Colin A. Ellis
A5039576451- Genomics and Rare Diseases
- Epilepsy research and treatment
- Genetics and Neurodevelopmental Disorders
- Pharmacological Effects and Toxicity Studies
- Genomic variations and chromosomal abnormalities
- Topic Modeling
- Machine Learning in Healthcare
- EEG and Brain-Computer Interfaces
- Biomedical Text Mining and Ontologies
- Cellular transport and secretion
- Neurological disorders and treatments
- Neonatal and fetal brain pathology
- Neuroscience and Neuropharmacology Research
- Traumatic Brain Injury Research
- Neurological Complications and Syndromes
- Artificial Intelligence in Healthcare and Education
- Machine Learning in Bioinformatics
- Metabolism and Genetic Disorders
- Genetic Associations and Epidemiology
- Retinal Development and Disorders
- Moyamoya disease diagnosis and treatment
- BRCA gene mutations in cancer
- Diet and metabolism studies
- Lysosomal Storage Disorders Research
- Traumatic Brain Injury and Neurovascular Disturbances
University of Pennsylvania
2016-2025
California University of Pennsylvania
2024-2025
Children's Hospital of Philadelphia
2020-2024
Hospital of the University of Pennsylvania
2024
Penn Center for AIDS Research
2023
VIB-UAntwerp Center for Molecular Neurology
2022
Antwerp University Hospital
2022
University of Antwerp
2022
Cleveland Clinic Lerner College of Medicine
2020
Austin Health
2018-2019
Disease-causing variants in STXBP1 are among the most common genetic causes of neurodevelopmental disorders. However, phenotypic spectrum STXBP1-related disorders is wide and clear correlations between variant type clinical features have not been observed so far. Here, we harmonized data across 534 individuals with analysed 19 973 derived terms, including phenotypes 253 previously unreported scientific literature. The overall landscape characterized by abnormalities 95% seizures 89%...
PurposePathogenic variants in SCN2A cause a wide range of neurodevelopmental phenotypes. Reports genotype–phenotype correlations are often anecdotal, and the available phenotypic data have not been systematically analyzed.MethodsWe extracted information from primary descriptions SCN2A-related disorders literature between 2001 2019, which we coded Human Phenotype Ontology (HPO) terms. With higher-level phenotype terms inferred by HPO structure, assessed frequencies clinical features...
Abstract Objective Seizure frequency and seizure freedom are among the most important outcome measures for patients with epilepsy. In this study, we aimed to automatically extract clinical information from unstructured text in notes. If successful, could improve decision-making epilepsy allow rapid, large-scale retrospective research. Materials Methods We developed a finetuning pipeline pretrained neural models classify as being seizure-free containing their date of last annotated 1000 notes...
Genetic testing is now the standard of care for many neurologic conditions. Health disparities are unfortunately widespread in US health system, but utilization genetic conditions have not been studied. We tested hypothesis that access to and results vary according race, ethnicity, sex, socioeconomic status, insurance status adults with
Pathogenic STXBP1 variants cause a severe early-onset developmental and epileptic encephalopathy (STXBP1-DEE). We aimed to investigate the natural history of STXBP1-DEE in adults focusing on seizure evolution, presence movement disorders, level functional (in)dependence. In this observational study, patients with minimum age 18 years carrying (likely) pathogenic variant were recruited through medical genetics departments epilepsy centers. Treating clinicians completed clinical questionnaires...
BackgroundThe developmental and epileptic encephalopathies (DEEs) are the most severe group of epilepsies which co-present with delay intellectual disability (ID). DEEs usually occur in people without a family history epilepsy have emerged as primarily monogenic, damaging rare mutations found 50% patients. Little is known about genetic architecture patients whom no pathogenic variant identified. Polygenic risk scoring (PRS) method that measures person's common burden for trait or condition....
Abstract Objective Large-language models (LLMs) can potentially revolutionize health care delivery and research, but risk propagating existing biases or introducing new ones. In epilepsy, social determinants of are associated with disparities in access, their impact on seizure outcomes among those access remains unclear. Here we (1) evaluated our validated, epilepsy-specific LLM for intrinsic bias, (2) used LLM-extracted to determine if different demographic groups have outcomes. Materials...
Abstract Objective Electronic medical records allow for retrospective clinical research with large patient cohorts. However, epilepsy outcomes are often contained in free text notes that difficult to mine. We recently developed and validated novel natural language processing (NLP) algorithms automatically extract key outcome measures from clinic notes. In this study, we assessed the feasibility of extracting these study history at our center. Methods applied previously NLP seizure freedom,...
More than 100 genetic etiologies have been identified in developmental and epileptic encephalopathies (DEEs), but correlating findings with clinical features at scale has remained a hurdle because of lack frameworks for analyzing heterogenous data. Here, we analyzed 31,742 Human Phenotype Ontology (HPO) terms 846 individuals existing whole-exome trio data assessed associated phenotypic relatedness by using HPO-based semantic similarity analysis de novo variants the same gene. Gene-specific...
The epilepsies are highly heritable conditions that commonly follow complex inheritance. While monogenic causes have been identified in rare familial epilepsies, most remain unsolved. We aimed to determine (1) whether common genetic variation contributes epilepsy risk, and (2) risk is enriched compared with non-familial (sporadic) epilepsies.Using variants derived from the largest genome-wide association study, we calculated polygenic scores (PRS) for patients (n = 1,818 1,181 families),...
Abstract Subcellular membrane systems are highly enriched in dolichol, whose role organelle homeostasis and endosomal-lysosomal pathway remains largely unclear besides being involved protein glycosylation. DHDDS encodes for the catalytic subunit (DHDDS) of enzyme cis-prenyltransferase (cis-PTase), dolichol biosynthesis dolichol-dependent glycosylation endoplasmic reticulum. An autosomal recessive form retinitis pigmentosa (retinitis 59) has been associated with a recurrent variant. Moreover,...
Abstract Objective Improvement in epilepsy care requires standardized methods to assess disease severity. We report the results of implementing common data elements (CDEs) document history electronic medical record (EMR) after 12 months clinical use outpatient encounters. Methods Data regarding seizure frequency were collected during routine encounters using a CDE‐based form within our EMR. extracted CDE from EMR and developed measurements for severity improvement scores. Seizure burden was...
Disease-causing variants in synaptic function genes are a common cause of neurodevelopmental disorders and epilepsy. Here, we describe 14 individuals with de novo disruptive BSN , which encodes the presynaptic protein Bassoon. To expand phenotypic spectrum, identified 15 additional protein-truncating (PTVs) from large biobanks. Clinical features were standardized using Human Phenotype Ontology (HPO) across all 29 individuals, revealed clinical characteristics including epilepsy (13/29 45%),...
Although previous research shows that generalized and focal epilepsies have at least some distinct genetic influences, it remains uncertain why families manifest both types of epilepsy. We tested two hypotheses: (1) with epilepsy carry separate risk alleles for types; (2) within mixed families, the type each individual manifests is influenced by relative burden epilepsies. The Epi4K cohort included 711 individuals from 257 (113 66 78 families). calculated polygenic scores (PRSs) (GGE_PRS)...