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Báo cáo y học: " Single-cell copy number variation detection"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Single-cell copy number variation detection. | Cheng et al. Genome Biology 2011 12 R80 http genomebiology.eom content 12 8 R80 Genome Biology METHOD Open Access Single-cell copy number variation detection 1.2 3 1.2 3 3 1.2 Jiqiu Cheng Evelyne Vanneste Peter Konings Thierry Voet Joris R Vermeesch and Yves Moreau 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. Background Array analysis of single-cell copy number variations CNVs is a recently developed experimental technique for the detection of chromosomal rearrangements in single cells 1-4 . Two-color single-cell array comparative genomic hybridization CGH assays the copy number difference between an euploid reference sample from genomic DNA and an unknown test sample from amplified single-cell DNA by comparing signal intensities using log2 ratios 5 . However the accurate detection of single-cell CNV has been hampered by the noise levels in the log2 ratios caused by the amplification of the minute quantities of DNA present in a single cell. Moreover since the reference DNA in single-cell array exp eriments is non-amplified genomic DNA extracted from a large number of cells 2 the biological nature of test and reference sample is different resulting in new genome artifacts 6 . Unfortunately existing normalization strategies do not provide clear guidelines for checking for these artifacts nor for handling