared with their controls. Plants supplemented with ZnO and DJ55 showed higher zinc content and iron content as compared to their respective controls. The expression patterns of the SLZIP5 and SLZIP4 genes were changed in the root and shoot. Application of ZnO stimulates both gene expression and protein synthesis in tomato roots and shoots. Inoculation of tomato plants with ZSB and insoluble ZnO reduced the expression of the SLZIP5 and SLZIP4 genes in the root and shoot. In conclusion, both strains can be considered as potential zinc-solubilizing bioinoculants to promote the growth and production yield of tomato.

Covid-induced thyroiditis.

Thyroiditis is one of the manifestations of novel Covid-19 virus. Thyroid function test (TFTs) shows typical features of hyperthyroidism. Inflammatory markers and thyroid scan give clue to the diagnosis. This report is about a 39-year-old female who presented with signs and symptoms of thyrotoxicosis along with pain in the neck, odynophagia, and intermittent fever after recovering from Covid-19 a few weeks back. She had no significant history of past medical or endocrine disease. TFTs revealed high T3 and T4 and low TSH. Thyroid scan revealed decrease uptake and ESR was 115. She was started on NSAID, steroids, and beta blocker. Four weeks later, she reverted with the resolution of symptoms and normal TFTs.

Reevaluating the Genetic Contribution of Monogenic Dilated Cardiomyopathy.

BACKGROUND: Dilated cardiomyopathy (DCM) is genetically heterogeneous, with >100 purported disease genes tested in clinical laboratories. However, many genes were originally identified based on candidate-gene studies that did not adequately account for background population variation. Here we define the frequency of rare variation in 2538 patients with DCM across protein-coding regions of 56 commonly tested genes and compare this to both 912 confirmed healthy controls and a reference population of 60 706 individuals to identify clinically interpretable genes robustly associated with dominant monogenic DCM. METHODS: We used the TruSight Cardio sequencing panel to evaluate the burden of rare variants in 56 putative DCM genes in 1040 patients with DCM and 912 healthy volunteers processed with identical sequencing and bioinformatics pipelines. We further aggregated data from 1498 patients with DCM sequenced in diagnostic laboratories and the Exome Aggregation Consortium database for replication and meta-analysis. RESULTS: Truncating variants in TTN and DSP were associated with DCM in all comparisons. Variants in MYH7, LMNA, BAG3, TNNT2, TNNC1, PLN, ACTC1, NEXN, TPM1, and VCL were significantly enriched in specific patient subsets, with the last 2 genes potentially contributing primarily to early-onset forms of DCM. Overall, rare variants in these 12 genes potentially explained 17% of cases in the outpatient clinic cohort representing a broad range of adult patients with DCM and 26% of cases in the diagnostic referral cohort enriched in familial and early-onset DCM. Although the absence of a significant excess in other genes cannot preclude a limited role in disease, such genes have limited diagnostic value because novel variants will be uninterpretable and their diagnostic yield is minimal. CONCLUSIONS: In the largest sequenced DCM cohort yet described, we observe robust disease association with 12 genes, highlighting their importance in DCM and translating into high interpretability in diagnostic testing. The other genes analyzed here will need to be rigorously evaluated in ongoing curation efforts to determine their validity as Mendelian DCM genes but have limited value in diagnostic testing in DCM at present. This data will contribute to community gene curation efforts and will reduce erroneous and inconclusive findings in diagnostic testing.

Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions.

PURPOSE: Accurate discrimination of benign and pathogenic rare variation remains a priority for clinical genome interpretation. State-of-the-art machine learning variant prioritization tools are imprecise and ignore important parameters defining gene-disease relationships, e.g., distinct consequences of gain-of-function versus loss-of-function variants. We hypothesized that incorporating disease-specific information would improve tool performance. METHODS: We developed a disease-specific variant classifier, CardioBoost, that estimates the probability of pathogenicity for rare missense variants in inherited cardiomyopathies and arrhythmias. We assessed CardioBoost's ability to discriminate known pathogenic from benign variants, prioritize disease-associated variants, and stratify patient outcomes. RESULTS: CardioBoost has high global discrimination accuracy (precision recall area under the curve [AUC] 0.91 for cardiomyopathies; 0.96 for arrhythmias), outperforming existing tools (4-24% improvement). CardioBoost obtains excellent accuracy (cardiomyopathies 90.2%; arrhythmias 91.9%) for variants classified with >90% confidence, and increases the proportion of variants classified with high confidence more than twofold compared with existing tools. Variants classified as disease-causing are associated with both disease status and clinical severity, including a 21% increased risk (95% confidence interval [CI] 11-29%) of severe adverse outcomes by age 60 in patients with hypertrophic cardiomyopathy. CONCLUSIONS: A disease-specific variant classifier outperforms state-of-the-art genome-wide tools for rare missense variants in inherited cardiac conditions ( https://www.cardiodb.org/cardioboost/ ), highlighting broad opportunities for improved pathogenicity prediction through disease specificity.

