What is the limit of detection for LOH/AOH for the CytoSNP 850K array?

The minimum detectable region of LOH/AOH (loss of heterozygosity/absence of heterozygosity) will vary from sample to sample, depending on the amount of noise in the data (Log R Deviation) and overall quality of the data from the sample (call rate). The detectable region size is also influenced by the coverage and distribution of the single nucleotide polymorphisms (SNP) markers across a given region.

In BlueFuse Multi analysis software, the default analysis algorithm sets a minimum LOH Region Size for CytoSNP-850K v1.2 and 1.3 of 3 Mb, assuming the sample meets the QC metrics for beadarray data of SD Autosome/Robust <0.20/0.17, Median Log R Dev of <0.20, and Median call rate of >0.98. The algorithm also sets a default minimum number of markers for a detectable region at 500 SNPs. Regions must meet both criteria in order to be detected as regions of LOH/AOH.

For any feedback or questions regarding this article (Illumina Knowledge Article #6024), contact Illumina Technical Support [e-mail].