A tool developed for tumor-only diagnostic sequencing using hybrid-capture protocols. It provides copy number adjusted for purity and ploidy and can classify mutations by somatic status and clonality. It requires a pool of process-matched normals for coverage normalization and artifact filtering. PureCN was parameterized using large collections of diverse samples, ranging from low coverage whole-exome to ultra-deep sequenced plasma gene-panels.
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("PureCN")
If your R/Bioconductor version is outdated, this will install an old and unsupported version.
For outdated R/Bioconductor versions, you can try backporting the latest stable version (this should work fine for Bioconductor 3.3 and later):
If you want the latest and greatest from the developer branch:
To get started:
For the R package and more detailed information:
Main paper describing the likelihood model:
Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D and Morrissey M (2016). “PureCN: Copy number calling and SNV classification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, pp. 13. doi: 10.1186/s13029-016-0060-z.
Validation paper, including description of novel additions, such as off-target support, tangent normalization and tweaks to the likelihood model:
Oh S, Geistlinger L, Ramos M, Morgan M, Waldron L, Riester M (2019). Reliable analysis of clinical tumor-only whole exome sequencing data. bioRxiv. doi: 10.1101/552711
Dagogo-Jack et al. (2018). "Tracking the evolution of resistance to ALK tyrosine kinase inhibitors through longitudinal analysis of circulating tumor DNA". JCO Precision Oncology. doi: 10.1200/PO.17.00160.
Orlando et al. (2018). "Genetic mechanisms of target antigen loss in CAR19 therapy of acute lymphoblastic leukemia". Nature Medicine. doi: 10.1038/s41591-018-0146-z.
Pal et al. (2018). "Efficacy of BGJ398, a fibroblast growth factor receptor 1-3 inhibitor, in patients with previously treated advanced urothelial carcinoma with FGFR3 alterations". Cancer Discovery. doi: 10.1158/2159-8290.CD-18-0229.
Pitt et al. (2018). "Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features". Nature Communications. doi: 10.1038/s41467-018-06616-0.