Fig. 2.

Detection of copy number variation using B-allele frequencies (BAF). a In case of heterozygosity, variant allele frequencies (or BAFs) are influenced by copy number variation at the respective loci. Here, for a hypothetical case with a neoplastic cell load of 50% the NGS-based BAF (y axis) is shown for an increasing number of alleles (x axis). b An example of BAFs of common SNPs at the gene loci of the NGS results of sample 2, presented in Fig. 1, in which Gene B is amplified. Every circle represents the variant allele frequency of a common SNP. Dark gray circles represent homozygous alleles. Blue circles represent heterozygous alleles for which the BAF is within the expected ~50% (40–60% range). Yellow circles represent heterozygous alleles for which the BAF is divergent from this range due to amplification of the reference allele (decreased BAF) or amplification of the variant allele (increased BAF)