Figure 2.

False discovery of CNLOH in unpaired studies. An SNP array analysis of 10 MDS patients for chromosomes 6, 10, and 18 is shown (Affymetrix StyI 250K arrays). Copy number analysis (only tumor samples are shown) reveals no deletions or amplifications (left panel), whereas inferred LOH analysis based on paired samples (Figure 1) reveals no LOH (right panel). However, an inferred LOH analysis of 10 patients based on 100 unrelated controls, processed in the same laboratory and core facility, reveals 9 large segments (and several short segments) of falsely discovered LOH resulting from the lack of matched normal samples. The segment sizes are: 4.3, 2.3, 5.6, and 3.5 Mb (chromosome 6, patients 2, 4, 6, and 7), 11.3, 10.6, and 12.6 Mb (chromosome 10, patients 7, 9, and 10), and 12.2 and 10.6 Mb (chromosome 18, patients 1 and 7). The organization of the figure corresponds to Supplemental Figure 3 in Radtke et al.¹⁸