2.7.2. Log R ratio (LRR) and B allele frequency (BAF) graphs

LRR and BAF graphs were used to further validate the diagnosis obtained by Karyomapping but also to provide a method to discriminate between loss of heterozygosity and monosomy and to detect certain trisomies of mitotic origin. The analysis pertaining to LRR and BAF graphs was conducted in R (R Core Team, 2014) and figures were produced using the package karyoploteR [35]. Samples identified as euploid by Karyomapping were used to calculate standard R and Theta values for each SNP combination (RAA, RAB, RBB, ThetaAA, ThetaAB, ThetaBB) from signal intensity data (X and Y) available from the SNP database itself. We employed the same R and Theta definitions recommended in Ref. [36]. These values (R and Theta) were then used to calculate the relevant data points for each LRR and BAF graph, as previously described [36]. A threshold was also employed so that only data points with GC > 0.60 were plotted.