Linkage of whole genome sequencing with administrative health, and electronic medical record data for the study of autism spectrum disorder: Feasibility, Opportunities and Challenges

Introduction Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder (NDD) that presents with a high degree of heterogeneity (e.g., co-occurrence of other NDDs and other co-morbid conditions), contributing to differential health system needs. Genetics are known to play an important role in ASD and may be associated with different disease trajectories. Objectives and Approach In this proof of principle project, our objective is to link >2,200 children with a confirmed diagnosis of a NDD from the Province of Ontario Neurodevelopmental (POND) Study to administrative health data and electronic medical record (EMR) data in order to identify subgroups of ASD with unique health system trajectories. POND includes detailed phenotype and whole genome sequencing (WGS) data. Identified subgroups will be characterized based on clinical phenotype and genetics. To meet this goal, consideration of WGS-specific privacy and data issues is needed to implement processes which are above and beyond traditional requirements for analyzing individual-level administrative health data. Results Linkage of WGS data with administrative health data is an emerging area of research. As such it has presented a number of initial challenges for our study of ASD. Privacy concerns surrounding the use of WGS data and rare-variant analysis are of particular importance. Practical issues required the need for analysts with expertise in administrative data, EMR data and genetic analyses, and specialized software and sufficient processing power to analyze WGS data. Transdisciplinary discussions of the scope and significance of research questions addressed through this linkage were crucial. The identification of genetic determinants of phenotypes and trajectories in ASD could support targeted early interventions; EMR linkage may inform algorithms to identify ASD in broader populations. These approaches could improve both patient outcome and family experience. Conclusion/Implications As the cost of genetic sequencing decreases, WGS data will become part of the routine clinical management of patients. Linkage of WGS, EMR and administrative data has tremendous potential that has largely not been realized; including population-level ASD research to improve our ability to predict long-term outcomes associated with ASD

Validating a novel deterministic privacy-preserving record linkage between administrative & clinical data: applications in stroke research

Introduction Research data combined with administrative data provides a robust resource capable of answering unique research questions. However, in cases where personal health data are encrypted, due to ethics requirements or institutional restrictions, traditional methods of deterministic and probabilistic record linkages are not feasible. Instead, privacy-preserving record linkages must be used to protect patients' personal data during data linkage. Objectives To determine the feasibility and validity of a deterministic privacy preserving data linkage protocol using homomorphically encrypted data. Methods Feasibility was measured by the number of records that successfully matched via direct identifiers. Validity was measured by the number of records that matched with multiple indirect identifiers. The threshold for feasibility and validity were both set at 95%. The datasets shared a single, direct identifier (health card number) and multiple indirect identifiers (sex and date of birth). Direct identifiers were encrypted in both datasets and then transferred to a third-party server capable of linking the encrypted identifiers without decrypting individual records. Once linked, the study team used indirect identifiers to verify the accuracy of the linkage in the final dataset. Results With a combination of manual and automated data transfer in a sample of 8,128 individuals, the privacy-preserving data linkage took 36 days to match to a population sample of over 3.2 million records. 99.9% of the records were successfully matched with direct identifiers, and 99.8% successfully matched with multiple indirect identifiers. We deemed the linkage both feasible and valid. Conclusions As combining administrative and research data becomes increasingly common, it is imperative to understand options for linking data when direct linkage is not feasible. The current linkage process ensured the privacy and security of patient data and improved data quality. While the initial implementations required significant computational and human resources, increased automation keeps the requirements within feasible bounds

Harmonizing data on correlates of sleep in children within and across neurodevelopmental disorders: lessons learned from an Ontario Brain Institute cross-program collaboration

