Example of cloneHD output for an MDS sample. (A) Read depth of genome-wide SNP loci (top) and the posterior probability of copy number state of the inferred clone (bottom) in sample MDS108; with karyotype 47, XY, +8, add (13q)[12]. Chromosomes 1 to 22 and chromosome X (23) are depicted. For chromosome 8 and for 13q, copy number gains reflect the karyotype as does the reduced coverage for X. (B) Genome-wide BAF for MDS108 (top) and posterior probability of the B-allele state of the inferred clone (bottom). The B-allele states of 0/2 at 2p and 11q indicate a loss of heterozygosity in these regions, thus in keeping with CN-LOH in these regions. This region includes the DNMT3A gene and CN-LOH explains the high VAF (0.97) for the R882C mutation that was also detected in MDS108. BAF, B-allele fraction.