OverUnder BeadStudio plugin
Introduction

Version 3.9 (2/26/2009)
Edward F. Attiyeh

OverUnder is an algorithm for determining genomic copy number from SNP microarray data. It is currently implemented as a plugin to the BeadStudio package from Illumina. It employs four complimentary methods to overcome some of the existing problems with genomic array analysis.

  1. Copy number is calculated based on the quantitative allelic ratio and not the probe intensity measurement.
  2. Copy number is calculated as a continuous variable which reflects the heterogeneity of genomes extracted from cancer tissues.
  3. Aneuploidy is detected, and the probe intensity values are corrected to account for the increased DNA content of many tumor samples. This ultimately allows for determination of absolute copy number as opposed to copy number relative to the DNA index.
  4. Gains are characterized by the number of minor alleles present.

Please cite uses of the algorithm as Attiyeh et al.(2009) Genome Res 19(2):276-28