Genetic Variants Associated With Cancer Therapy-Induced Cardiomyopathy.

BACKGROUND: Cancer therapy-induced cardiomyopathy (CCM) is associated with cumulative drug exposures and preexisting cardiovascular disorders. These parameters incompletely account for substantial interindividual susceptibility to CCM. We hypothesized that rare variants in cardiomyopathy genes contribute to CCM. METHODS: We studied 213 patients with CCM from 3 cohorts: retrospectively recruited adults with diverse cancers (n=99), prospectively phenotyped adults with breast cancer (n=73), and prospectively phenotyped children with acute myeloid leukemia (n=41). Cardiomyopathy genes, including 9 prespecified genes, were sequenced. The prevalence of rare variants was compared between CCM cohorts and The Cancer Genome Atlas participants (n=2053), healthy volunteers (n=445), and an ancestry-matched reference population. Clinical characteristics and outcomes were assessed and stratified by genotypes. A prevalent CCM genotype was modeled in anthracycline-treated mice. RESULTS: CCM was diagnosed 0.4 to 9 years after chemotherapy; 90% of these patients received anthracyclines. Adult patients with CCM had cardiovascular risk factors similar to the US population. Among 9 prioritized genes, patients with CCM had more rare protein-altering variants than comparative cohorts ( P≤1.98e-04). Titin-truncating variants (TTNtvs) predominated, occurring in 7.5% of patients with CCM versus 1.1% of The Cancer Genome Atlas participants ( P=7.36e-08), 0.7% of healthy volunteers ( P=3.42e-06), and 0.6% of the reference population ( P=5.87e-14). Adult patients who had CCM with TTNtvs experienced more heart failure and atrial fibrillation ( P=0.003) and impaired myocardial recovery ( P=0.03) than those without. Consistent with human data, anthracycline-treated TTNtv mice and isolated TTNtv cardiomyocytes showed sustained contractile dysfunction unlike wild-type ( P=0.0004 and P<0.002, respectively). CONCLUSIONS: Unrecognized rare variants in cardiomyopathy-associated genes, particularly TTNtvs, increased the risk for CCM in children and adults, and adverse cardiac events in adults. Genotype, along with cumulative chemotherapy dosage and traditional cardiovascular risk factors, improves the identification of patients who have cancer at highest risk for CCM. CLINICAL TRIAL REGISTRATION: URL: https://www.clinicaltrials.gov . Unique identifiers: NCT01173341; AAML1031; NCT01371981.

CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation.

PURPOSE: Internationally adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier ( http://www.cardioclassifier.org ), a semiautomated decision-support tool for inherited cardiac conditions (ICCs). METHODS: CardioClassifier integrates data retrieved from multiple sources with user-input case-specific information, through an interactive interface, to support variant interpretation. Combining disease- and gene-specific knowledge with variant observations in large cohorts of cases and controls, we refined 14 computational ACMG criteria and created three ICC-specific rules. RESULTS: We benchmarked CardioClassifier on 57 expertly curated variants and show full retrieval of all computational data, concordantly activating 87.3% of rules. A generic annotation tool identified fewer than half as many clinically actionable variants (64/219 vs. 156/219, Fisher's P = 1.1 × 10-18), with important false positives, illustrating the critical importance of disease and gene-specific annotations. CardioClassifier identified putatively disease-causing variants in 33.7% of 327 cardiomyopathy cases, comparable with leading ICC laboratories. Through addition of manually curated data, variants found in over 40% of cardiomyopathy cases are fully annotated, without requiring additional user-input data. CONCLUSION: CardioClassifier is an ICC-specific decision-support tool that integrates expertly curated computational annotations with case-specific data to generate fast, reproducible, and interactive variant pathogenicity reports, according to best practice guidelines.

