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OJBTM
Online
Journal of Bioinformatics ©
Volume 11 (2):
224-244, 2010
Analysis of array CGH data for the detection of
single-cell chromosomal imbalances
Michele Ampe1 (MSc) ,
Geert Verbeke1 (PhD), Evelyne Vanneste2(MSc), Joris Robert Vermeesch2(PhD)
1 Interuniversity Institute
for Biostatistics and statistical Bioinformatics, Katholieke
Universiteit Leuven and Universiteit
Hasselt and, 2Centre for Human Genetics (CME), Katholieke
Universiteit Leuven, Belgium
ABSTRACT
Ampe M, Verbeke G, Vanneste E, Vermeesch JR.,
Analysis of array CGH data for the detection of single-cell chromosomal
imbalances, Online J Bioinformatics, 11 (2):
224-244, 2010. Array comparative genomic hybridization (array CGH) can be used to
detect genome-wide changes in the chromosomal copy number in single cells.
Single cell array CGH has the specific problem of bias introduced by the
amplification of the DNA. To increase the resolution and the accuracy of the
detection of chromosomal imbalances in single cells, we developed a finite
mixture model with a clone-specific correction enabling the detection of
chromosomal and segmental aneuploidies. The clone-specific correction is
derived from a reference set of normal chromosomes. The detection of
aneuploidies is equivalent to searching for regions of successive clones that
belong to one of the mixture groups. To obtain these regions, the posterior
probabilities of the clones are smoothed by means of a loess smoothing. We
tested our methodology on single cells with known aberrations as well as
through simulations and could detect both chromosomal and segmental
aneuploidies.
Key
words: Single-cell chromosomal imbalances, array CGH ,
Finite Mixture, Clone-specific correction
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