HSCRs were derived from segmental estimates of phased multipoint allelic copy-ratios at heterozygous loci using the program HAPSEG 53 on data from Affymetrix SNP arrays. As part of this procedure, haplotype panels from population linkage analysis HAPMAP3 54 were used in conjunction with statistical phasing software BEAGLE 55 in order to estimate the phased germline genotypes at SNP markers in each cancer sample. This increased our sensitivity for resolving these genotypes, since it naturally exploits the local statistical dependencies between SNPs 53. In addition, this allowed greater resolution of small differences between homologous copy-ratios, since phase information from allelic imbalance of heterozygous markers due to SCNA could be combined with the statistical phasing from the haplotype panels 53.
