Arun Ramani
YOU?
Author Swipe
View article: Assessing the diagnostic impact of blood transcriptome profiling in a pediatric cohort previously assessed by genome sequencing
Assessing the diagnostic impact of blood transcriptome profiling in a pediatric cohort previously assessed by genome sequencing Open
Despite advances in genome sequencing, many individuals with rare genetic disorders remain undiagnosed. Transcriptional profiling via RNA-seq can reveal functional impacts of DNA variants and improve diagnosis. We assessed blood-derived RN…
View article: Assessing the diagnostic impact of blood transcriptome profiling in a pediatric cohort previously assessed by genome sequencing
Assessing the diagnostic impact of blood transcriptome profiling in a pediatric cohort previously assessed by genome sequencing Open
Despite advances in diagnostic testing and genome sequencing, the majority of individuals with rare genetic disorders remain undiagnosed. As a complement to genome sequencing, transcriptional profiling can provide insight into the function…
View article: Investigating instructors’ and students’ perceived knowledge and attitudes in using generative AI tools for teaching and learning
Investigating instructors’ and students’ perceived knowledge and attitudes in using generative AI tools for teaching and learning Open
This preliminary study surveys university instructors’ reported experiences of generative artificial intelligence (GenAI) knowledge and attitudes. The collective perceptual information from this study aims to provide the University with in…
View article: Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon
Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon Open
View article: DIPG-86. INVESTIGATING THE TUMOR ENVIRONMENT AND SIGNALING DEPENDENCIES DRIVING DIFFUSE MIDLINE GLIOMA TUMOR INITIATION, PROGRESSION, AND RESISTANCE: A COMPREHENSIVE APPROACH LEVERAGING BULK MULTIOMICS DECONVOLUTION AND SINGLE-CELL OMICS VALIDATION
DIPG-86. INVESTIGATING THE TUMOR ENVIRONMENT AND SIGNALING DEPENDENCIES DRIVING DIFFUSE MIDLINE GLIOMA TUMOR INITIATION, PROGRESSION, AND RESISTANCE: A COMPREHENSIVE APPROACH LEVERAGING BULK MULTIOMICS DECONVOLUTION AND SINGLE-CELL OMICS VALIDATION Open
BACKGROUND Diffuse Midline Glioma (DMG) is a incurable tumor affecting children. Recent genomic investigations have identified a recurrent H3K27M mutation which induces global alterations in histone methylation patterns and DNA methylation…
View article: Clinical Implementation of MetaFusion for Accurate Cancer-Driving Fusion Detection from RNA Sequencing
Clinical Implementation of MetaFusion for Accurate Cancer-Driving Fusion Detection from RNA Sequencing Open
View article: RNAget: an API to securely retrieve RNA quantifications
RNAget: an API to securely retrieve RNA quantifications Open
Summary Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in ma…
View article: The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations
The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations Open
View article: EPCO-17. UNMASKING CLONAL EVOLUTION OF DIFFUSE INTRINSIC GLIOMA USING MULTI-MODAL GENOMIC DATA
EPCO-17. UNMASKING CLONAL EVOLUTION OF DIFFUSE INTRINSIC GLIOMA USING MULTI-MODAL GENOMIC DATA Open
Diffuse intrinsic pontine glioma (DIPG) is an infiltrative incurable tumor affecting children. DIPG tumors often harbor a recurrent H3K27M mutation which leads to a global loss of H3K27me2/3 and overall DNA hypomethylation, suggesting an i…
View article: Conserved transcriptional programming across sex and species after peripheral nerve injury predicts treatments for neuropathic pain
Conserved transcriptional programming across sex and species after peripheral nerve injury predicts treatments for neuropathic pain Open
Background and Purpose: Chronic pain is a devastating problem affecting 1 in 5 individuals around the globe, with neuropathic pain the most debilitating and poorly treated type of chronic pain. Advances in transcriptomics and data mining h…
View article: Genomics4RD: An integrated platform to share Canadian deep-phenotype and multiomic data for international rare disease gene discovery.
