Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity
Fig 3
Analysis of CRUK0063 multi-sample and multi-time point NSCLC case.
a) MEDICC2 phylogeny. Multi-sample reference phased allele-specific copy number output from Refphase can be passed directly to MEDICC2 to produce a phylogenetic reconstruction. b) SCNA summary tracks for all samples—primary and metastases—from patient CRUK0063. c) BAF profiles and SCNA summary tracks for the primary samples from CRUK0063 are indicated by a red border. d) SCNA summary tracks and BAF profiles from five post-mortem metastatic samples with a blue border. Sample BAF tracks are ordered by their position in the MEDICC2 phylogenetic reconstruction. Green boxes, arrowheads and associated Roman numerals highlight selected examples of MSAI on chromosomes 2p, 6q, 4p and 10q, described in the main text. WGD indicates whole genome doubling events inferred by MEDICC2.