title: Single-cell copy number variation detection.
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.
authors.affiliation: Department of Electrical Engineering, Esat-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven 3001, Belgium.
authors.forename: Jiqiu
authors.initials: J
authors.lastname: Cheng
authors.forename: Evelyne
authors.initials: E
authors.lastname: Vanneste
authors.forename: Peter
authors.initials: P
authors.lastname: Konings
authors.forename: Thierry
authors.initials: T
authors.lastname: Voet
authors.forename: Joris R
authors.initials: JR
authors.lastname: Vermeesch
authors.forename: Yves
authors.initials: Y
authors.lastname: Moreau
mesh_terms: D000465:Algorithms; D016477:Artifacts; D002869:Chromosome Aberrations; D002877:Chromosomes, Human / Q000235:genetics; D055028:Comparative Genomic Hybridization / Q000379:methods*; D003198:Computer Simulation; D056915:DNA Copy Number Variations; D018628:Gene Dosage; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D059010:Single-Cell Analysis / Q000379:methods*