Molecular charactarization of wheat advanced lines for leaf rust resistant genes using SSR markers.

A total of fifty seven wheat advanced lines were screened to detect the existence of leaf rust resistant genes (Lr9, Lr13, Lr19, Lr24, Lr26, Lr28, Lr32, Lr34, Lr35, Lr36, Lr37, Lr39 and Lr46) using thirteen SSR markers. Only four markers for Lr13, Lr32, Lr34 and Lr35 produced separate, reproducible bands which indicated the positive linkage of leaf rust resistance with these SSR markers. The highest frequency was observed for Lr32 (100%), as it was detected in all fifty seven lines, followed by Lr34 (89.4%) in 51 lines, Lr35 (87.7%) in 50 lines and Lr13 (31.5%) in 18 lines respectively. All the four resistant genes were identified in fifteen lines which is only 26% of the studied population. These results indicate that there are limited number of variant genes for leaf rust resistance in the studied wheat advanced lines. Therefore, strategies for arraying these genes to lengthen infection resistance are advised to eliminate wheat rust diseases. In addition, more reliable and capable markers are essential to be settled for marker assisted selection of these and other genes.

Rice seeds biofortification using biogenic iron oxide nanoparticles synthesized by using Glycyrrhiza glabra: a study on growth and yield improvement.

Iron, a crucial micronutrient, is an integral element of biotic vitality. The scarcity of iron in the soil creates agronomic challenges and has a detrimental impact on crop vigour and chlorophyll formation. Utilizing iron oxide nanoparticles (IONPs) via nanopriming emerges as an innovative method to enhance agricultural efficiency and crop health. The objective of this study was to synthesize biogenic IONPs from Glycyrrhiza glabra (G. glabra) plant extract using green chemistry and to evaluate their nanopriming effects on rice seed iron levels and growth. The synthesized IONPs were analyzed using UV-Vis spectroscopy, Fourier-transform infrared spectroscopy (FTIR), Scanning electron microscope (SEM), Transmission electron microscopy (TEM), and Energy-dispersive X-ray (EDX) techniques. The UV-Vis peak at 280 nm revealed the formation of IONPs. SEM and TEM showed that the nanoparticles were spherical and had an average diameter of 23.8 nm. Nanopriming resulted in a substantial enhancement in growth, as seen by a 9.25% and 22.8% increase in shoot lengths for the 50 ppm and 100 ppm treatments, respectively. The yield metrics showed a positive correlation with the concentrations of IONPs. The 1000-grain weight and spike length observed a maximum increase of 193.75% and 97.73%, respectively, at the highest concentration of IONPs. The study indicates that G. glabra synthesized IONPs as a nanopriming agent significantly increased rice seeds' growth and iron content. This suggests that there is a relationship between the dosage of IONPs and their potential for improving agricultural biofortification.

Prevalence, Clinical Characteristics, and Clinical Outcomes of New-onset Diabetes Mellitus among COVID-19 Patients in Developing and Developed Countries: A Systematic Review.

Diabetes mellitus (DM) is linked to poor clinical outcomes and high mortality in Coronavirus patients. The primary objective of this systematic review was to determine the prevalence, clinical features, glycemic parameters, and outcomes of newly diagnosed diabetes in individuals with COVID-19 in developing and developed countries. By searching PubMed, Medline, Scopus, Embase, Google Scholar, and PakMediNet databases, an online literature search was conducted from March 2020 to November 2021. Guidelines for reporting systematic reviews and meta-analyses (PRISMA) were used. There were 660 publications found, of which 27 were original studies involving 3241 COVID-19 patients were selected. In the COVID-19 patients with new-onset diabetes, mean age was 43.21±21.00 years. Fever, cough, polyuria, and polydipsia were the most frequently reported symptoms, followed by shortness of breath, arthralgia, and myalgia. The developed world reported (109/1119) new diabetes cases (9.74%), while the developing world reported (415/2122) (19.5%). COVID-19 new-onset diabetic mortality rate was 470/3241 (14.5%). Key Words: COVID-19, New onset diabetes mellitus, SARS-CoV-2, Prevalence, Clinical outcomes, Developing countries, Developed countries.

Heavy metal ATPase genes (HMAs) expression induced by endophytic bacteria, "AI001, and AI002" mediate cadmium translocation and phytoremediation.

