Supplementary Figure 11: No validation of suggested cases of GOY using low-coverage (∼5×) whole-genome next-generation sequencing.

Of 100 sequenced participants, 3 had a positive median LRR on the SNP array in the male-specific part of chromosome Y (mLRR-Y), indicating possible GOY. In panels a–c are plotted the SNP array and next-generation sequencing data from chromosomes 22, X and Y for each of these three subjects. The LRR and BAF 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 diploid state, and chromosome X probes (residing outside PAR regions) with ambiguous clustering (scored as heterozygotes) are excluded from analyses. The ploidy 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.