Supplementary Figure 5: Detailed individual validations of LOY in ULSAM subjects 98 and 279 using low-coverage whole-genome next-generation sequencing.
In panels a and b are plotted SNP array and next-generation sequencing data from chromosomes 22, X and Y for each subject. LRR (blue dots) and BAF (red dots) values from SNP array data are plotted overlaid, and the percentages of cells affected were calculated using MAD software35. LRR values on sex chromosomes were normalized to a diploid state, and chromosome X probes (residing outside PAR regions) with ambiguous clustering (scored as heterozygotes) are excluded from analyses. The ploidy value, estimated from next-generation sequencing data, was calculated using FREEC software39. Blue lines indicate the normal copy number state, and the red line indicates the observed LOY. SNP array data within MSY include clusters of probes for known highly repetitive genes and loci, e.g., the TSPYA, TSPYB and RBMY1 genes16,17. Therefore, probes covering these loci do not reflect the true copy number state of chromosome Y. These regions are not included in the mapping of next-generation sequencing reads.
