Case-control Dataset Research Articles

Networks extracted from nonlinear fMRI connectivity exhibit unique spatial variation and enhanced sensitivity to differences between individuals with schizophrenia and controls

Schizophrenia is a chronic brain disorder associated with widespread alterations in functional brain connectivity. Although data-driven approaches such as independent component analysis are often used to study how schizophrenia impacts linearly connected networks, alterations within the underlying nonlinear functional connectivity structure remain largely unknown. Here we report the analysis of networks from explicitly nonlinear functional magnetic resonance imaging connectivity in a case–control dataset. We found systematic spatial variation, with higher nonlinear weight within core regions, suggesting that linear analyses underestimate functional connectivity within network centers. We also found that a unique nonlinear network incorporating default-mode, cingulo-opercular and central executive regions exhibits hypoconnectivity in schizophrenia, indicating that typically hidden connectivity patterns may reflect inefficient network integration in psychosis. Moreover, nonlinear networks including those previously implicated in auditory, linguistic and self-referential cognition exhibit heightened statistical sensitivity to schizophrenia diagnosis, collectively underscoring the potential of our methodology to resolve complex brain phenomena and transform clinical connectivity analysis.

Evidence-based approach for the generation of a multivariate logistic regression model that predicts instrument failure.

Identification of instrument failure (IF) represents a point to improve the quality of services provided by medical laboratories. Here, a logistic regression model was created to define the relationship between instrument downtime and laboratory quality management systems. Interval-level quality control (QC) and categorical quality assurance data from 3 identical chemistry analyzers was utilized to generate a logistic regression model able to predict IF. A case-control approach and the forward stepwise likelihood-ratio method was used to develop the logistic regression model. The model was tested using a case-control dataset and again using the complete sample. A total of 650 downtime events were identified. A total of 22,880 QC data points, 187 calibrations, 24 proficiency testing events, and 107 maintenance records were analyzed. The regression model was able to correctly predict 59.2% of no instrument downtime events and 69.2% of instrument downtime events using the case-control data. Using the entire data set, the sensitivity of the model was 69.2% and the specificity was 58.2%. A logistic regression model can predict instrument downtime nearly 70% of the time. This study acts as a proof of concept using a limited data set collected by the chemistry laboratory.

OSTEO18, a novel urinary proteomic signature, associated with osteoporosis in heart transplant recipients

Abstract Background Immunosuppressive treatment in heart transplant (HTx) recipient causes osteoporosis. The urinary proteomic profile (UPP) includes peptide fragments derived from the bone extracellular matrix. Purpose Study aims were to develop and validate a multidimensional UPP biomarker for osteoporosis in HTx patients from single sequenced urinary peptides identifying the parent proteins. Methods A single-center HTx cohort was analyzed. Urine samples were measured by capillary electrophoresis coupled with mass spectrometry. Cases with osteoporosis and matching controls were randomly selected from all available 389 patients. In derivation case-control dataset, 1576 sequenced peptides detectable in ≥30% of patients. Applying statistical analysis on these, an 18-peptide multidimensional osteoporosis UPP biomarker (OSTEO18) was generated by support vector modeling. The 2 replication datasets included 118 and 94 patients. For further validation, the whole cohort was analyzed. Statistical methods included logistic regression and receiver operating characteristic curve (ROC) analysis. Results In derivation dataset, the AUC, sensitivity and specificity of OSTEO18 were 0.83 (95% CI: 0.76-0.90), 74.3% and 87.1%, respectively. In replication datasets, results were confirmatory. In the whole cohort (154 osteoporotic patients [39.6%]), the ORs for osteoporosis increased (p < 0.0001) across OSTEO18 quartiles from 0.39 (95% CI: 0.25-0.61) to 3.14 (2.08-4.75). With full adjustment for known osteoporosis risk factors, OSTEO18 improved AUC from 0.708 to 0.786 (p = 0.0003) for OSTEO18 categorized (optimized threshold: 0.095) and to 0.784 (p = 0.0004) for OSTEO18 as continuously distributed classifier. Conclusion OSTEO18 is a clinically meaningful novel biomarker indicative of osteoporosis in HTx recipients and is being certified as in-vitro diagnostic.

Tracking the pre-clinical progression of transthyretin amyloid cardiomyopathy using artificial intelligence-enabled electrocardiography and echocardiography.