Genomics4RD: An integrated platform to share Canadian deep-phenotype and multiomic data for international rare disease gene discovery. Open
Despite recent progress in the understanding of the genetic etiologies of rare diseases (RDs), a significant number remain intractable to diagnostic and discovery efforts. Broad data collection and sharing of information among RD researche…
View article: Conserved transcriptional programming across sex and species after peripheral nerve injury predicts treatments for neuropathic pain
Conserved transcriptional programming across sex and species after peripheral nerve injury predicts treatments for neuropathic pain Open
Chronic pain is a devastating problem affecting 1 in 5 individuals around the globe, with neuropathic pain the most debilitating and poorly treated type of chronic pain. Advances in transcriptomics and data mining have contributed to catal…
View article: Large scale genotype‐ and phenotype‐driven machine learning in Von Hippel‐Lindau disease
Large scale genotype‐ and phenotype‐driven machine learning in Von Hippel‐Lindau disease Open
Von Hippel-Lindau (VHL) disease is a hereditary cancer syndrome where individuals are predisposed to tumor development in the brain, adrenal gland, kidney, and other organs. It is caused by pathogenic variants in the VHL tumor suppressor g…
View article: A Machine Learning Approach to Identifying Causal Monogenic Variants in Inflammatory Bowel Disease
A Machine Learning Approach to Identifying Causal Monogenic Variants in Inflammatory Bowel Disease Open
Leveraging a large WES data set, we demonstrate a statistically rigorous strategy for prioritization of variants for monogenic IBD diagnosis.
View article: Evaluation of single-cell RNA-seq clustering algorithms on cancer tumor datasets
Evaluation of single-cell RNA-seq clustering algorithms on cancer tumor datasets Open
View article: Whole genome analysis for 163 guide RNAs in Cas9 edited mice reveals minimal off-target activity
Whole genome analysis for 163 guide RNAs in Cas9 edited mice reveals minimal off-target activity Open
Introductory Paragraph The Knockout Mouse Phenotyping Program (KOMP 2 ) uses CRISRPR/Cas9 for high-throughput mouse line production to generate null alleles in the inbred C57BL/6N strain for broad-based in vivo phenotyping. In order to ass…
View article: HGG-39. ALTERNATIVE SPLICING OF <i>NEUROFIBROMIN 1</i> IS ASSOCIATED WITH ELEVATED MAPK ACTIVITY AND POOR PROGNOSIS IN HIGH-GRADE GLIOMA
HGG-39. ALTERNATIVE SPLICING OF <i>NEUROFIBROMIN 1</i> IS ASSOCIATED WITH ELEVATED MAPK ACTIVITY AND POOR PROGNOSIS IN HIGH-GRADE GLIOMA Open
Despite a good understanding of the coding mutations underlying high-grade gliomas (HGG), their prognosis remains poor. We sought to characterize their transcriptional alterations and how this contributes to pathogenesis. We analyzed a lar…
View article: Child Neurology: RNA Sequencing for the Diagnosis of Lissencephaly
Child Neurology: RNA Sequencing for the Diagnosis of Lissencephaly Open
Malformations of cortical development represent an important cause of developmental disability and neurologic morbidity and mortality.1 Advances in genetic methodology, particularly the widespread implementation of next-generation DNA sequ…
View article: UTILIZATION OF WHOLE EXOME SEQUENCING DATA TO IDENTIFY CLINICALLY RELEVANT PHARMACOGENOMIC VARIANTS IN INFLAMMATORY BOWEL DISEASE
UTILIZATION OF WHOLE EXOME SEQUENCING DATA TO IDENTIFY CLINICALLY RELEVANT PHARMACOGENOMIC VARIANTS IN INFLAMMATORY BOWEL DISEASE Open
Objectives We hypothesized that variants within clinically relevant pharmacogenes could be identified using a whole exome sequencing (WES) dataset derived from a cohort of over 1000 IBD patients. Methods Pediatric patients diagnosed with I…
View article: Utilization of Whole Exome Sequencing Data to Identify Clinically Relevant Pharmacogenomic Variants in Pediatric Inflammatory Bowel Disease
Utilization of Whole Exome Sequencing Data to Identify Clinically Relevant Pharmacogenomic Variants in Pediatric Inflammatory Bowel Disease Open
