Machine Learning-based Cerebral Venous Thrombosis Diagnosis with Clinical Data.

OBJECTIVES: Cerebral Venous Thrombosis (CVT) poses diagnostic challenges due to the variability in disease course and symptoms. The prognosis of CVT relies on early diagnosis. Our study focuses on developing a machine learning-based screening algorithm using clinical data from a large neurology referral center in southern Iran. METHODS: The Iran Cerebral Venous Thrombosis Registry (ICVTR code: 9001013381) provided data on 382 CVT cases from Namazi Hospital. The control group comprised of adult headache patients without CVT as confirmed by neuroimaging and was retrospectively selected from those admitted to the same hospital. We collected 60 clinical and demographic features for model development and validation. Our modeling pipeline involved imputing missing values and evaluating four machine learning algorithms: generalized linear model, random forest, support vector machine, and extreme gradient boosting. RESULTS: A total of 314 CVT cases and 575 controls were included. The highest AUROC was reached when imputation was used to estimate missing values for all the variables, combined with the support vector machine model (AUROC=0.910, Recall=0.73, Precision=0.88). The best recall was achieved also by the support vector machine model when only variables with less than 50% missing rate were included (AUROC=0.887, Recall=0.77, Precision=0.86). The random forest model yielded the best precision by using variables with less than 50% missing rate (AUROC=0.882, Recall=0.61, Precision=0.94). CONCLUSION: The application of machine learning techniques using clinical data showed promising results in accurately diagnosing CVT within our study population. This approach offers a valuable complementary assistive tool or an alternative to resource-intensive imaging methods.

Automated detection of early signs of irreversible ischemic change on CTA source images in patients with large vessel occlusion.

PURPOSE: To create and validate an automated pipeline for detection of early signs of irreversible ischemic change from admission CTA in patients with large vessel occlusion (LVO) stroke. METHODS: We retrospectively included 368 patients for training and 143 for external validation. All patients had anterior circulation LVO stroke, endovascular therapy with successful reperfusion, and follow-up diffusion-weighted imaging (DWI). We devised a pipeline to automatically segment Alberta Stroke Program Early CT Score (ASPECTS) regions and extracted their relative Hounsfield unit (rHU) values. We determined the optimal rHU cut points for prediction of final infarction in each ASPECT region, performed 10-fold cross-validation in the training set, and measured the performance via external validation in patients from another institute. We compared the model with an expert neuroradiologist for prediction of final infarct volume and poor functional outcome. RESULTS: We achieved a mean area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity of 0.69±0.13, 0.69±0.09, 0.61±0.23, and 0.72±0.11 across all regions and folds in cross-validation. In the external validation cohort, we achieved a median [interquartile] AUC, accuracy, sensitivity, and specificity of 0.71 [0.68-0.72], 0.70 [0.68-0.73], 0.55 [0.50-0.63], and 0.74 [0.73-0.77], respectively. The rHU-based ASPECTS showed significant correlation with DWI-based ASPECTS (rS = 0.39, p<0.001) and final infarct volume (rS = -0.36, p<0.001). The AUC for predicting poor functional outcome was 0.66 (95%CI: 0.57-0.75). The predictive capabilities of rHU-based ASPECTS were not significantly different from the neuroradiologist's visual ASPECTS for either final infarct volume or functional outcome. CONCLUSIONS: Our study demonstrates the feasibility of an automated pipeline and predictive model based on relative HU attenuation of ASPECTS regions on baseline CTA and its non-inferior performance in predicting final infarction on post-stroke DWI compared to an expert human reader.

Comparative analysis of machine learning versus traditional method for early detection of parental depression symptoms in the NICU.

