This tool was created in collaboration with the sequencing staff (James McKenna, Lesley Neill, Derek Fairley, Tanya Curran) at the Belfast Health and Social Care Trust (BHSCT) Regional Virology Laboratory, Belfast, to produce bespoke HIV-1 drug resistant clinical reports containing both patient information and Stanford's University HIV-1 resistance database HIVdb interpretation to help our clinicians in patient management of HIV-1 infection.
Although 'raw JSON report' outputs are available following submission of paired FASTQs to the HIVdb-NGS pipeline, these are not in a user friendly format for our clinical colleagues. Therefore using an overarching R script HIV_resistance_report_online_only.R(overview below), different bespoke clinical reports (created by R Markdown scripts) are generated based on the suffix following the lab number.
Clone the HIV-1_DR_RJ_Analysis folder into your working directory
git clone https://github.com/BHSCT-Bioinformatics/HIV-1_DR_RJ_Analysis.git
This tool uses a folder of raw JSON files which have previously been downloaded from Stanford's University HIV-1 resistance webpage which are outputs from their HIV-1 NGS pipeline. The raw JSON folder needs to be copied into the HIV-1_DR_RJ_Analysis folder. Additionally within the raw JSON folder needs to be the relevant patient metadata file (xlsx format).
Note: The patient metadata (Name, DOB, H&C number, Laboratory number, Type of specimen, Date of specimen collection, Date of specimen received) are desirable fields for our BHSCT clinicians and might not be relevant for other users. Furthmore within the HIV-1_DR_RJ_Analysis folder is the BHSCT logo (belfast_trust_logo.png) which will only be applicable to BHSCT users.
Running the test_dataset folder included in this Github repository
Rscript HIV_resistance_report_online_only.R test_dataset
- Bespoke clinical reports (
.pdf) - Combined drug susceptibilities to ARVs and HIV-1 subtype for run samples (
combined_drug_susceptibilities.csv) - Combined technical log files for run samples (
combined_technical_logs.csv)
Examples are available in test_dataset_output
Column headers of combined_technical_logs.csv file
| Sample_ID | Metadata_added | Minimum_Read_Depth | Nucleotide_Mixture_Threshold | Mutation_Detection_Threshold | Sierra_version_date | HIVdb_version_date |
|---|---|---|---|---|---|---|
Note: In the combined_technical_logs.csv the Metadata_added column is crucial to investigate as a clinical report will be generated irrespective of metadata being present.
The two options are:
- 'Yes'
- 'Problems were encountered when joining patient data. Verify that the lab number is accurate' (Will need to be adressed).
This tool is dependent on various R packages (currently tested with R version 4.3.1) which are all available on CRAN
HIV-1_DR_RJ_Analysis is licensed under GPL v3
- Marc Niebel (Bioinformatician at Regional Virology Laboratory, Belfast)
- Email address: Marc.Niebel@belfasttrust.hscni.net