Whole pathogen genome sequencing, phylogenetics and modelling in viral diagnostics
Lead Research Organisation:
University College London
Department Name: Great Ormond St. Instit of Child Health
Abstract
Using Bioinformatics to analyse whole genome pathogen sequences from patients in GOSH & wider, starting with norovirus & adenovirus. Aim to drive improvements in diagnostics for personalised medical care, better handle transmission in outbreaks and study effects of experimental drugs.
Organisations
| Title | cmvdrg - Human Cytomegalovirus Drug Resistance Genotyping database and application |
| Description | The first Comprehensive database of Human Cytomegalovirus Drug Resistance Mutations to All clinically relevant drugs. Ganciclovir, Cidofovir, Foscarnet, Letermovir, Tomeglovir. - Text database - R package - Web server - Only open source verifiable dataset Processes sequence and variant data, allowing use of minor variant frequencies known to be crucial for analysis of immunosuppressed patients. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | - Now the GOSH standard - Although still in pre-print it receives ~5 downloads a week and the web server has been used in 10 countries. - Was required for an upcoming paper in the lab (confidential) on longitudinal patient sequencing and prognosis. - Was required for an upcoming paper on Machine Learning to predict Resistance Mutations in the herpesviruses in general. |
| URL | https://github.com/ucl-pathgenomics/cmvdrg |