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Single-cell copy number variation detection

Jiqiu Cheng12, Evelyne Vanneste3, Peter Konings12, Thierry Voet3, Joris R Vermeesch3 and Yves Moreau12*

Author Affiliations

1 Department of Electrical Engineering, Esat-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven 3001, Belgium

2 IBBT-K.U.Leuven Future Health Department, Kasteelpark Arenberg 10, Leuven 3001, Belgium

3 Center for Human Genetics, Katholieke Universiteit Leuven, Herestraat 49, Leuven 3000, Belgium

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Genome Biology 2011, 12:R80  doi:10.1186/gb-2011-12-8-r80

Published: 19 August 2011

Abstract

Detection of chromosomal aberrations from a single cell by array comparative genomic hybridization (single-cell array CGH), instead of from a population of cells, is an emerging technique. However, such detection is challenging because of the genome artifacts and the DNA amplification process inherent to the single cell approach. Current normalization algorithms result in inaccurate aberration detection for single-cell data. We propose a normalization method based on channel, genome composition and recurrent genome artifact corrections. We demonstrate that the proposed channel clone normalization significantly improves the copy number variation detection in both simulated and real single-cell array CGH data.