Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays (original) (raw)
Figure 3
Comparison of LOH Inferred from Unpaired Tumors to LOH Observed in Tumor/Normal Pairs
(A) Results from 10 K SNP array data. Each column represents a sample, with SNP markers from Chromosome 10 displayed from the p terminus (top) to the q terminus (bottom) (not all markers are displayed at this resolution). Tumor/normal observations (left) represent direct comparisons of tumor to normal genotypes. Here, SNP markers observed as having undergone LOH are indicated in blue, retention is shown in yellow, and noninformative SNPs are indicated in grey. Inferences from unpaired tumor data represent the probability of each SNP having undergone LOH, as made by the basic HMM (center) and HC/LD-HMM (right). Here, a high probability of LOH (LOSS) is also indicated in blue, a high probability of retention (RET) is indicated in yellow, and indeterminate SNPs with an almost equal probability of either state are indicated in white. Occasionally, regions that are noninformative in the tumor/normal comparison are falsely inferred as LOH by the basic HMM in the unpaired data (red arrows); some of these false regions are corrected by the HC/LD-HMM (green arrows).
(B) Results from 100 K SNP array data, shown as in (A). Data from Chromosome 21 are shown to highlight the detection of false LOH in the analysis of unpaired tumor data, and are not representative of the frequency of true LOH events in this sample set. Almost all regions falsely inferred as LOH by the basic HMM are correctly inferred by the HC/LD-HMM. The blue arrows indicate a region of true LOH, which is correctly identified by both the basic and HC/LD-HMM.