Introduction: Neonatal intensive care unit (NICU) admission is a stressful experience for parents. NICU parents are twice at risk of depression symptoms compared to the general birthing population. Parental mental health problems have harmful long-term effects on both parents and infants. Timely screening and treatment can reduce these negative consequences. Objective: Our objective is to compare the performance of the traditional logistic regression with other machine learning (ML) models in identifying parents who are more likely to have depression symptoms to prioritize screening of at-risk parents. We used data obtained from parents of infants discharged from the NICU at Children's National Hospital (n = 300) from 2016 to 2017. This dataset includes a comprehensive list of demographic characteristics, depression and stress symptoms, social support, and parent/infant factors. Study design: Our study design optimized eight ML algorithms - Logistic Regression, Support Vector Machine, Decision Tree, Random Forest, XGBoost, Naïve Bayes, K-Nearest Neighbor, and Artificial Neural Network - to identify the main risk factors associated with parental depression. We compared models based on the area under the receiver operating characteristic curve (AUC), positive predicted value (PPV), sensitivity, and F-score. Results: The results showed that all eight models achieved an AUC above 0.8, suggesting that the logistic regression-based model's performance is comparable to other common ML models. Conclusion: Logistic regression is effective in identifying parents at risk of depression for targeted screening with a performance comparable to common ML-based models.

Machine Learning-Based Prediction of Stroke in Emergency Departments.

Background: Stroke misdiagnosis, associated with poor outcomes, is estimated to occur in 9% of all stroke patients. Objectives: We hypothesized that machine learning (ML) could assist in the diagnosis of ischemic stroke in emergency departments (EDs). Design: The study was conducted and reported according to the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis guidelines. We performed model development and prospective temporal validation, using data from pre- and post-COVID periods; we also performed a case study on a small cohort of previously misdiagnosed stroke patients. Methods: We used structured and unstructured electronic health records (EHRs) of 56,452 patient encounters from 13 hospitals in Pennsylvania, from September 2003 to January 2021. ML pipelines, including natural language processing, were created using pre-event clinical data and provider notes in the EDs. Results: Using pre-event information, our model's area under the receiver operating characteristics curve (AUROC) ranged from 0.88 to 0.92 with a similar range accuracy (0.87-0.90). Using provider notes, we identified five models that reached a balanced performance in terms of AUROC, sensitivity, and specificity. Model AUROC ranged from 0.93 to 0.99. Model sensitivity and specificity reached 0.90 and 0.99, respectively. Four of the top five performing models were based on the post-COVID provider notes; however, no performance difference between models tested on pre- and post-COVID was observed. Conclusion: This study leveraged pre-event and at-encounter level EHR for stroke prediction. The results indicate that available clinical information can be used for building EHR-based stroke prediction models and ED stroke alert systems.

Many Models, Little Adoption-What Accounts for Low Uptake of Machine Learning Models for Atrial Fibrillation Prediction and Detection?

(1) Background: Atrial fibrillation (AF) is a major risk factor for stroke and is often underdiagnosed, despite being present in 13-26% of ischemic stroke patients. Recently, a significant number of machine learning (ML)-based models have been proposed for AF prediction and detection for primary and secondary stroke prevention. However, clinical translation of these technological innovations to close the AF care gap has been scant. Herein, we sought to systematically examine studies, employing ML models to predict incident AF in a population without prior AF or to detect paroxysmal AF in stroke cohorts to identify key reasons for the lack of translation into the clinical workflow. We conclude with a set of recommendations to improve the clinical translatability of ML-based models for AF. (2) Methods: MEDLINE, Embase, Web of Science, Clinicaltrials.gov, and ICTRP databases were searched for relevant articles from the inception of the databases up to September 2022 to identify peer-reviewed articles in English that used ML methods to predict incident AF or detect AF after stroke and reported adequate performance metrics. The search yielded 2815 articles, of which 16 studies using ML models to predict incident AF and three studies focusing on ML models to detect AF post-stroke were included. (3) Conclusions: This study highlights that (1) many models utilized only a limited subset of variables available from patients' health records; (2) only 37% of models were externally validated, and stratified analysis was often lacking; (3) 0% of models and 53% of datasets were explicitly made available, limiting reproducibility and transparency; and (4) data pre-processing did not include bias mitigation and sufficient details, leading to potential selection bias. Low generalizability, high false alarm rate, and lack of interpretability were identified as additional factors to be addressed before ML models can be widely deployed in the clinical care setting. Given these limitations, our recommendations to improve the uptake of ML models for better AF outcomes include improving generalizability, reducing potential systemic biases, and investing in external validation studies whilst developing a transparent modeling pipeline to ensure reproducibility.