Diagnosing transthyretin amyloid cardiomyopathy (ATTR-CM) requires advanced imaging, precluding large-scale testing for pre-clinical disease. We examined the application of artificial intelligence (AI) to echocardiography (TTE) and electrocardiography (ECG) as a scalable strategy to quantify pre-clinical trends in ATTR-CM. Across age/sex-matched case-control datasets in the Yale-New Haven Health System (YNHHS) we trained deep learning models to identify ATTR-CM-specific signatures on TTE videos and ECG images (area under the curve of 0.93 and 0.91, respectively). We deployed these across all studies of individuals referred for cardiac nuclear amyloid imaging in an independent population at YNHHS and an external population from the Houston Methodist Hospitals (HMH) to define longitudinal trends in AI-defined probabilities for ATTR-CM using age/sex-adjusted linear mixed models, and describe discrimination metrics during the early pre-clinical stage. Among 984 participants referred for cardiac nuclear amyloid imaging at YNHHS (median age 74 years, 44.3% female) and 806 at HMH (69 years, 34.5% female), 112 (11.4%) and 174 (21.6%) tested positive for ATTR-CM, respectively. Across both cohorts and modalities, AI-defined ATTR-CM probabilities derived from 7,423 TTEs and 32,205 ECGs showed significantly faster progression rates in the years before clinical diagnosis in cases versus controls (p time × group interaction ≤0.004). In the one-to-three-year window before cardiac nuclear amyloid imaging sensitivity/specificity metrics were estimated at 86.2%/44.2% [YNHHS] vs 65.7%/65.5% [HMH] for AI-Echo, and 89.8%/40.6% [YNHHS] vs 88.5%/35.1% [HMH] for AI-ECG. We demonstrate that AI tools for echocardiographic videos and ECG images can enable scalable identification of pre-clinical ATTR-CM, flagging individuals who may benefit from risk-modifying therapies.

Identifying neuroimaging biomarkers in major depressive disorder using machine learning algorithms and functional near-infrared spectroscopy (fNIRS) during verbal fluency task

One of the most prevalent psychiatric disorders is major depressive disorder (MDD), which increases the probability of suicidal ideation or untimely demise. Abnormal frontal hemodynamic changes detected by functional near-infrared spectroscopy (fNIRS) during verbal fluency task (VFT) have the potential to be used as an objective indicator for assessing clinical symptoms. However, comprehensive quantitative and objective assessment instruments for individuals who exhibit symptoms suggestive of depression remain undeveloped. Drawing from a total of 467 samples in a large-scale dataset comprising 289 MDD patients and 178 healthy controls, fNIRS measurements were obtained throughout the VFT. To identify unique MDD biomarkers, this research introduced a data representation approach for extracting spatiotemporal features from fNIRS signals, which were subsequently utilized as potential predictors. Machine learning classifiers (e.g., Gradient Boosted Decision Trees (GBDT) and Multilayer Perceptron) were implemented to assess the ability to predict selected features. The mean and standard deviation of the cross-validation indicated that the GBDT model, when combined with the 180-feature pattern, distinguishes patients with MDD from healthy controls in the most effective manner. The accuracy of correct classification for the test set was 0.829 ± 0.053, with an AUC of 0.895 (95 % CI: 0.864–0.925) and a sensitivity of 0.914 ± 0.051. Channels that made the most important contribution to the identification of MDD were identified using Shapley Additive Explanations method, located in the frontopolar area and the dorsolateral prefrontal cortex, as well as pars triangularis Broca's area. Assessment of abnormal prefrontal activity during the VFT in MDD serves as an objectively measurable biomarker that could be utilized to evaluate cognitive deficits and facilitate early screening for MDD. The model suggested in this research could be applied to large-scale case-control fNIRS datasets to detect unique characteristics of MDD and offer clinicians an objective biomarker-based analytical instrument to assist in the evaluation of suspicious cases.

