A Nextflow based software tool to run the INVAR (Integration of VAriant Reads) analysis pipeline. Previously available here.
The pipeline seeks to detect minimal residual disease signal in patient liquid biopsy data, and outputs a classifcation based on a threshold score established on a cohort of healthy samples. A general cohort size should range from around 20+ individual patients.
More details are available in the links below. Test data is available at the EGA accession numbers EGAS00001004447 and EGAS00001005246 with results available in the following publications:
[1] Wan J, Heider K, Gale D et al. ctDNA monitoring using patient-specific sequencing and integration of variant reads. Sci Transl Med. 2020;12(548). doi:10.1126/scitranslmed.aaz8084
[2] Heider K, Wan J, Gale D. ctDNA detection by personalised assays in early-stage NSCLC. MedRxiv. doi:https://doi.org/10.1101/2021.06.01.21258171
Contact: Hui.zhao@cruk.cam.ac.uk, emma-jane.ditter@cruk.cam.ac.uk