A very fast and accurate method for calling aberrations in array-CGH data.
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.
Benelli
Matteo
M
Diagnostic Genetic Unit, Careggi Hospital, Azienda Ospedaliera Universitaria Careggi, University of Florence, Florence, Italy. matteo.benelli@gmail.com
Marseglia
Giuseppina
G
Nannetti
Genni
G
Paravidino
Roberta
R
Zara
Federico
F
Bricarelli
Franca Dagna
FD
Torricelli
Francesca
F
Magi
Alberto
A
D000465:Algorithms; D055028:Comparative Genomic Hybridization / Q000379:methods*; D003198:Computer Simulation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*