Balancing the efforts of chart review and gains in PRS prediction accuracy: An empirical study

ObjectivePhenotypic misclassification in genetic association analyses can impact the accuracy of PRS-based prediction models. The bias reduction method proposed by Tong et al. (2019) has demonstrated its efficacy in reducing the effects of bias on the estimation of association parameters between genotype and phenotype while minimizing variance by employing chart reviews on a subset of the data for validating phenotypes, however its improvement of subsequent PRS prediction accuracy remains unclear. Our study aims to fill this gap by assessing the performance of simulated PRS models and estimating the optimal number of chart reviews needed for validation. MethodsTo comprehensively assess the efficacy of the bias reduction method proposed by Tong et al. in enhancing the accuracy of PRS-based prediction models, we simulated each phenotype under different correlation structures (an independent model, a weakly correlated model, a strongly correlated model) and introduced error-prone phenotypes using two distinct error mechanisms (differential and non-differential phenotyping errors). To facilitate this, we used genotype and phenotype data from 12 case-control datasets in the Alzheimer’s Disease Genetics Consortium (ADGC) to produce simulated phenotypes. The evaluation included analyses across various misclassification rates of original phenotypes as well as quantities of validation set. Additionally, we determined the median threshold, identifying the minimal validation size required for a meaningful improvement in the accuracy of PRS-based predictions across a broad spectrum. ResultsThis simulation study demonstrated that incorporating chart review does not universally guarantee enhanced performance of PRS-based prediction models. Specifically, in scenarios with minimal misclassification rates and limited validation sizes, PRS models utilizing debiased regression coefficients demonstrated inferior predictive capabilities compared to models using error-prone phenotypes. Put differently, the effectiveness of the bias reduction method is contingent upon the misclassification rates of phenotypes and the size of the validation set employed during chart reviews. Notably, when dealing with datasets featuring higher misclassification rates, the advantages of utilizing this bias reduction method become more evident, requiring a smaller validation set to achieve better performance. ConclusionThis study highlights the importance of choosing an appropriate validation set size to balance between the efforts of chart review and the gain in PRS prediction accuracy. Consequently, our study establishes a valuable guidance for validation planning, across a diverse array of sensitivity and specificity combinations.

Harnessing transcriptomic signals for amyotrophic lateral sclerosis to identify novel drugs and enhance risk prediction

IntroductionAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. This study integrates common genetic association results from the latest ALS genome-wide association study (GWAS) summary statistics with functional genomic annotations with the aim of providing mechanistic insights into ALS risk loci, inferring drug repurposing opportunities, and enhancing prediction of ALS risk and clinical characteristics. MethodsGenes associated with ALS were identified using GWAS summary statistic methodology including SuSiE SNP-based fine-mapping, and transcriptome- and proteome-wide association study (TWAS/PWAS) analyses. Using several approaches, gene associations were integrated with the DrugTargetor drug-gene interaction database to identify drugs that could be repurposed for the treatment of ALS. Furthermore, ALS gene associations from TWAS were combined with observed blood expression in two external ALS case-control datasets to calculate polytranscriptomic scores and evaluate their utility for prediction of ALS risk and clinical characteristics, including site of onset, age at onset, and survival. ResultsSNP-based fine-mapping, TWAS and PWAS identified 118 genes associated with ALS, with TWAS and PWAS providing novel mechanistic insights. Drug repurposing analyses identified six drugs significantly enriched for interactions with ALS associated genes, though directionality could not be determined. Additionally, drug class enrichment analysis showed gene signatures linked to calcium channel blockers may reduce ALS risk, whereas antiepileptic drugs may increase ALS risk. Across the two observed expression target samples, ALS polytranscriptomic scores significantly predicted ALS risk (R2 = 5.1 %; p-value = 3.2 × 10−27) and clinical characteristics. ConclusionsFunctionally-informed analyses of ALS GWAS summary statistics identified novel mechanistic insights into ALS aetiology, highlighted several therapeutic research avenues, and enabled statistically significant prediction of ALS risk.

Detecting outliers in case-control cohorts for improving deep learning networks on Schizophrenia prediction.

This study delves into the intricate genetic and clinical aspects of Schizophrenia, a complex mental disorder with uncertain etiology. Deep Learning (DL) holds promise for analyzing large genomic datasets to uncover new risk factors. However, based on reports of non-negligible misdiagnosis rates for SCZ, case-control cohorts may contain outlying genetic profiles, hindering compelling performances of classification models. The research employed a case-control dataset sourced from the Swedish populace. A gene-annotation-based DL architecture was developed and employed in two stages. First, the model was trained on the entire dataset to highlight differences between cases and controls. Then, samples likely to be misclassified were excluded, and the model was retrained on the refined dataset for performance evaluation. The results indicate that SCZ prevalence and misdiagnosis rates can affect case-control cohorts, potentially compromising future studies reliant on such datasets. However, by detecting and filtering outliers, the study demonstrates the feasibility of adapting DL methodologies to large-scale biological problems, producing results more aligned with existing heritability estimates for SCZ. This approach not only advances the comprehension of the genetic background of SCZ but also opens doors for adapting DL techniques in complex research for precision medicine in mental health.