Development and internal validation of machine learning-based models and external validation of existing risk scores for outcome prediction in patients with ischaemic stroke.

Aims: We developed new machine learning (ML) models and externally validated existing statistical models [ischaemic stroke predictive risk score (iScore) and totalled health risks in vascular events (THRIVE) scores] for predicting the composite of recurrent stroke or all-cause mortality at 90 days and at 3 years after hospitalization for first acute ischaemic stroke (AIS). Methods and results: In adults hospitalized with AIS from January 2005 to November 2016, with follow-up until November 2019, we developed three ML models [random forest (RF), support vector machine (SVM), and extreme gradient boosting (XGBOOST)] and externally validated the iScore and THRIVE scores for predicting the composite outcomes after AIS hospitalization, using data from 721 patients and 90 potential predictor variables. At 90 days and 3 years, 11 and 34% of patients, respectively, reached the composite outcome. For the 90-day prediction, the area under the receiver operating characteristic curve (AUC) was 0.779 for RF, 0.771 for SVM, 0.772 for XGBOOST, 0.720 for iScore, and 0.664 for THRIVE. For 3-year prediction, the AUC was 0.743 for RF, 0.777 for SVM, 0.773 for XGBOOST, 0.710 for iScore, and 0.675 for THRIVE. Conclusion: The study provided three ML-based predictive models that achieved good discrimination and clinical usefulness in outcome prediction after AIS and broadened the application of the iScore and THRIVE scoring system for long-term outcome prediction. Our findings warrant comparative analyses of ML and existing statistical method-based risk prediction tools for outcome prediction after AIS in new data sets.

Prevalence and Determinants of Long-Term Post-COVID Conditions in the United States: 2022 Behavioral Risk Factor Surveillance System.

BACKGROUND: A significant proportion of COVID survivors experience lingering and debilitating symptoms following acute COVID-19 infection. According to the national research plan on long COVID, it is a national priority to identify the prevalence of post-COVID conditions and their associated factors. METHOD: We performed a cross-sectional analysis of the Prevention Behavioral Risk Factor Surveillance System (BRFSS) 2022, the largest continuously gathered health survey dataset worldwide by the Centers for Disease Control. After identifying individuals with a positive history of COVID-19, we grouped COVID-19 survivors based on whether they experienced long-term post-COVID conditions. Using survey-specific R packages, we compared the two groups' socio-demographics, comorbidities, and lifestyle-related factors. A logistic regression model was used to identify factors associated with post-COVID conditions. RESULTS: The overall estimated prevalence of long-term post-COVID conditions among COVID survivors was 21.7%. Fatigue (5.7%), dyspnea (4.2%), and anosmia/ageusia (3.8%) were the most frequent symptoms. Based on multivariate logistic regression analysis, female sex, body mass index (BMI)≥25, lack of insurance, history of pulmonary disease, depression, and arthritis, being a former smoker, and sleep duration <7 h/d were associated with higher odds of post-COVID conditions. On the other hand, age >64 y/o, Black race, and annual household income ≥$100k were associated with lower odds of post-COVID conditions. CONCLUSION: Our findings indicate a notable prevalence of post-COVID conditions, particularly among middle-aged women and individuals with comorbidities or adverse lifestyles. This high-risk demographic may require long-term follow-up and support. Further investigations are essential to facilitate the development of specified healthcare and therapeutic strategies for those suffering from post-COVID conditions.

Prevalence and associated factors of cerebral microbleeds in a rural population of the United States.

