A5049856137- Bioinformatics and Genomic Networks
- Alzheimer's disease research and treatments
- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
- Renal Transplantation Outcomes and Treatments
- Machine Learning in Bioinformatics
- Organ Transplantation Techniques and Outcomes
- Genomics and Phylogenetic Studies
- Liver Disease and Transplantation
- Neuroinflammation and Neurodegeneration Mechanisms
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Nutrition, Genetics, and Disease
- Genomic variations and chromosomal abnormalities
- Epigenetics and DNA Methylation
- Cholesterol and Lipid Metabolism
- Organ Donation and Transplantation
- Neurological Disease Mechanisms and Treatments
- Liver Disease Diagnosis and Treatment
- Healthcare Policy and Management
- Molecular Biology Techniques and Applications
- Biological Research and Disease Studies
- Heart Failure Treatment and Management
- Inflammation biomarkers and pathways
- Dementia and Cognitive Impairment Research
University of Colorado Hospital
2025
University of Colorado Denver
2023-2025
University of Pennsylvania
2014-2024
University of Colorado Anschutz Medical Campus
2022-2024
University of Colorado Boulder
2023-2024
University of Colorado System
2023
Penn Center for AIDS Research
2022
Genomics (United Kingdom)
2022
Alzheimer’s Disease Neuroimaging Initiative
2020
Drexel University
2018-2020
Despite the acceptance of living-donor liver transplant (LDLT) as a lifesaving procedure for end-stage disease, it remains underused in United States. Quantification lifetime survival benefit and Model End-stage Liver Disease incorporating sodium levels (MELD-Na) score range at which outweighs risk LDLT is necessary to demonstrate its safety effectiveness.To assess benefit, life-years saved, MELD-Na that was obtained individuals who received an compared with remained on wait list.This...
Abstract Summary: We implemented a high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA–DNA fragments with high confidence and quality control, detecting histone modifications DNase hypersensitive enrichments in putative elements, ultimately extracting possible intra- inter-chromosomal enhancer–target gene relationships. Availability implementation: This software package is designed run on...
Introduction Late-onset Alzheimer’s disease (LOAD, onset age > 60 years) is the most prevalent dementia in elderly 1 , and risk partially driven by genetics 2 . Many of loci responsible for this genetic were identified genome-wide association studies (GWAS) 3–8 To identify additional LOAD loci, we performed largest GWAS to date (89,769 individuals), analyzing both common rare variants. We confirm 20 previous four new ( IQCK ACE ADAM10 ADAMTS1 ). Pathway analysis these data implicates...
Summary Work in the past 10 years has greatly expanded our understanding of Alzheimer's disease (AD) genetics, with more than 20 susceptibility genetic loci discovered large genome‐wide association and sequencing studies. The NIA Genetics Disease Data Storage Site (NIAGADS) is funded by National Institute on Aging to serve as a one‐stop portal for community access research data findings generated from AD genetics projects. In this article, we describe mission NIAGADS, available resources,...
Background The cytomegalovirus (CMV) mismatch rate in deceased donor kidney transplant (DDKT) recipients the US remains above 40%. Since CMV mismatching is common DDKT recipients, cumulative effects may be significant context of overall patient and graft survival. Our primary objective was to describe short- long-term risks associated with high-risk positive/recipient negative (D+/R-) among explicit goal deriving a mathematical penalty. Methods We conducted retrospective, secondary analysis...
The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to joint analysis. Here we bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten capture kits in fourteen centers Alzheimer's Disease Sequencing Project. joint-genotype called variant-called format (VCF) file contains only positions within union kits. VCF was then processed specifically account batch effects arising from use different...
Detecting structural variants (SVs) in whole-genome sequencing poses significant challenges. We present a protocol for variant calling, merging, genotyping, sensitivity analysis, and laboratory validation generating high-quality SV call set from the Alzheimer’s Disease Sequencing Project comprising 578 individuals 111 families. Employing two complementary pipelines, Scalpel Parliament, SV/indel we assessed through sample replicates (N = 9) with silico spike-ins. developed novel metric,...
Structural variations (SVs) are important contributors to the genetics of numerous human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due challenges accurately detecting SVs. Here, we analyzed whole-genome sequencing data from Disease Sequencing Project (ADSP, N=16,905 subjects) and identified 400,234 (168,223 high-quality) We found a significant burden deletions duplications AD cases (OR=1.05, P=0.03), particularly for singletons (OR=1.12, P=0.0002)...
Currently in the United States, deceased donor liver transplant (DDLT) allocation priority is based on model for end-stage disease including sodium (MELD-Na) score. The Network organ sharing's 'Share-15' policy states that candidates with MELD-Na scores of 15 or greater have to receive local offers compared lower scores. Since inception this policy, major changes primary etiologies occurred and previous assumptions need be recalibrated.The authors retrospectively analyzed Scientific Registry...
We have applied a novel and integrative analysis framework for next-generation sequencing (NGS) data to 503 human subjects provided by the Religious Orders Study Memory Aging Project (ROSMAP) examine changes in transcriptomic organization common variants association with late-onset Alzheimer's disease (Wijsman et al.). Our identified seven reproducible, co-regulated modules after quality control, clinical segregation, preservation filtering, functional ontology analysis. These were...
NIAGADS is a national genetics data repository that facilitates access of genotypic to qualified investigators for the study late-onset AD. It expected all derived from NIA funded AD studies be deposited at or another approved site whenever possible (https://www.niagads.org/sites/all/public_files/NIAGADS_DOCUMENTS/NIA%20AD%20genetics%20sharing%20plan%2020121026.pdf). supported by under cooperative agreement (U24 AG041689) expand its storage and sharing capacity large-scale sequencing...
Biliary anastomotic stricture (BAS) is a frequent complication of liver transplantation and associated with reduced graft survival patient morbidity. Existing treatments for BAS involve dilation the though placement 1 or more catheters 6 to 24 months yielding limited effectiveness in transplant patients. In this case series, we present preliminary safety efficacy novel percutaneous laser stricturotomy treatment cohort 5 posttransplant patients refractory long-term large bore catheterization....
In this issue of Transplantation, Tsapepas et al1 revealed several important inconsistencies in the OPTN/UNOS national transplantation data registry, including miscoding primary diagnosis patients who are listed for a second transplant, temporal change reporting symptomatic peripheral vascular disease, "strategic coding" patient variables used to adjust OPTN's transplant program evaluation model, an absence auditing codes and procedures, general lack technological progress terms collection,...
Structural variations (SVs) are important contributors to the genetics of human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due challenges accurately detecting SVs. We analyzed whole-genome sequencing data from Disease Sequencing Project (N = 16,905) and identified 400,234 (168,223 high-quality) Laboratory validation yielded a sensitivity 82% (85% for high-quality). found significant burden deletions duplications AD cases, particularly singletons...
Abstract In 1948, Claude Shannon published a mathematical system describing the probabilistic relationships between letters of natural language and their subsequent order or syntax structure. By counting unique, reoccurring sequences called N-grams, this model was used to generate recognizable English sentences from N-gram frequency probability tables. More recently, analysis methodologies have been successful in addressing many complex problems variety domains, processing genomics. One such...
Currently, there is no mathematical model used nationally to determine the medical urgency of patients on heart transplant waitlist in United States. While current organ distribution system accounts for many patient factors, a truly objective needed more reliably stratify by their acuity.