Heritability of sudden cardiac death in Thoroughbred racehorses.

Sudden cardiac death (SCD) is an important cause of exercise-associated fatalities in Thoroughbred racehorses. Equine deaths share similarities with fatalities in human athletes that result from inherited cardiac disease. Whilst genetic causes have been postulated in horses, these have not been confirmed and heritability of SCD has not previously been estimated in Thoroughbred racehorses. To determine the heritability of SCD in a sample population of Thoroughbred racehorses. Retrospective case-control study. Steward and post-mortem reports of Thoroughbred racehorses in Australia between 2007 and 2020 were reviewed to identify horses with SCD. Control horses were randomly selected from races in which SCD occurred or from races on the date of the case fatality. A five-generation integrated pedigree chart was collected for each horse. Estimates of heritability were obtained using an animal model in the ASReml-R program with variance components estimated assuming SCD was normally distributed, and on the logit transformed scale. Inbreeding coefficients were calculated and the risk of producing SCD-affected progeny was calculated for stallions that sired ≥5 individuals in the case-control population. Ninety-three horses with SCD and 465 control horses were identified. Heritability on the underlying scale was 0.15 ± 0.09 (logit animal) and 0.24 ± 0.12 (normal animal). Inbreeding coefficients were not significantly different between groups. Of the 16 first generation sires that appeared ≥5 times in the case-control data set, two sires more frequently produced affected progeny (OR 7.95-10.41). Challenges in definitively confirming SCD may lead to misclassification of some cases. Some control horses may have not been exposed to environmental influences of SCD. Case numbers are low and the studied population may not represent the entire Thoroughbred genetic pool. The heritability of SCD in this population was relatively low. However, individual stallions appear more likely to produce affected progeny. Further studies are required to understand the genetic and environmental influences that contribute to disease expression.

Polygenic inheritance and its interplay with smoking history in predicting lung cancer diagnosis: a French-Canadian case-control cohort

The most near-term clinical application of genome-wide association studies in lung cancer is a polygenic risk score (PRS). A case-control dataset was generated consisting of 4002 lung cancer cases from the LORD project and 20,010 ethnically matched controls from CARTaGENE. A genome-wide PRS including >1.1 million genetic variants was derived and validated in UK Biobank (n=5419 lung cancer cases). The predictive ability and diagnostic discrimination performance of the PRS was tested in LORD/CARTaGENE and benchmarked against previous PRSs from the literature. Stratified analyses were performed by smoking status and genetic risk groups defined as low (<20th percentile), intermediate (20-80th percentile) and high (>80th percentile) PRS. The phenotypic variance explained and the effect size of the genome-wide PRS numerically outperformed previous PRSs. Individuals with high genetic risk had a 2-fold odds of lung cancer compared to low genetic risk. The PRS was an independent predictor of lung cancer beyond conventional clinical risk factors, but its diagnostic discrimination performance was incremental in an integrated risk model. Smoking increased the odds of lung cancer by 7.7-fold in low genetic risk and by 11.3-fold in high genetic risk. Smoking with high genetic risk was associated with a 17-fold increase in the odds of lung cancer compared to individuals who never smoked and with low genetic risk. Individuals at low genetic risk are not protected against the smoking-related risk of lung cancer. The joint multiplicative effect of PRS and smoking increases the odds of lung cancer by nearly 20-fold. This work was supported by the CQDM and the IUCPQ Foundation owing to a generous donation from Mr. Normand Lord.

Statistical Methods for Best and Worst Eye Measurements.

The focus is often on the best and worst eyes to detect early predictive and non-invasive biomarkers of diabetic retinopathy. Typically, such data have been dealt with in a case-control setting, which applies two-sample tests and ignores the correlation between the fellow eyes. Practitioners are mostly unaware that such measurements hide the labels of the fellow eyes, which rules out standard tools, such as paired t or signed-rank tests. This report discusses the problems with such data on best and worst eye measurements, and illustrates alternative paired tests for equality of means or locations using a case-control dataset. This report illustrates that methods which ignore the correlation between fellow eyes result in grossly conservative tests. A battery of Z-tests which consider this correlation can resolve this issue. This finding emphasizes the importance of selecting an appropriate control group for the detection of possible markers. Further, it cites an example to show that using data from fellow eyes and adjusting for their correlation may not always be the best option, contrary to common perception.

