Figure 3

An example of applying gtBCR on samples with CNAs. (a) A and B allele log-intensity plot with samples colored by the genotypes of their paired normal samples: blue, green and red representing “AA”, “AB” and “BB” genotype, respectively. (b) The copy number status plot for each sample: red squares represent samples with copy number loss, green squares represent samples with copy number gain, and gray squares are samples without CNAs. (c) Genotypes called by BCRgt, with colors being the same as (a). Both the black and red arrows point to the observations that have “AB” genotype in the paired normal sample (see (a)) and have copy number loss (see (b)). They are both correctly called “AA” by BCRgt, which agrees with their copy number status. (d) Genotypes called by BRLMM: no call on the observation pointed by the black arrow, and “AB” call on the observation pointed by the red arrow, which is inconsistent to its copy number status.