Motivation: Identification of structural variants (SVs) in sequence data results in a large number of false positive calls using existing software, which overburdens subsequent validation.
Results: Simulations using RAPTR-SV and other, similar algorithms for SV detection revealed that RAPTR-SV had superior sensitivity and precision, as it recovered 66.4% of simulated tandem duplications with a precision of 99.2%. When compared with calls made by Delly and LUMPY on available datasets from the 1000 genomes project, RAPTR-SV showed superior sensitivity for tandem duplications, as it identified 2-fold more duplications than Delly, while making ∼85% fewer duplication predictions.
Availability And Implementation: RAPTR-SV is written in Java and uses new features in the collections framework in the latest release of the Java version 8 language specifications. A compiled version of the software, instructions for usage and test results files are available on the GitHub repository page: https://github.com/njdbickhart/RAPTR-SV.
Contact: derek.bickhart@ars.usda.gov.
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http://dx.doi.org/10.1093/bioinformatics/btv086 | DOI Listing |
Background: Convergent evidence indicates that deficits in the endosomal recycling pathway underlies pathogenesis of Alzheimer's disease (AD). SORL1 encodes the retromer-associated receptor SORLA that plays an essential role in recycling of AD-associated cargos such as the amyloid precursor protein and the glutamatergic AMPA receptor. Importantly, loss of function pathogenic SORL1 variants are associated with AD.
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Indiana University School of Medicine, Indianapolis, IN, USA.
Background: The goal of the TREAT-AD Center is to enable drug discovery by developing assays and providing tool compounds for novel and emerging targets. The role of microglia in neuroinflammation has been implicated in the pathogenesis of Alzheimer's disease (AD). Genome-wide association studies, whole genome sequencing, and gene-expression network analyses comparing normal to AD brain have identified risk and protective variants in genes essential to microglial function.
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December 2024
University of Sydney, Camperdown, NSW, Australia.
Background: Dementia, including its younger-onset variant, increasingly challenges diverse workplaces, affecting both employees living with dementia and their employers. With a growing global trend of individuals extending their working years, it becomes crucial to understand the specific challenges and implications for those with dementia within various employment contexts. This review delves into the cognitive, interpersonal, and organizational challenges faced by employees living with dementia across a broad range of workplaces, reflecting the evolving dynamics of today's work environment.
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December 2024
Grupo de Neurociencias de Antioquia, Universidad de Antioquia, Medellin, Colombia.
Background: Genetic testing for individuals with dominantly inherited Alzheimer's disease (DIAD) is now of greater relevance due to the existence of therapeutic trials available to this population. However, the impact and main drivers influencing the decision to seek genetic testing are relatively unknown in Latin America (LatAm). Here we present results from a regional genetic counseling and testing protocol implemented in LatAm.
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Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima, Peru.
Background: Frontotemporal dementia (FTD) is a clinical syndrome characterized by progressive changes in behavior, executive function, or language. In Latin America, persons with FTD are underrecognized or diagnosed late. There is a lack of knowledge about the experiences have on families.
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