There is an increasing desire to study neurodevelopmental disorders (NDDs) together to understand commonalities to develop generic health promotion strategies and improve clinical treatment. Common data elements (CDEs) collected across studies involving children with NDDs afford an opportunity to answer clinically meaningful questions. We undertook a retrospective, secondary analysis of data pertaining to sleep in children with different NDDs collected through various research studies. The objective of this paper is to share lessons learned for data management, collation, and harmonization from a sleep study in children within and across NDDs from large, collaborative research networks in the Ontario Brain Institute (OBI). Three collaborative research networks contributed demographic data and data pertaining to sleep, internalizing symptoms, health-related quality of life, and severity of disorder for children with six different NDDs: autism spectrum disorder; attention deficit/hyperactivity disorder; obsessive compulsive disorder; intellectual disability; cerebral palsy; and epilepsy. Procedures for data harmonization, derivations, and merging were shared and examples pertaining to severity of disorder and sleep disturbances were described in detail. Important lessons emerged from data harmonizing procedures: prioritizing the collection of CDEs to ensure data completeness; ensuring unprocessed data are uploaded for harmonization in order to facilitate timely analytic procedures; the value of maintaining variable naming that is consistent with data dictionaries at time of project validation; and the value of regular meetings with the research networks to discuss and overcome challenges with data harmonization. Buy-in from all research networks involved at study inception and oversight from a centralized infrastructure (OBI) identified the importance of collaboration to collect CDEs and facilitate data harmonization to improve outcomes for children with NDDs

Local Suppression of T Cell Responses by Arginase-Induced L-Arginine Depletion in Nonhealing Leishmaniasis

The balance between T helper (Th) 1 and Th2 cell responses is a major determinant of the outcome of experimental leishmaniasis, but polarized Th1 or Th2 responses are not sufficient to account for healing or nonhealing. Here we show that high arginase activity, a hallmark of nonhealing disease, is primarily expressed locally at the site of pathology. The high arginase activity causes local depletion of L-arginine, which impairs the capacity of T cells in the lesion to proliferate and to produce interferon-γ, while T cells in the local draining lymph nodes respond normally. Healing, induced by chemotherapy, resulted in control of arginase activity and reversal of local immunosuppression. Moreover, competitive inhibition of arginase as well as supplementation with L-arginine restored T cell effector functions and reduced pathology and parasite growth at the site of lesions. These results demonstrate that in nonhealing leishmaniasis, arginase-induced L-arginine depletion results in impaired T cell responses. Our results identify a novel mechanism in leishmaniasis that contributes to the failure to heal persistent lesions and suggest new approaches to therapy

The Effect of a Ketogenic Diet in the Treatment of Succinic Semialdehyde Dehydrogenase Deficiency in Mice

Succinic semialdehyde dehydrogenase (ALDH5A1) deficiency (SSADH-d) is an autosomal recessive, inborn error of gamma-aminobutyric acid (GABA) metabolism that results in psychomotor retardation, ataxia and seizures. A mouse model of SSADH-d (the Aldh5a1-/- mouse) was created to study the pathophysiology and treatment of SSADH-d. Aldh5a1-/- mice have psychomotor retardation and a progressive seizure phenotype results in death around P25. The present experiments tested the effects of a ketogenic diet in the treatment of Aldh5a1-/- mice. The KD was found to prolong the lives of Aldh5a1-/- mice by >300% while significantly delaying the onset the ataxia and preventing weight loss that is seen in untreated Aldh5a1-/- mice. Electrophysiological recordings revealed a corresponding decrease in seizures in KD fed mutants, as compared to control diet (CD) fed mutants. We assessed spontaneous miniature postsynaptic currents (mPSC) in CD and KD fed mutants. We found that CD fed mutants had significantly decreased inhibitory mPSC (mIPSC) activity compared to CD fed wildtype controls. mIPSC activity was restored in KD fed Aldh5a1-/- mice. A similar effect was found in [35S]TBPS binding experiments. TBPS binding was significantly reduced in CD fed Aldh5a1-/- mice, but restored in KD fed mutants. Plasma analysis revealed that an elevation of serum beta-hydroxybutyrate may play a role in the KD’s effects. The KD led to a significant elevation in the number of hippocampal mitochondria in mutant mice. Further, the KD was able to normalize the deficiencies in the hippocampal ATP levels seen in the Aldh5a1-/- mice. The present data suggest that the KD is able to significantly improve the Aldh5a1-/- phenotype. The effect of the KD on mIPSC activity is novel and furthers our understanding of how the KD may exert its effects. The mitochondrial studies confirm the findings of others, that the KD elevates the number of mitochondria. The KD also restores ATP deficiencies in Aldh5a1-/- mice, which is a novel finding. Together, these show that the KD may be an effective treatment for SSADH-d in humans. These data also further our understanding of the KD’s mechanisms of action.Ph

