cloneMap: a R package to visualise clonal heterogeneity

Genomic evolution and clonal heterogeneity in the soma are widespread and are involved in various pathologies with devastating consequences to human health, most prominently in neoplasia. Tools to interrogate and visualise the diversity of clonal populations in malignant or non-malignant tissues are currently lacking. cloneMap is a tool to represent clonal heterogeneity in a sample or set of samples, accounting for the clone size and phylogenetic relationships between clones. We apply cloneMap to several publicly available cancer sequencing datasets to demonstrate its ability to provide biological inferences of clonal heterogeneity. cloneMap is an R package available on github (). ### Competing Interest Statement A.M.F. is a co-inventor on a patent application to determine methods and systems for tumour monitoring (GB2114434.0). N.M. has stock options in and has consulted for Achilles Therapeutics and holds a European patent in determining HLA LOH (PCT/GB2018/052004), and is a co-inventor to a patent to identifying responders to cancer treatment (PCT/GB2018/051912). C.S. acknowledges grant support from Pfizer, AstraZeneca, Bristol Myers Squibb, Roche-Ventana, Boehringer-Ingelheim, Archer Dx Inc. (collaboration in minimal residual disease sequencing technologies) and Ono Pharmaceutical; is an AstraZeneca Advisory Board Member and Chief Investigator for the MeRmaiD1 clinical trial; has consulted for Amgen, Pfizer, Novartis, GlaxoSmithKline, MSD, Bristol Myers Squibb, AstraZeneca, Illumina, Genentech, Roche-Ventana, GRAIL, Medicxi, Bicycle Therapeutics, Metabomed and the Sarah Cannon Research Institute; has stock options in Apogen Biotechnologies, Epic Bioscience and GRAIL; and has stock options and is co-founder of Achilles Therapeutics. C.S. holds patents relating to assay technology to detect tumour recurrence (PCT/GB2017/053289); to targeting neoantigens (PCT/EP2016/059401), identifying patent response to immune checkpoint blockade (PCT/EP2016/071471), determining HLA LOH (PCT/GB2018/052004), predicting survival rates of patients with cancer (PCT/GB2020/050221), to treating cancer by targeting Insertion/deletion mutations (PCT/GB2018/051893), identifying insertion/deletion mutation targets (PCT/GB2018/051892); methods for lung cancer detection (PCT/US2017/028013), identifying responders to cancer treatment (PCT/GB2018/051912); and a patent application to determine methods and systems for tumour monitoring (GB2114434.0).