Method Overview
Sapio's Loss of Heterozygosity experiments perform analysis on high density genotyping datasets.
LOH in Exemplar is calculated via a probability-based method. This method computes the probability that a string of homozygous genotypes would occur by chance alone. If a block of homozygous neighboring SNP’s in the analysis set has a very low probability of being homozygous in the reference set, then that block is shown to have a high probability of LOH.
LOH is calculated for each individual SNP in the input dataset, and then the results are'smoothed' across user-specified blocks of SNP’s to reduce noise. The results are presented in a high quality graphical interface that includes interactive charts, tables, and visual mapping of the results onto a chromosome viewer.
The software allows the user to specify their own reference set to use against a set of samples to be analyzed for LOH. The results are computed across blocks of homozygous SNP's or optionally by using a user-defined block size.
Results
Results are graphically displayed in both chart and tabular displays. Some examples of the graphical output are illustrated below:
