Who else is using CNVkit?¶
Google Scholar lists some of the studies where CNVkit has been used by other researchers. We’d like to highlight:
- TRACERx Renal Consortium studies:
- Turajlic, S. et al. (2018). Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal. Cell, 173(3), 581-594.e12
- Turajlic, S. et al. (2018). Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal. Cell, 173(3), 595-610.e11
- Seed, G. et al. (2017). Gene copy number estimation from targeted next generation sequencing of prostate cancer biopsies: Analytic validation and clinical qualification. Clinical Cancer Research, 23(20), 6070–6077
- McCreery, M.Q. et al. (2015). Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers. Nature Medicine, 21, 1514–1520
- Shain, A.H. et al. (2015). Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nature Genetics, 47(10), 1194-1199
- Shain, A.H. et al. (2015). The Genetic Evolution of Melanoma from Precursor Lesions. New England Journal of Medicine, 373(20), 1926-1936
Specific support for CNVkit is included in bcbio-nextgen, PureCN, THetA2, and MetaSV. CNVkit is also available on the commercial platforms DNAnexus, Bina RAVE, and Diploid InHelix.
Finally, CNVkit can export files to several standard formats that can be used with many other software packages, including BioDiscovery Nexus Copy Number and Integrative Genomics Viewer (IGV).