The shadow of HIV
Data of WGS-based non-invasive prenatal testing (NIPT) or cell-free DNA testing contains exogenous DNA (bacterial and viral). This information is too fragmentary to conduct full microbiome studies, but still interesting for expanding NIPT functionality.
Being a retrovirus, HIV can not be directly detected in cell-free DNA data.
Steps of the study:
1. Extraction of unmapped reads
2. Assigning taxonomic labels
3. Creating residual virus and microbiome profiles of two datasets 4. Analysis of the HIV-positive sequencing data
5. Finding the differences in exogenous DNA composition between HIV- and HIV+ NIPT samples
The results are published in The-shadow-of-HIV repository.