OBJECTIVE: Cerebral microbleeds (CMBs) can carry an advanced risk for the development and burden of cerebrovascular and cognitive disorders. Large-scale population-based studies are required to identify the at-risk population. METHOD: Ten percent (N = 3,056) of the Geisinger DiscovEHR Initiative Cohort participants who had brain magnetic resonance imaging (MRI) for any indication were randomly selected. Patients with CMBs were compared to an age-, gender-, body mass index-, and hypertension-matched cohort of patients without CMB. The prevalence of comorbidities and use of anticoagulation therapy was investigated in association with CMB presence (binary logistic regression), quantity (ordinal regression), and topography (multinomial regression). RESULTS: Among 3,056 selected participants, 477 (15.6 %) had CMBs in their MRI. Patients with CMBs were older and were more prevalently hypertensive, with ischemic stroke, arrhythmia, dyslipidemia, coronary artery disease, and the use of warfarin. After propensity-score matching, 477 patients with CMBs and 974 without were included for further analyses. Predictors of ≥5 CMBs were ischemic stroke (OR, 1.6; 95 % CI, 1.2 -2.0), peripheral vascular disease (OR, 1.6; 95 % CI, 1.1-2.3), and thrombocytopenia (OR, 1.9; 95 % CI, 1.2-2.9). Ischemic stroke was associated with strictly lobar CMBs more strongly than deep/infra-tentorial CMBs (OR, 2.1; 95 % CI, 1.5-3.1; vs. OR, 1.4; CI, 1.1-1.8). CONCLUSIONS: CMBs were prevalent in our white population. Old age, hypertension, anticoagulant treatment, thrombocytopenia, and a history of vascular diseases including stroke, were associated with CMBs.

An integrated pipeline for prediction of Clostridioides difficile infection.

With the expansion of electronic health records(EHR)-linked genomic data comes the development of machine learning-enable models. There is a pressing need to develop robust pipelines to evaluate the performance of integrated models and minimize systemic bias. We developed a prediction model of symptomatic Clostridioides difficile infection(CDI) by integrating common EHR-based and genetic risk factors(rs2227306/IL8). Our pipeline includes (1) leveraging phenotyping algorithm to minimize temporal bias, (2) performing simulation studies to determine the predictive power in samples without genetic information, (3) propensity score matching to control for the confoundings, (4) selecting machine learning algorithms to capture complex feature interactions, (5) performing oversampling to address data imbalance, and (6) optimizing models and ensuring proper bias-variance trade-off. We evaluate the performance of prediction models of CDI when including common clinical risk factors and the benefit of incorporating genetic feature(s) into the models. We emphasize the importance of building a robust integrated pipeline to avoid systemic bias and thoroughly evaluating genetic features when integrated into the prediction models in the general population and subgroups.

The Phenotypic Spectrum of COL4A3 Heterozygotes.

Introduction: The penetrance and phenotypic spectrum of autosomal dominant Alport Syndrome (ADAS), affecting 1 in 106, remains understudied. Methods: Using data from 174,418 participants in the Geisinger MyCode/DiscovEHR study, an unselected health system-based cohort with whole exome sequencing, we identified 403 participants who were heterozygous for likely pathogenic COL4A3 variants. Phenotypic data was evaluated using International Classification of Diseases (ICD) codes, laboratory data, and chart review. To evaluate the phenotypic spectrum of genetically-determined ADAS, we matched COL4A3 heterozygotes 1:5 to nonheterozygotes using propensity scores by demographics, hypertension, diabetes, and nephrolithiasis. Results: COL4A3 heterozygotes were at significantly increased risks of hematuria, decreased estimated glomerular filtration rate (eGFR), albuminuria, and kidney failure (P < 0.05 for all comparisons) but not bilateral sensorineural hearing loss (P = 0.9). Phenotypic severity was more severe for collagenous domain glycine missense variants than protein truncating variants (PTVs). For example, patients with Gly695Arg (n = 161) had markedly increased risk of dipstick hematuria (odds ratio [OR] 9.50; 95% confidence interval [CI]: 6.32, 14.28) and kidney failure (OR 7.02; 95% CI: 3.48, 14.16) whereas those with PTVs (n = 119) had moderately increased risks of dipstick hematuria (OR 1.64; 95% CI: 1.03, 2.59) and kidney failure (OR 3.44; 95% CI: 1.28, 9.22). Less than a third of patients had albuminuria screening completed, and fewer than 1 of 3 were taking inhibitors of the renin-angiotensin-aldosterone system. Conclusion: This study demonstrates a wide spectrum of phenotypic severity in ADAS due to COL4A3 with phenotypic variability by genotype. Future studies are needed to evaluate the impact of earlier diagnosis, appropriate evaluation, and treatment of ADAS.

