Comparative Analysis of Copy Number Alterations

Reads were aligned to the 1000 genomes phase 2 reference genome (hs37d5) which includes build GRCh37 and decoy sequences: (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz) using the Illumina Dragen 3.7.3 aligner. The ichorCNA algorithm was subsequently applied using the depth of coverage obtained from 500 kb bins across the genome^{38 (link)}. When available, LP-WGS data from the LB samples were compared with CNA profiles of the matching primary tumors generated from CMA assays (CytoScanHD or OncoScan, Thermo Fisher Scientific, Waltham, MA). Briefly, all 59 Cytoscan or OncoScan arrays performed on the tumor tissue were processed using ASCAT and NxClinical (BioDiscovery, El Segundo, CA) using the default settings, except that the Piecewise Constant Fitting (PCF) penalty was increased to 95 to account for FFPE degradation of samples. Subsequently, the segmented calls from LP-WGS and CMA were binned into 1 Mb regions across the entire genome. Pearson’s correlation for each pair of samples across all bins over autosomes was calculated for all CMA samples and LP-WGS samples with purity greater than 10%. All samples with a Pearson’s correlation coefficient (r²) less than 0.7 were manually examined.