Contamination of heavy metals is a serious threat, which causes threats to the environment. Our study aimed to determine the role of endophytic bacteria in Cd phytoremediation and heavy metal ATPase gene expression. Cadmium (Cd) resistant endophytic bacteria were isolated from Solanum nigrum on LB agar plates, contaminated with 0-30 mg/L Cd. The phosphate solubilization and indole-3-acetic acid (IAA) production of endophytes were estimated by growing them on Pikovskaya agar medium and GC-MS analysis, respectively. An experiment in a pot was performed to evaluate the effects of bacteria on rice plants contaminated with 5-25 mg/L of Cd. Expression of Cd response genes was quantified through qRT-PCR and Cd translocation from one part to another part of the plant was measured through the ICP. BLAST alignment of 16 S-rDNA gene sequences confirmed the bacterial isolates as Serratia sp. AI001 and Klebsiella sp. Strain AI002. Both strains tolerated Cd up to 25 mg/L and produced 27-30 µg/mL of IAA. Inoculation of AI001 and AI002 improved plant growth dynamics (i.e., plant length, biomass, chlorophyll contents), relieved electrolyte leakage, and improved reduced glutathione significantly (P < 0.05). The inoculation of AI001 and AI002 significantly (P < 0.05) induced the expression of heavy metal ATPase genes ie., "HMA2, HMA3, and HMA4" and Cd translocation compared to uninoculated plants. Both AI001 and AI002 exhibited very prominent plant-growth-promoting and Cd phytoremediation properties. The results revealed that isolates also contributed a lot to the expression of rice plant heavy metal ATPase genes and in the Cd translocation in the plant.

Are fiducial registration error and target registration error correlated? SciKit-SurgeryFRED for teaching and research.

Understanding the relationship between fiducial registration error (FRE) and target registration error (TRE) is important for the correct use of interventional guidance systems. Whilst it is well established that TRE is statistically independent of FRE, system users still struggle against the intuitive assumption that a low FRE indicates a low TRE. We present the SciKit-Surgery Fiducial Registration Educational Demonstrator and describe its use. SciKit-SurgeryFRED was developed to enable remote teaching of key concepts in image registration. SciKit-SurgeryFRED also supports research into user interface design for image registration systems. SciKit-SurgeryFRED can be used to enable remote tutorials covering the statistics relevant to image guided interventions. Students are able to place fiducial markers on pre and intra-operative images and observe the effects of changes in marker geometry, marker count, and fiducial localisation error on TRE and FRE. SciKit-SurgeryFRED also calculates statistical measures for the expected values of TRE and FRE. Because many registrations can be performed quickly the students can then explore potential correlations between the different statistics. SciKit-SurgeryFRED also implements a registration based game, where participants are rewarded for complete treatment of a clinical target, whilst minimising the treatment margin. We used this game to perform a remote study on registration and simulated ablation, measuring how user performance changes depending on what error statistics are made available. The results support the assumption that knowing the exact value of target registration error leads to better treatment. Display of other statistics did not have a significant impact on the treatment performance.

Comparing the phosphorus use efficiency of pre-treated (organically) rock phosphate with soluble P fertilizers in maize under calcareous soils.

In calcareous soils, phosphorus (P) availability to plant is impaired due to the formation of insoluble complexes with calcium and magnesium. Therefore, this study was executed to compare the P use efficiency (PUE) of four different P sources [rock phosphate (RP), acidulated rock phosphate (ARP), single super phosphate (SSP) and di ammonium phosphate (DAP)] alone or pre-treated with organic amendments (farm yard manure (FYM) enriched compost, simple compost and humic acid (HA)) along with control in maize crop under calcareous soils. All treatments irrespective of P sources received 90 kg P2O5 ha-1. Phosphorus application regardless of its sources and combination with organic amendments significantly improved maize growth, yield as well as P uptake and PUE. Rock phosphate when applied alone was recorded inferior but its performance significantly improved with compost or its pre-addition with FYM and HA, that further enhanced upon acidulation. Maize grain yield increased by 21, 22.2, 67.9 and 94% with RP, ARP, ARP enriched compost and ARP+ compost respectively, over control. Similarly, PUE of DAP improved from 31.7 to 43.1 and 39 with sample and enriched compost correspondingly. Post-harvest soil and grain P were at par for SSP, ARP and DAP alone or in conjugation with organic amendments when averaged across the amendments. These results suggested that pretreatment of P sources with organic amendments is an economical and more feasible approach to improve maize yield and PUE. Moreover, on-farm acidulation of RP may give at par results with SSP and DAP with cheaper rate and hence recommended for P management in maize in alkaline calcareous soils.