Cysteine-Altering NOTCH3 Variants Are Associated with an Increased Risk of Autoimmune Diseases.

Autoimmune conditions have been reported among patients with cysteine-altering NOTCH3 variants and CADASIL. This study aimed to investigate the occurrence of autoimmune illnesses and markers of inflammation in such populations. Cases were identified who had a NOTCH3 cysteine-altering variant from the Geisinger MyCode® Community Health Initiative (MyCode®). We further performed external validation using the UK Biobank cohort. A cohort of 121 individuals with a NOTCH3 cysteine-altering variant from MyCode® was compared to a control group with no non-synonymous variation in NOTCH3 (n = 184). Medical records were evaluated for inflammatory markers and autoimmune conditions, which were grouped by the organ systems involved. A similar analysis was conducted using data from the UK Biobank (n~450,000). An overall increase in inflammatory markers among participants with a NOTCH3 cysteine-altering variant was observed when compared to an age- and sex-matched MyCode® control group (out of participants with laboratory testing: 50.9% versus 26.7%; p = 0.0047; out of total participants: 23.1% versus 10.9%; p = 0.004). Analysis of UK Biobank data indicated any autoimmune diagnosis (1.63 [1.14, 2.09], p= 2.665 × 10-3) and multiple sclerosis (3.42 [1.67, 6.02], p = 9.681 × 10-4) are associated with a NOTCH3 cysteine-altering variant in any domain. Our findings suggest a possible association between NOTCH3 cysteine-altering variants and autoimmune conditions.

Transient Ischemic Attack Outpatient Clinic: Past Journey and Future Adventure.

A transient ischemic attack (TIA), a constellation of temporary neurological symptoms, precedes stroke in one-fifth of patients. Thus far, many clinical models have been introduced to optimize the quality, time to treatment, and cost of acute TIA care, either in an inpatient or outpatient setting. In this article, we aim to review the characteristics and outcomes of outpatient TIA clinics across the globe. In addition, we discussed the main challenges for outpatient management of TIA, including triage and diagnosis, and the system dynamics of the clinics. We further reviewed the potential developments in TIA care, such as telemedicine, predictive analytics, personalized medicine, and advanced imaging.

The Phenotypic Spectrum of COL4A3 Heterozygotes.

Most data on Alport Syndrome (AS) due to COL4A3 are limited to families with autosomal recessive AS or severe manifestations such as focal segmental glomerulosclerosis (FSGS). Using data from 174,418 participants in the Geisinger MyCode/DiscovEHR study, an unselected health system-based cohort with whole exome sequencing, we identified 403 participants (0.2%) who were heterozygous for likely pathogenic COL4A3 variants. Phenotypic data was evaluated using International Classification of Diseases (ICD) codes, laboratory data, and chart review. To evaluate the phenotypic spectrum of genetically-determined autosomal dominant AS, we matched COL4A3 heterozygotes 1:5 to non-heterozygotes using propensity scores by demographics, hypertension, diabetes, and nephrolithiasis. COL4A3 heterozygotes were at significantly increased risks of hematuria, decreased estimated glomerular filtration rate (eGFR), albuminuria, and end-stage kidney disease (ESKD) (p<0.05 for all comparisons) but not bilateral sensorineural hearing loss (p=0.9). Phenotypic severity tended to be more severe among patients with glycine missense variants located within the collagenous domain. For example, patients with Gly695Arg (n=161) had markedly increased risk of dipstick hematuria (OR 9.47, 95% CI: 6.30, 14.22) and ESKD diagnosis (OR 7.01, 95% CI: 3.48, 14.12) whereas those with PTVs (n=119) had moderately increased risks of dipstick hematuria (OR 1.63, 95% CI: 1.03, 2.58) and ESKD diagnosis (OR 3.43, 95% CI: 1.28, 9.19). Less than a third of patients had albuminuria screening completed, and fewer than 1/3 were taking inhibitors of the renin-angiotensin-aldosterone system (RAASi). Future studies are needed to evaluate the impact of earlier diagnosis, appropriate evaluation, and treatment of ADAS.