Comparison of Bayesian approaches for developing prediction models in rare disease: application to the identification of patients with Maturity-Onset Diabetes of the Young

BackgroundClinical prediction models can help identify high-risk patients and facilitate timely interventions. However, developing such models for rare diseases presents challenges due to the scarcity of affected patients for developing and calibrating models. Methods that pool information from multiple sources can help with these challenges.MethodsWe compared three approaches for developing clinical prediction models for population screening based on an example of discriminating a rare form of diabetes (Maturity-Onset Diabetes of the Young - MODY) in insulin-treated patients from the more common Type 1 diabetes (T1D). Two datasets were used: a case-control dataset (278 T1D, 177 MODY) and a population-representative dataset (1418 patients, 96 MODY tested with biomarker testing, 7 MODY positive). To build a population-level prediction model, we compared three methods for recalibrating models developed in case-control data. These were prevalence adjustment (“offset”), shrinkage recalibration in the population-level dataset (“recalibration”), and a refitting of the model to the population-level dataset (“re-estimation”). We then developed a Bayesian hierarchical mixture model combining shrinkage recalibration with additional informative biomarker information only available in the population-representative dataset. We developed a method for dealing with missing biomarker and outcome information using prior information from the literature and other data sources to ensure the clinical validity of predictions for certain biomarker combinations.ResultsThe offset, re-estimation, and recalibration methods showed good calibration in the population-representative dataset. The offset and recalibration methods displayed the lowest predictive uncertainty due to borrowing information from the fitted case-control model. We demonstrate the potential of a mixture model for incorporating informative biomarkers, which significantly enhanced the model’s predictive accuracy, reduced uncertainty, and showed higher stability in all ranges of predictive outcome probabilities.ConclusionWe have compared several approaches that could be used to develop prediction models for rare diseases. Our findings highlight the recalibration mixture model as the optimal strategy if a population-level dataset is available. This approach offers the flexibility to incorporate additional predictors and informed prior probabilities, contributing to enhanced prediction accuracy for rare diseases. It also allows predictions without these additional tests, providing additional information on whether a patient should undergo further biomarker testing before genetic testing.

Joint modeling of gene-environment correlations and interactions using polygenic risk scores in case-control studies.

Polygenic risk scores (PRSs) are rapidly emerging as a way to measure disease risk by aggregating multiple genetic variants. Understanding the interplay of the PRS with environmental factors is critical for interpreting and applying PRSs in a wide variety of settings. We develop an efficient method for simultaneously modeling gene-environment correlations and interactions using the PRS in case-control studies. We use a logistic-normal regression modeling framework to specify the disease risk and PRS distribution in the underlying population and propose joint inference across the 2 models using the retrospective likelihood of the case-control data. Extensive simulation studies demonstrate the flexibility of the method in trading-off bias and efficiency for the estimation of various model parameters compared with standard logistic regression or a case-only analysis for gene-environment interactions, or a control-only analysis, for gene-environment correlations. Finally, using simulated case-control data sets within the UK Biobank study, we demonstrate the power of our method for its ability to recover results from the full prospective cohort for the detection of an interaction between long-term oral contraceptive use and the PRS on the risk of breast cancer. This method is computationally efficient and implemented in a user-friendly R package.

Polygenic Risk Scores Validated in Patient-Derived Cells Stratify for Mitochondrial Subtypes of Parkinson's Disease.