SciKit-Surgery: compact libraries for surgical navigation.

PURPOSE: This paper introduces the SciKit-Surgery libraries, designed to enable rapid development of clinical applications for image-guided interventions. SciKit-Surgery implements a family of compact, orthogonal, libraries accompanied by robust testing, documentation, and quality control. SciKit-Surgery libraries can be rapidly assembled into testable clinical applications and subsequently translated to production software without the need for software reimplementation. The aim is to support translation from single surgeon trials to multicentre trials in under 2 years. METHODS: At the time of publication, there were 13 SciKit-Surgery libraries provide functionality for visualisation and augmented reality in surgery, together with hardware interfaces for video, tracking, and ultrasound sources. The libraries are stand-alone, open source, and provide Python interfaces. This design approach enables fast development of robust applications and subsequent translation. The paper compares the libraries with existing platforms and uses two example applications to show how SciKit-Surgery libraries can be used in practice. RESULTS: Using the number of lines of code and the occurrence of cross-dependencies as proxy measurements of code complexity, two example applications using SciKit-Surgery libraries are analysed. The SciKit-Surgery libraries demonstrate ability to support rapid development of testable clinical applications. By maintaining stricter orthogonality between libraries, the number, and complexity of dependencies can be reduced. The SciKit-Surgery libraries also demonstrate the potential to support wider dissemination of novel research. CONCLUSION: The SciKit-Surgery libraries utilise the modularity of the Python language and the standard data types of the NumPy package to provide an easy-to-use, well-tested, and extensible set of tools for the development of applications for image-guided interventions. The example application built on SciKit-Surgery has a simpler dependency structure than the same application built using a monolithic platform, making ongoing clinical translation more feasible.

SnappySonic: An Ultrasound Acquisition Replay Simulator.

SnappySonic provides an ultrasound acquisition replay simulator designed for public engagement and training. It provides a simple interface to allow users to experience ultrasound acquisition without the need for specialist hardware or acoustically compatible phantoms. The software is implemented in Python, built on top of a set of open source Python modules targeted at surgical innovation. The library has high potential for reuse, most obviously for those who want to simulate ultrasound acquisition, but it could also be used as a user interface for displaying high dimensional images or video data.

Identification and characterization of a novel multi-stress responsive gene in Arabidopsis.

Abiotic stresses especially salinity, drought and high temperature result in considerable reduction of crop productivity. In this study, we identified AT4G18280 annotated as a glycine-rich cell wall protein-like (hereafter refer to as GRPL1) protein as a potential multistress-responsive gene. Analysis of public transcriptome data and GUS assay of pGRPL1::GUS showed a strong induction of GRPL1 under drought, salinity and heat stresses. Transgenic plants overexpressing GRPL1-3HA showed significantly higher germination, root elongation and survival rate under salt stress. Moreover, the 35S::GRPL1-3HA transgenic lines also showed higher survival rates under drought and heat stresses. GRPL1 showed similar expression patterns with Abscisic acid (ABA)-pathway genes under different growth and stress conditions, suggesting a possibility that GRPL1 might act in the ABA pathway that is further supported by the inability of ABA-deficient mutant (aba2-1) to induce GRPL1 under drought stress. Taken together, our data presents GRPL1 as a potential multi-stress responsive gene working downstream of ABA.

A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach.

The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. The urgency of the situation requires the development of SARS-CoV-2-based vaccines. Immunoinformatic and molecular modelling are time-efficient methods that are generally used to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines has proved to be a promising immunization strategy against viruses and pathogens, thus inducing more comprehensive protective immunity. The current study demonstrated a comprehensive in silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in Escherichia coli. Despite that this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can be present as a better prophylactic solution against COVID-19.

Feasible regeneration and agro bacterium-mediated transformation of Brassica juncea with Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) gene.