INTRODUCTION: We hypothesized that variants within clinically relevant pharmacogenes could be identified using a whole exome sequencing data set derived from a cohort of more than 1,000 patients with inflammatory bowel disease (IBD). METHO…
View article: MetaFusion: A high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates
MetaFusion: A high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates Open
Motivation Current fusion detection tools use diverse calling approaches and provide varying results, making selection of the appropriate tool challenging. Ensemble fusion calling techniques appear promising; however, current options have …
View article: Modelling the conversion between specific IgE test platforms for nut allergens in children and adolescents
Modelling the conversion between specific IgE test platforms for nut allergens in children and adolescents Open
Background: Multiplex tests allow for measurement of allergen-specific IgE responses to multiple allergen extracts and components and have several advantages for large cohort studies. Due to significant methodological differences, test sys…
View article: FORCAST: a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments
FORCAST: a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments Open
Cas-mediated genome editing has enabled researchers to perform mutagenesis experiments with relative ease. Effective genome editing requires tools for guide RNA selection, off-target prediction, and genotyping assay design. While independe…
View article: CReSCENT: CanceR Single Cell ExpressioN Toolkit
CReSCENT: CanceR Single Cell ExpressioN Toolkit Open
CReSCENT CanceR Single Cell ExpressioN Toolkit ( https://crescent.cloud ), is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing (scRNA-seq) …
View article: Prevalence and Clinical Features of Inflammatory Bowel Diseases Associated With Monogenic Variants, Identified by Whole-Exome Sequencing in 1000 Children at a Single Center
Prevalence and Clinical Features of Inflammatory Bowel Diseases Associated With Monogenic Variants, Identified by Whole-Exome Sequencing in 1000 Children at a Single Center Open
View article: Found in Transcription: Gene fusions arise through defects in RNA processing in the absence of chromosomal rearrangements
Found in Transcription: Gene fusions arise through defects in RNA processing in the absence of chromosomal rearrangements Open
Recent advancements in high throughput sequencing analysis have enabled the characterization of cancer-driving fusions, improving our understanding of cancer development. Most fusion calling methods, however, examine either RNA or DNA info…
View article: Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease
Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease Open
View article: HGG-18. ALTERNATIVE SPLICING OF NEUROFIBROMIN 1 IS ASSOCIATED WITH ELEVATED MAPK ACTIVITY AND POOR PROGNOSIS IN HIGH-GRADE GLIOMA
HGG-18. ALTERNATIVE SPLICING OF NEUROFIBROMIN 1 IS ASSOCIATED WITH ELEVATED MAPK ACTIVITY AND POOR PROGNOSIS IN HIGH-GRADE GLIOMA Open
Pediatric high-grade gliomas (pHGG) are invasive tumors with poor prognosis. In particular, diffuse intrinsic pontine glioma (DIPG), arising in the brainstem, is incurable and the leading cause of brain-tumor death in children. Previous ge…
View article: Characterization of Key Sexually Dimorphic Regulators in Pain Processing
Characterization of Key Sexually Dimorphic Regulators in Pain Processing Open
Introduction/Aim: Chronic pain affects 1 in 5 Canadians and costs over $43B annually, yet effective and safe treatment options remain elusive. Recent discoveries have brought to the forefront sex differences in mechanisms of pain as a pote…
View article: Characterization Of Allergen Sensitization Patterns In Canadian Preschool Children With Severe Wheezing
Characterization Of Allergen Sensitization Patterns In Canadian Preschool Children With Severe Wheezing Open