Allele Specific Computation Module

This module provides access to BioDiscovery’s SNPRank Segmentation as well SNP-FASST algorithms. Both of these methods are designed to take advantage of the allele specific measurements provided by SNP arrays. The processing combines the Log ratio values for each probe with the B-Allele Frequency (BAF) to identify regions of genomic change. These changes are both in terms of copy number: gain and loss, as well as allelic events: Imbalance and Loss of Heterozygousity (LOH). Nexus Copy Number will then report these events in all tables as well as display them graphically as shown below:

Single sample view of Chromosome 4 showing a one copy loss (marked by red bar) as well as areas of LOH (marked by light brown bars). Note that the LOH area around the centromer is a “copy neutral LOH” event since there is no corresponding copy number loss detected.

Frequency plot of LOH events across the genome. A recurrent copy neutral LOH event is seen around the centromer of chromosome 4