An illustration of log R Ratio (LRR) and B Allele Freq (BAF) values for the chromosome 15 q-arm of an individual. A normal chromosome region has three BAF genotype clusters, as represented as AA, AB, and BB genotypes in boxes, and with LRR values centered around zero. The copy-neutral LOH region has normal LRR values, but without the AB genotype cluster. The increased copy number for a CNV region can be detected based on an increased number of peaks in the BAF distribution, as well as increased LRR values. The patterns of LRR and BAF for different CNV regions, normal regions, and copy-neutral LOH regions are distinct from each other, thus the combination of LRR and BAF can be used to generate CNV calls.