The aim of our study is to better understand the genetic architecture and pathological mechanisms underlying neurodegeneration in idiopathic Parkinson's disease (iPD). We hypothesized that a fraction of iPD patients may harbor a combination of common variants in nuclear-encoded mitochondrial genes ultimately resulting in neurodegeneration. We used mitochondria-specific polygenic risk scores (mitoPRSs) and created pathway-specific mitoPRSs using genotype data from different iPD case-control datasets worldwide, including the Luxembourg Parkinson's Study (412 iPD patients and 576 healthy controls) and COURAGE-PD cohorts (7,270 iPD cases and 6,819 healthy controls). Cellular models from individuals stratified according to the most significant mitoPRS were subsequently used to characterize different aspects of mitochondrial function. Common variants in genes regulating Oxidative Phosphorylation (OXPHOS-PRS) were significantly associated with a higher PD risk in independent cohorts (Luxembourg Parkinson's Study odds ratio, OR = 1.31[1.14-1.50], p-value = 5.4e-04; COURAGE-PD OR = 1.23[1.18-1.27], p-value = 1.5e-29). Functional analyses in fibroblasts and induced pluripotent stem cells-derived neuronal progenitors revealed significant differences in mitochondrial respiration between iPD patients with high or low OXPHOS-PRS (p-values < 0.05). Clinically, iPD patients with high OXPHOS-PRS have a significantly earlier age at disease onset compared to low-risk patients (false discovery rate [FDR]-adj p-value = 0.015), similar to prototypic monogenic forms of PD. Finally, iPD patients with high OXPHOS-PRS responded more effectively to treatment with mitochondrially active ursodeoxycholic acid. OXPHOS-PRS may provide a precision medicine tool to stratify iPD patients into a pathogenic subgroup genetically defined by specific mitochondrial impairment, making these individuals eligible for future intelligent clinical trial designs. ANN NEUROL 2024;96:133-149.

Genome-wide meta-analysis of short-tandem repeats for Parkinson's disease risk using genotype imputation.

Idiopathic Parkinson's disease is determined by a combination of genetic and environmental factors. Recently, the first genome-wide association study on short-tandem repeats in Parkinson's disease reported on eight suggestive short-tandem repeat-based risk loci (α = 5.3 × 10-6), of which four were novel, i.e. they had not been implicated in Parkinson's disease risk by genome-wide association analyses of single-nucleotide polymorphisms before. Here, we tested these eight candidate short-tandem repeats in a large, independent Parkinson's disease case-control dataset (n = 4757). Furthermore, we combined the results from both studies by meta-analysis resulting in the largest Parkinson's disease genome-wide association study of short-tandem repeats to date (n = 43 844). Lastly, we investigated whether leading short-tandem repeat risk variants exert functional effects on gene expression regulation based on methylation quantitative trait locus data in human 'post-mortem' brain (n = 142). None of the eight previously reported short-tandem repeats were significantly associated with Parkinson's disease in our independent dataset after multiple testing correction (α = 6.25 × 10-3). However, we observed modest support for short-tandem repeats near CCAR2 and NCOR1 in the updated meta-analyses of all available data. While the genome-wide meta-analysis did not reveal additional study-wide significant (α = 6.3 × 10-7) short-tandem repeat signals, we identified seven novel suggestive Parkinson's disease short-tandem repeat risk loci (α = 5.3 × 10-6). Of these, especially a short-tandem repeat near MEIOSIN showed consistent evidence for association across datasets. CCAR2, NCOR1 and one novel suggestive locus identified here (LINC01012) emerged from colocalization analyses showing evidence for a shared causal short-tandem repeat variant affecting both Parkinson's disease risk and cis DNA methylation in brain. Larger studies, ideally using short-tandem repeats called from whole-sequencing data, are needed to more fully investigate their role in Parkinson's disease.

Artificial intelligence for automated detection and measurements of carpal instability signs on conventional radiographs

ObjectivesTo develop and validate an artificial intelligence (AI) system for measuring and detecting signs of carpal instability on conventional radiographs.Materials and methodsTwo case-control datasets of hand and wrist radiographs were retrospectively acquired at three hospitals (hospitals A, B, and C). Dataset 1 (2178 radiographs from 1993 patients, hospitals A and B, 2018–2019) was used for developing an AI system for measuring scapholunate (SL) joint distances, SL and capitolunate (CL) angles, and carpal arc interruptions. Dataset 2 (481 radiographs from 217 patients, hospital C, 2017–2021) was used for testing, and with a subsample (174 radiographs from 87 patients), an observer study was conducted to compare its performance to five clinicians. Evaluation metrics included mean absolute error (MAE), sensitivity, and specificity.ResultsDataset 2 included 258 SL distances, 189 SL angles, 191 CL angles, and 217 carpal arc labels obtained from 217 patients (mean age, 51 years ± 23 [standard deviation]; 133 women). The MAE in measuring SL distances, SL angles, and CL angles was respectively 0.65 mm (95%CI: 0.59, 0.72), 7.9 degrees (95%CI: 7.0, 8.9), and 5.9 degrees (95%CI: 5.2, 6.6). The sensitivity and specificity for detecting arc interruptions were 83% (95%CI: 74, 91) and 64% (95%CI: 56, 71). The measurements were largely comparable to those of the clinicians, while arc interruption detections were more accurate than those of most clinicians.ConclusionThis study demonstrates that a newly developed automated AI system accurately measures and detects signs of carpal instability on conventional radiographs.Clinical relevance statementThis system has the potential to improve detections of carpal arc interruptions and could be a promising tool for supporting clinicians in detecting carpal instability.