FAIR in action: Brain-CODE - A neuroscience data sharing platform to accelerate brain research

The effective sharing of health research data within the healthcare ecosystem can have tremendous impact on the advancement of disease understanding, prevention, treatment, and monitoring. By combining and reusing health research data, increasingly rich insights can be made about patients and populations that feed back into the health system resulting in more effective best practices and better patient outcomes. To achieve the promise of a learning health system, data needs to meet the FAIR principles of findability, accessibility, interoperability, and reusability. Since the inception of the Brain-CODE platform and services in 2012, the Ontario Brain Institute (OBI) has pioneered data sharing activities aligned with FAIR principles in neuroscience. Here, we describe how Brain-CODE has operationalized data sharing according to the FAIR principles. Findable—Brain-CODE offers an interactive and itemized approach for requesters to generate data cuts of interest that align with their research questions. Accessible—Brain-CODE offers multiple data access mechanisms. These mechanisms—that distinguish between metadata access, data access within a secure computing environment on Brain-CODE and data access via export will be discussed. Interoperable—Standardization happens at the data capture level and the data release stage to allow integration with similar data elements. Reusable - Brain-CODE implements several quality assurances measures and controls to maximize data value for reusability. We will highlight the successes and challenges of a FAIR-focused neuroinformatics platform that facilitates the widespread collection and sharing of neuroscience research data for learning health systems

Formulation of evidence-based messages to promote the use of physical activity to prevent and manage Alzheimer’s disease

Background: The impending public health impact of Alzheimer’s disease is tremendous. Physical activity is a promising intervention for preventing and managing Alzheimer’s disease. However, there is a lack of evidence-based public health messaging to support this position. This paper describes the application of the Appraisal of Guidelines Research and Evaluation II (AGREE-II) principles to formulate an evidence-based message to promote physical activity for the purposes of preventing and managing Alzheimer’s disease. Methods A messaging statement was developed using the AGREE-II instrument as guidance. Methods included (a) conducting a systematic review of reviews summarizing research on physical activity to prevent and manage Alzheimer’s disease, and (b) engaging stakeholders to deliberate the evidence and formulate the messaging statement. Results The evidence base consisted of seven systematic reviews focused on Alzheimer’s disease prevention and 20 reviews focused on symptom management. Virtually all of the reviews of symptom management conflated patients with Alzheimer’s disease and patients with other dementias, and this limitation was reflected in the second part of the messaging statement. After deliberating the evidence base, an expert panel achieved consensus on the following statement: “Regular participation in physical activity is associated with a reduced risk of developing Alzheimer’s disease. Among older adults with Alzheimer’s disease and other dementias, regular physical activity can improve performance of activities of daily living and mobility, and may improve general cognition and balance.” The statement was rated favourably by a sample of older adults and physicians who treat Alzheimer’s disease patients in terms of its appropriateness, utility, and clarity. Conclusion Public health and other organizations that promote physical activity, health and well-being to older adults are encouraged to use the evidence-based statement in their programs and resources. Researchers, clinicians, people with Alzheimer’s disease and caregivers are encouraged to adopt the messaging statement and the recommendations in the companion informational resource.Health and Social Development, Faculty of (Okanagan)Non UBCHealth and Exercise Sciences, School of (Okanagan)ReviewedFacult