Defining the Age of Young Ischemic Stroke Using Data-Driven Approaches.

Introduction: The cut-point for defining the age of young ischemic stroke (IS) is clinically and epidemiologically important, yet it is arbitrary and differs across studies. In this study, we leveraged electronic health records (EHRs) and data science techniques to estimate an optimal cut-point for defining the age of young IS. Methods: Patient-level EHRs were extracted from 13 hospitals in Pennsylvania, and used in two parallel approaches. The first approach included ICD9/10, from IS patients to group comorbidities, and computed similarity scores between every patient pair. We determined the optimal age of young IS by analyzing the trend of patient similarity with respect to their clinical profile for different ages of index IS. The second approach used the IS cohort and control (without IS), and built three sets of machine-learning models-generalized linear regression (GLM), random forest (RF), and XGBoost (XGB)-to classify patients for seventeen age groups. After extracting feature importance from the models, we determined the optimal age of young IS by analyzing the pattern of comorbidity with respect to the age of index IS. Both approaches were completed separately for male and female patients. Results: The stroke cohort contained 7555 ISs, and the control included 31,067 patients. In the first approach, the optimal age of young stroke was 53.7 and 51.0 years in female and male patients, respectively. In the second approach, we created 102 models, based on three algorithms, 17 age brackets, and two sexes. The optimal age was 53 (GLM), 52 (RF), and 54 (XGB) for female, and 52 (GLM and RF) and 53 (RF) for male patients. Different age and sex groups exhibited different comorbidity patterns. Discussion: Using a data-driven approach, we determined the age of young stroke to be 54 years for women and 52 years for men in our mainly rural population, in central Pennsylvania. Future validation studies should include more diverse populations.

An updated review and meta-analysis of screening tools for stroke in the emergency room and prehospital setting.

BACKGROUND: Stroke screening tools should have good diagnostic performance for early diagnosis and a proper therapeutic plan. This paper describes and compares various diagnostic tools used to identify stroke in emergency departments and prehospital setting. METHODS: The meta-analysis was conducted according to the Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies (PRISMA-DTA) guidelines. The PubMed and Scopus databases were searched until December 31, 2021, for studies published on stroke screening tools. These tools' diagnostic performance (sensitivity and specificity) was pooled using a bivariate random-effects model whenever appropriate. RESULTS: Eleven screening tools for stroke were identified in 29 different studies. The various tools had a wide range of sensitivity and specificity in different studies. In the meta-analysis, the Cincinnati Pre-hospital Stroke Scale, Face Arm Speech Test, and Recognition of Stroke in the Emergency Room (ROSIER) had sensitivity (between 83 and 91%) but poor specificity (all below 64%). When comparing all the tools, ROSIER had the highest sensitivity 90.5%. Los Angeles Pre-hospital Stroke Screen performed best in terms of specificity 88.7% but had low sensitivity (73.9%). Melbourne Ambulance Stroke Screen had a balanced performance in terms of sensitivity (86%) and specificity (76%). Sensitivity analysis consisting of only prospective studies showed a similar range of sensitivity and specificity. CONCLUSION: All the stroke screening tools included in the review were comparable, but no clear superior screening tool could be identified. Simple screening tools like Cincinnati prehospital stroke scale (CPSS) have similar performance compared to more complex tools.

