<i>CDKN2A</i> and <i>IKZF1</i> SNP allele proportions in tumor DNA relative to genomic control copy number.

Abstract

<p>Stacked histograms showing tumor DNA copy number of (A) <i>CDKN2A</i> and (B) <i>IKZF1</i> SNPs relative to a genomic control locus (<i>SLC24A3</i>). Black and grey bars represent the proportions of normalized SNP copy number accounted for by the risk and protective alleles respectively. White bars represent the difference between <i>CDKN2A</i>/<i>IKZF1</i> SNP copy number and the genomic control gene copy number. SMART-ddPCR was used to measure copy number of SNP risk/protective alleles, as well as the genomic control locus, in 35 leukemia bone marrow (tumor) DNA samples for <i>CDKN2A</i> (SNP rs3731249) and 75 tumor DNA samples for <i>IKZF1</i> (SNP rs4132601). Samples are grouped into those with allelic imbalance (AI) and those without AI, and arranged in order of normalized gene copy number relative to the genomic control.</p