Genome-wide concordance of aberration estimates.

We present aberration call concordance for different methods at different tumor purities (30%, 21%, 14%, 10%). We defined the concordance rate as the percentage of markers with calls consistent with GAP, in terms of the following: (left) Copy number and LOH status, i.e. matching both total allele copy number and existence of LOH; (middle) Gain or loss status in the aberrant cells of the two germline alleles (inherited as 1-1), i.e. “gain/gain” (2-2), “gain/normal” (3-1); or (right) Allelic imbalance, i.e. presence or absence of AI. Missing entries (“-”) indicate either no output or a small value (less than 0.01). Some cells contain “n/a” due to limits of the output from certain methods, i.e. PSCN allows comparison of gain or loss concordance only, and hapLOH simply outputs probability of allelic imbalance.
Genome-wide concordance of aberration estimates.