In the present study an effort has been made to optimize the in vitro regeneration protocol for Agrobacterium-mediated transformation of Brassica juncea, because of its importance as oilseed crops. The highest callus induction frequency of 87% was observed on MS (Murashige and Skoog, 1962) medium supplemented with 4 µM 6-benzyladenine (BA) after four weeks of culture period. Subculturing of organogenic calli in MS media with a similar hormonal composition resulted in shoot organogenesis after six weeks of culture cultivation. The highest shoot induction frequency (92%) was recorded on MS medium containing 4 µM BA in combination with 1 µM of α-naphthalene acetic acid (NAA). Further, well-developed roots were formed in MS media augmented with 6 µM of Indole acetic acid (IAA) in combination with 1 µM Kinetin (Kn). Cotyledon explants were exploited in vitro for the successful transformation of B. juncea. A binary vector comprised of the Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) gene under the transcriptional control of a glycinin promoter and with a basta selection marker was introduced into A. tumefaciens strain GV3101 via electroporation. EaDAcT gene is responsible for unusual triacylglycerol's production where the sn-3 position is esterified with acetate instead of the long-chain fatty acid found in the triacylglycerol's. The highest regeneration frequency (100%) of transgenic shoots was observed on MS medium supplemented with 4 µM BA plus 1 µM NAA in the presence of 25 mg l-1 basta and 160 mg l-1 timintin. The efficiency of stable transformation was found to be approximately 7% in the transgenic plants. Moreover, the transformed regenerated shoots were confirmed by PCR analysis using EaDAcT gene-specific primers.

Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: the case of hypertrophic cardiomyopathy.

BACKGROUND: International guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false-positive rate over test sensitivity and diagnostic yield. Genetic testing is also more likely informative in individuals with well-characterised variants from extensively studied European-ancestry populations. Inherited cardiomyopathies are relatively common Mendelian diseases that allow empirical calibration and assessment of this framework. METHODS: We compared rare variants in large hypertrophic cardiomyopathy (HCM) cohorts (up to 6179 cases) to reference populations to identify variant classes with high prior likelihoods of pathogenicity, as defined by etiological fraction (EF). We analysed the distribution of variants using a bespoke unsupervised clustering algorithm to identify gene regions in which variants are significantly clustered in cases. RESULTS: Analysis of variant distribution identified regions in which variants are significantly enriched in cases and variant location was a better discriminator of pathogenicity than generic computational functional prediction algorithms. Non-truncating variant classes with an EF ≥ 0.95 were identified in five established HCM genes. Applying this approach leads to an estimated 14-20% increase in cases with actionable HCM variants, i.e. variants classified as pathogenic/likely pathogenic that might be used for predictive testing in probands' relatives. CONCLUSIONS: When found in a patient confirmed to have disease, novel variants in some genes and regions are empirically shown to have a sufficiently high probability of pathogenicity to support a "likely pathogenic" classification, even without additional segregation or functional data. This could increase the yield of high confidence actionable variants, consistent with the framework and recommendations of current guidelines. The techniques outlined offer a consistent and unbiased approach to variant interpretation for Mendelian disease genetic testing. We propose adaptations to ACMG/AMP guidelines to incorporate such evidence in a quantitative and transparent manner.

Comparison of mucosal B- and T-cell responses in Helicobacter pylori-infected subjects in a developing and a developed country.

Helicobacter pylori is highly endemic in developing countries, but comparatively little is known about mucosal immune responses to H. pylori in these settings. Therefore, we have compared B- and T-cell responses, with a focus on the gastrointestinal mucosa, in H. pylori-infected adults in a developing (Bangladesh) and a developed (Sweden) country. We found comparable numbers of CD19(+) B cells and CD4 (+)T cells and similar levels of H. pylori-specific IgA antibodies in gastric mucosa from Bangladeshi and Swedish volunteers. However, about threefold higher numbers of CD19(+) B cells and 12-fold increased levels of H. pylori-specific IgA antibodies were found in the duodenum of Bangladeshi subjects. The gastric and duodenal immune responses in Bangladeshi asymptomatic carriers and duodenal ulcer patients were comparable. Bangladeshi subjects had about twofold lower titers of H. pylori-specific IgA and IgG antibodies in the circulation compared with Swedish volunteers. In conclusion, our findings suggest that Bangladeshi individuals have comparable gastric immune responses, but lower systemic antibody responses to H. pylori, compared with Swedish volunteers. Increased inflammation is present in the duodenum of Bangladeshi volunteers, maybe as a result of frequent exposure to enteric infections in these individuals.