Copy number variation (CNV) calculation

Raw sequencing data (fastq files) were first mapped to the human genome (hg19) (DNASTAR, Madison, WI). Read counts from the mapped sequence files were then binned into 60kb windows (total 51672 genomic bins) and adjusted to the global mean count for each sample. The read count ratio in each genomic bin was calculated by dividing cfDNA with peripheral blood mononuclear cell germline DNA (gDNA) in the same patient [20]. The resulting ratios were further transformed with log2 and corrected for GC content [40]. The fully normalized log2 ratios in genomic bins were subjected to segmentation using the copy number analysis method (CNAM) algorithm (Golden Helix, Bozeman, MT).