Risk factors for tick attachment in companion animals in Great Britain: a spatiotemporal analysis covering 2014-2021.

Ticks are an important driver of veterinary health care, causing irritation and sometimes infection to their hosts. We explored epidemiological and geo-referenced data from > 7 million electronic health records (EHRs) from cats and dogs collected by the Small Animal Veterinary Surveillance Network (SAVSNET) in Great Britain (GB) between 2014 and 2021 to assess the factors affecting tick attachment in an individual and at a spatiotemporal level. EHRs in which ticks were mentioned were identified by text mining; domain experts confirmed those with ticks on the animal. Tick presence/absence records were overlaid with a spatiotemporal series of climate, environment, anthropogenic and host distribution factors to produce a spatiotemporal regression matrix. An ensemble machine learning spatiotemporal model was used to fine-tune hyperparameters for Random Forest, Gradient-boosted Trees and Generalized Linear Model regression algorithms, which were then used to produce a final ensemble meta-learner to predict the probability of tick attachment across GB at a monthly interval and averaged long-term through 2014-2021 at a spatial resolution of 1km. Individual host factors associated with tick attachment were also assessed by conditional logistic regression on a matched case-control dataset. In total, 11,741 consultations were identified in which a tick was recorded. The frequency of tick records was low (0.16% EHRs), suggesting an underestimation of risk. That said, increased odds for tick attachment in cats and dogs were associated with younger adult ages, longer coat length, crossbreeds and unclassified breeds. In cats, males and entire animals had significantly increased odds of recorded tick attachment. The key variables controlling the spatiotemporal risk for tick attachment were climatic (precipitation and temperature) and vegetation type (Enhanced Vegetation Index). Suitable areas for tick attachment were predicted across GB, especially in forests and grassland areas, mainly during summer, particularly in June. Our results can inform targeted health messages to owners and veterinary practitioners, identifying those animals, seasons and areas of higher risk for tick attachment and allowing for more tailored prophylaxis to reduce tick burden, inappropriate parasiticide treatment and potentially TBDs in companion animals and humans. Sentinel networks like SAVSNET represent a novel complementary data source to improve our understanding of tick attachment risk for companion animals and as a proxy of risk to humans.

Individualized Texture Similarity Network in Schizophrenia

BackgroundStructural covariance network disruption has been considered an important pathophysiological indicator for schizophrenia. Here, we introduced a novel individualized structural covariance network measure, referred to as a texture similarity network (TSN), and hypothesized that the TSN could reliably reveal unique intersubject heterogeneity and complex dysconnectivity patterns in schizophrenia. MethodsThe TSN was constructed by measuring the covariance of 180 three-dimensional voxelwise gray-level co-occurrence matrix feature maps between brain areas in each participant. We first tested the validity and reproducibility of the TSN in characterizing the intersubject variability in 2 longitudinal test-retest healthy cohorts. The TSN was further applied to elucidate intersubject variability and dysconnectivity patterns in 10 schizophrenia case-control datasets (609 schizophrenia cases vs. 579 controls) as well as in a first-episode depression dataset (69 patients with depression vs. 69 control participants). ResultsThe test-retest analysis demonstrated higher TSN intersubject than intrasubject variability. Moreover, the TSN reliably revealed higher intersubject variability in both chronic and first-episode schizophrenia, but not in depression. The TSN also reproducibly detected coexistent increased and decreased TSN strength in widespread brain areas, increased global small-worldness, and the coexistence of both structural hyposynchronization in the central networks and hypersynchronization in peripheral networks in patients with schizophrenia but not in patients with depression. Finally, aberrant intersubject variability and covariance strength patterns revealed by the TSN showed a missing or weak correlation with other individualized structural covariance network measures, functional connectivity, and regional volume changes. ConclusionsThese findings support the reliability of a TSN in revealing unique structural heterogeneity and complex dysconnectivity in patients with schizophrenia.

Genetic interactions of schizophrenia using gene-based statistical epistasis exclusively identify nervous system-related pathways and key hub genes.

