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.
Overview plot showing both copy number aberrations and allelic Events. The blue and red bars next to the ideograms depict gain and loss regions respectively and the allelic event aberrations are shown with the gold (LOH) and purple (allelic imbalance) highlighting on the ideograms.
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 Heterozygosity (LOH). Nexus Copy Number will then report these events in all tables as well as display them graphically as shown below:
Features
Special processing for SNP arrays
Segmentation algorithm takes into account B-allele frequency values along with log ratio values
Allele-specific calls such as LOH, copy neutral LOH, allelic imbalance
ASCAT (Allele Specific Copy Number Analysis of Tumors) processing for cancer samples
Applications
The module is necessary for those working with SNP arrays such as those from Affymetrix, Agilent, and Illumina. It will allow processing of B-allele frequency results which allow for reporting of allelic event calls such as LOH. Copy neutral LOH can be identified by utilizing the log ratio data as well as the B-allele frequency values. Both copy number and allelic events are displayed alongside each other in a fully interactive browser. Filtering options allow the user to display only the large areas of allelic imbalances or only the copy neutral LOH regions, for example. The report table shows the type of call as well as percent heterozygosity. This module is also quite useful for cancer studies for its ASCAT processing to generate estimates of sample ploidy, copy number, and extent of normal cell contamination of the tumor samples.
An area of copy neutral LOH on chromosome 15. Lack of a corresponding red bar above the gold bar indicates it’s a copy neutral LOH.
A drill down view of a single chromosome with an interactive graphical display along the top containing annotation tracks and plots with a report table on the bottom.
