A very fast and accurate method for calling aberrations in array-CGH data

Biostatistics. 2010 Jul;11(3):515-8. doi: 10.1093/biostatistics/kxq008. Epub 2010 Mar 5.

Abstract

Array comparative genomic hybridization (aCGH) is a microarray technology that allows one to detect and map genomic alterations. The standard workflow of the aCGH data analysis consists of 2 steps: detecting the boundaries of the regions of changed copy number by means of a segmentation algorithm (break point identification) and then labeling each region as loss, neutral, or gain with a probabilistic framework (calling procedure). In this paper, we introduce a novel calling procedure based on a mixture of truncated normal distributions, named FastCall, that aims to give aberration probabilities to segmented aCGH data in a very fast and accurate way. Both on synthetic and real aCGH data, FastCall obtains excellent performances in terms of classification accuracy and running time.

MeSH terms

  • Algorithms
  • Comparative Genomic Hybridization / methods*
  • Computer Simulation
  • Oligonucleotide Array Sequence Analysis / methods*