CytoSure™ Interpret Software — Tips and Tricks

Tuesday 29 January 2013
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B-Allele Frequency display and analysis

In order to facilitate more in-depth analysis of allelic imbalance within samples that have been assayed with one of OGT’s CytoSure CNV +SNP arrays, CytoSure Interpret Software v4.3 (and above) includes the display and analysis of the B-Allele Frequency (BAF) of each SNP included in the design.

B-Allele Frequency

The B-Allele Frequency is a normalized measure of the allelic intensity ratio of two alleles (A and B), such that a BAF of 1 or 0 indicates the complete absence of one of the two alleles (e.g. AA or BB), and a BAF of 0.5 indicates the equal presence of both alleles (e.g. AB).

 Image 1


Figure 1: A screenshot of a section of the Overview section of the Genomic View showing, from top to bottom, the chromosome ideogram, the CNV probe log ratio scatter plot, and the SNP probe B-Allele Frequency plot.

Previous visualisation and analysis of SNP data within CytoSure Interpret Software enabled detection of regions of LOH (containing only BAF values around 0 or 1), but did not enable detection of allelic imbalances such as those caused by duplications (e.g. AAB/BBA) or mosaic deletions in the sample. Such imbalances can be identified on a BAF plot by the presence of SNPs at frequencies between 0.5 and 0 or 1. For example, the theoretical BAF values of triploid regions (AAA, AAB, ABB or BBB) are 0, 0.33, 0.66 and 1 respectively.

 Image 2

Figure 2: An example of a duplication of 2p resulting in BAF values of approx 0, 0.33, 0.66 and 1, and a hemizygous deletion on 2q resulting in BAF values of 0 and 1.

In order to automatically detect such regions, CytoSure Interpret Software segments the BAF data mirrored at 0.5 (see Staaf et al, Genome Biology 2008, 9:R136) and highlights regions showing an absence of heterozygous SNPs (i.e. SNPs with BAF values of approx. 0.5). In the case of losses and copy neutral events, the software also calculates the theoretical fraction of cells showing the allelic imbalance and displays this value in the BAF plot.

 Image 3


Figure 3: An example of a mosaic deletion of 18q resulting in BAF values of 0, 1 and approx. 0.32 and 0.68, indicating ~54% aberrant cells.

Please also note that areas shaded in red indicate regions of LOH.

Display options

The B-Allele Frequency plot can be displayed in both the Genomic View tab (next to the summary of the CNV probes for the selected chromosome) and the CNVs/SNPs tab (on selecting an individual chromosome from the ideogram view grid). To toggle the display of the B-Allele Frequency plot in the Genomic View tab, right-click on the CNV probe summary plot in the Overview section and select Show/Hide B-Allele Frequency Plot. In the CNVs/SNPs tab, ensure that the Ideogram View and the Show CNVs? checkbox are selected, select a chromosome containing SNP probes, then right-click anywhere in the Detected CNVs/SNPs section. This will provide the option to either Show B-Allele Frequency Plot or Show Distribution Plot depending on your current configuration.

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CytoSure™ products are for research use only; not for use in diagnostic procedures.