A Simple Review of Small Vessel Disease Manifestation in the Brain, Retina, and Kidneys.

Small blood vessels express specific phenotypical and functional characteristics throughout the body. Alterations in the microcirculation contribute to many correlated physiological and pathological events in related organs. Factors such as comorbidities and genetics contribute to the complexity of this topic. Small vessel disease primarily affects end organs that receive significant cardiac output, such as the brain, kidney, and retina. Despite the differences in location, concurrent changes are seen in the micro-vasculature of the brain, retina, and kidneys under pathological conditions due to their common histological, functional, and embryological characteristics. While the cardiovascular basis of pathology in association with the brain, retina, or kidneys has been well documented, this is a simple review that uniquely considers the relationship between all three organs and highlights the prevalence of coexisting end organ injuries in an attempt to elucidate connections between the brain, retina, and kidneys, which has the potential to transform diagnostic and therapeutic approaches.

Dissecting Polygenic Etiology of Ischemic Stroke in the Era of Precision Medicine.

Ischemic stroke (IS), the leading cause of death and disability worldwide, is caused by many modifiable and non-modifiable risk factors. This complex disease is also known for its multiple etiologies with moderate heritability. Polygenic risk scores (PRSs), which have been used to establish a common genetic basis for IS, may contribute to IS risk stratification for disease/outcome prediction and personalized management. Statistical modeling and machine learning algorithms have contributed significantly to this field. For instance, multiple algorithms have been successfully applied to PRS construction and integration of genetic and non-genetic features for outcome prediction to aid in risk stratification for personalized management and prevention measures. PRS derived from variants with effect size estimated based on the summary statistics of a specific subtype shows a stronger association with the matched subtype. The disruption of the extracellular matrix and amyloidosis account for the pathogenesis of cerebral small vessel disease (CSVD). Pathway-specific PRS analyses confirm known and identify novel etiologies related to IS. Some of these specific PRSs (e.g., derived from endothelial cell apoptosis pathway) individually contribute to post-IS mortality and, together with clinical risk factors, better predict post-IS mortality. In this review, we summarize the genetic basis of IS, emphasizing the application of methodologies and algorithms used to construct PRSs and integrate genetics into risk models.

Contribution of Common Genetic Variants to Risk of Early Onset Ischemic Stroke.

BACKGROUND AND OBJECTIVES: Current genome-wide association studies of ischemic stroke have focused primarily on late onset disease. As a complement to these studies, we sought to identifythe contribution of common genetic variants to risk of early onset ischemic stroke. METHODS: We performed a meta-analysis of genome-wide association studies of early onset stroke (EOS), ages 18-59, using individual level data or summary statistics in 16,730 cases and 599,237 non-stroke controls obtained across 48 different studies. We further compared effect sizes at associated loci between EOS and late onset stroke (LOS) and compared polygenic risk scores for venous thromboembolism between EOS and LOS. RESULTS: We observed genome-wide significant associations of EOS with two variants in ABO, a known stroke locus. These variants tag blood subgroups O1 and A1, and the effect sizes of both variants were significantly larger in EOS compared to LOS. The odds ratio (OR) for rs529565, tagging O1, 0.88 (95% CI: 0.85-0.91) in EOS vs 0.96 (95% CI: 0.92-1.00) in LOS, and the OR for rs635634, tagging A1, was 1.16 (1.11-1.21) for EOS vs 1.05 (0.99-1.11) in LOS; p-values for interaction = 0.001 and 0.005, respectively. Using polygenic risk scores, we observed that greater genetic risk for venous thromboembolism, another prothrombotic condition, was more strongly associated with EOS compared to LOS (p=0.008). DISCUSSION: The ABO locus, genetically predicted blood group A, and higher genetic propensity for venous thrombosis are more strongly associated with EOS than with LOS, supporting a stronger role of prothrombotic factors in EOS.

Stroke genetics informs drug discovery and risk prediction across ancestries.

Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries.