Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
Figure 4
Accounting for LD by the LD-HMM Significantly Reduces False LOH Inferences from Data Obtained at High Marker Density
(A) Inferences from the basic HMM applied to 100 K SNP array data are shown for Chromosome 4 in normal samples. Data are shown as in Figure 3.
(B) The genotypes of one region of falsely inferred LOH reveal a region of linkage disequilibrium (dashed red box), also identified by the HapMap project. The sample in column “D” contains one haplotype, the samples in columns “E” through “K” contain another haplotype, and the samples in columns “A” through “C” are heterozygous.
(C) Improved LOH inferences after application of the LD-HMM.