<p>Allelic copy number was measured in constitutional DNA and leukemia bone marrow (tumor) DNA from HeH ALL patients heterozygous for ALL-associated SNPs on chromosomes frequently gained in HeH ALL: <i>CEBPE</i> SNP rs2239633 (A), <i>ARID5B</i> SNP rs7089424 (B), <i>PIP4K2A</i> SNP rs10764338 (C), and <i>GATA3</i> SNP rs3824662 (D). Risk allele proportions are displayed as a fraction of the total allelic copy number measured in each patient using ddPCR. Each subject was assayed in duplicate, and error bars represent the standard error of the mean (some error bars not visible due to their range falling within boundaries of the data point). Upper/lower thresholds of allelic imbalance (AI) were +/- 3 SDs from the mean allelic proportion from repeat measurements in constitutional DNA samples (white squares). For rs2239633, 19 tumor samples showed AI favoring the risk allele versus 13 patients with AI favoring the protective allele (P = 0.19). For rs7089424, 20 tumor samples showed AI favoring the risk allele versus 15 patients with AI favoring the protective allele (P = 0.25). For rs10764338, 4 tumor samples showed AI favoring the risk allele versus 5 patients with AI favoring the protective allele (P = 0.50). For rs3824662, 10 tumor samples showed AI favoring the risk allele versus 9 patients with AI favoring the protective allele (P = 0.50). Data points clustering at ~0.66 and ~0.33 represent a 3:2 or 2:3 risk:protective allele proportion due to chromosomal copy number shifting from diploid (n = 2) to triploid (n = 3). Data points at ~0.75 represents a 3:1 risk:protective allele proportion due to a diploid to tetraploid (n = 4) shift in chromosome ploidy. Data points at 1 and 0 likely represent HeH ALL that has arisen via near-haploidy, leading to chromosomal LOH (Paulsson <i>et al</i>. 2005) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143343#pone.0143343.ref031" target="_blank">31</a>].</p