Background: The relationship between genotype and phenotype is governed by numerous genetic interactions (GIs), and the mapping of GI networks is of interest for two main reasons: 1) By modelling biological robustness, GIs provide a powerful opportunity to infer compensatory biological mechanisms via the identification of functional relationships between genes, which is of interest for biological discovery and translational research. Biological systems have evolved to compensate for genetic (i.e., variations and mutations) and environmental (i.e., drug efficacy) perturbations by exploiting compensatory relationships between genes, pathways and biological processes; 2) GI facilitates the identification of the direction (alleviating or aggravating interactions) and magnitude of epistatic interactions that influence the phenotypic outcome. The generation of GIs for human diseases is impossible using experimental biology approaches such as systematic deletion analysis. Moreover, the generation of disease-specific GIs has never been undertaken in humans. Methods: We used our Indian schizophrenia case-control (case-816, controls-900) genetic dataset to implement the workflow. Standard GWAS sample quality control procedure was followed. We used the imputed genetic data to increase the SNP coverage to analyse epistatic interactions across the genome comprehensively. Using the odds ratio (OR), we identified the GIs that increase or decrease the risk of a disease phenotype. The SNP-based epistatic results were transformed into gene-based epistatic results. Results: We have developed a novel approach by conducting gene-based statistical epistatic analysis using an Indian schizophrenia case-control genetic dataset and transforming these results to infer GIs that increase the risk of schizophrenia. There were ∼9.5 million GIs with a p-value 1 10-5. Approximately 4.8 million GIs showed an increased risk (OR > 1.0), while ∼4.75 million GIs had a decreased risk (OR <1.0) for schizophrenia. Conclusion: Unlike model organisms, this approach is specifically viable in humans due to the availability of abundant disease-specific genome-wide genotype datasets. The study exclusively identified brain/nervous system-related processes, affirming the findings. This computational approach fills a critical gap by generating practically non-existent heritable disease-specific human GIs from human genetic data. These novel datasets can train innovative deep-learning models, potentially surpassing the limitations of conventional GWAS.

Replication of a neuroimaging biomarker for striatal dysfunction in psychosis.

To bring biomarkers closer to clinical application, they should be generalizable, reliable, and maintain performance within the constraints of routine clinical conditions. The functional striatal abnormalities (FSA), is among the most advanced neuroimaging biomarkers in schizophrenia, trained to discriminate diagnosis, with post-hoc analyses indicating prognostic properties. Here, we attempt to replicate its diagnostic capabilities measured by the area under the curve (AUC) in receiver operator characteristic curves discriminating individuals with psychosis (n = 101) from healthy controls (n = 51) in the Human Connectome Project for Early Psychosis. We also measured the test-retest (run 1 vs 2) and phase encoding direction (i.e., AP vs PA) reliability with intraclass correlation coefficients (ICC). Additionally, we measured effects of scan length on classification accuracy (i.e., AUCs) and reliability (i.e., ICCs). Finally, we tested the prognostic capability of the FSA by the correlation between baseline scores and symptom improvement over 12 weeks of antipsychotic treatment in a separate cohort (n = 97). Similar analyses were conducted for the Yeo networks intrinsic connectivity as a reference. The FSA had good/excellent diagnostic discrimination (AUC = 75.4%, 95% CI = 67.0-83.3%; in non-affective psychosis AUC = 80.5%, 95% CI = 72.1-88.0%, and in affective psychosis AUC = 58.7%, 95% CI = 44.2-72.0%). Test-retest reliability ranged between ICC = 0.48 (95% CI = 0.35-0.59) and ICC = 0.22 (95% CI = 0.06-0.36), which was comparable to that of networks intrinsic connectivity. Phase encoding direction reliability for the FSA was ICC = 0.51 (95% CI = 0.42-0.59), generally lower than for networks intrinsic connectivity. By increasing scan length from 2 to 10 min, diagnostic classification of the FSA increased from AUC = 71.7% (95% CI = 63.1-80.3%) to 75.4% (95% CI = 67.0-83.3%) and phase encoding direction reliability from ICC = 0.29 (95% CI = 0.14-0.43) to ICC = 0.51 (95% CI = 0.42-0.59). FSA scores did not correlate with symptom improvement. These results reassure that the FSA is a generalizable diagnostic - but not prognostic - biomarker. Given the replicable results of the FSA as a diagnostic biomarker trained on case-control datasets, next the development of prognostic biomarkers should be on treatment-response data.