Genome-wide sensitivity and specificity for low purity simulations.

(†) With a limited state space (normal, cn-LOH, hemizygous deletion only) and no use of LRR, approximating the settings for hapLOH. Sensitivity is defined as the proportion of simulated aberrant markers that are called correctly. Specificity (shown in parentheses) is defined as the proportion of simulated non-aberrant markers that are called correctly. GPHMM has sensitivity less than 0.01 for purities less than 9%. Blank table entries (“-”) are due to either zero output or sensitivities <0.01. PSCN, genoCN, and ASCAT failed to produce meaningful output at all purity levels. Genome-wide sensitivity and specificity for low purity simulations.