How to create region not called by the algorithm for BeadArray data in BlueFuse Multi

BlueFuse Multi uses the CGH (Comparative Genomic Hybridization) and LOH (Loss of Heterozygosity) Region Calling algorithm for BeadChip Arrays. This algorithm simultaneously detects regions of copy number imbalance and regions of copy number neutral LOH. Each copy number, LOH, and mosaic state is associated with a specific pattern in both the Log R Ratio chart and the B Allele Frequency chart. This algorithm simultaneously uses the direction and magnitude of the Log R Ratio intensity signal, along with the distribution of B Allele Frequency signal. Therefore, the algorithm can segment the genome into regions where the joint Log R Ratio and B Allele Frequency patterns differ.

How to create a region manually in BlueFuse Multi

There may be instances when the user identifies a region of imbalance that is not detected by the algorithm. The "Create Region" feature allows the manual creation of:

• a region of imbalance in the CGH/CNV and Fused charts

• a region of LOH in the Fused SNP Copy Number chart for SNP experiments

In the Log R Ratio or B-Allele Frequency Chart, the user can select and manually create a region from a series of probes that have not been automatically called.

Log R Ratio Graph

In the Log R Ratio graph

1. Highlight the region by left-clicking and dragging (highlighted probe datapoints will turn yellow).

2. Right-click to open context menu and select "Create Region".

3. Specify whether the region is a Gain, Loss, or No Change.

B Allele Frequency Graph

In the B Allele Frequency graph

1. Highlight the region by left-clicking and dragging.

2. Right-click to open context menu and select "Create Region".

3. Specify whether the region is LOH, heterozygous, hemizygous, or nullizygous for SNP experiments

If the selected probes are already included in a region, the options for the region type are grayed out. Multiple existing regions can be merged into a single region.

The "Create Region Query", available in the same pulldowns, allows the user to search the current database for other experiments that contain the same imbalance.

SeeBlueFuse Multi Software Guide for additional information.

For any feedback or questions regarding this article (Illumina Knowledge Article #5044), contact Illumina Technical Support [email protected].