a robust penalized method for the analysis of noisy dna copy number data一个健壮的处罚方法,嘈杂的dna拷贝数的分析数据.pdfVIP

Gao and Huang BMC Genomics 2010, 11:517 /1471-2164/11/517 RESEARCH ARTICLE Open Access A robust penalized method for the analysis of noisy DNA copy number data Xiaoli Gao1*, Jian Huang2,3 Abstract Background: Deletions and amplifications of the human genomic DNA copy number are the causes of numerous diseases, such as, various forms of cancer. Therefore, the detection of DNA copy number variations (CNV) is important in understanding the genetic basis of many diseases. Various techniques and platforms have been developed for genome-wide analysis of DNA copy number, such as, array-based comparative genomic hybridization (aCGH) and high-resolution mapping with high-density tiling oligonucleotide arrays. Since complicated biological and experimental processes are often associated with these platforms, data can be potentially contaminated by outliers. Results: We propose a penalized LAD regression model with the adaptive fused lasso penalty for detecting CNV. This method contains robust properties and incorporates both the spatial dependence and sparsity of CNV into the analysis. Our simulation studies and real data analysis indicate that the proposed method can correctly detect the numbers and locations of the true breakpoints while appropriately controlling the false positives. Conclusions: The proposed method has three advantages for detecting CNV change points: it contains robustness properties; incorporates both spatial dependence and sparsity; and estimates the true values at each marker accurately. Background DNA sample of interest (test sample), and a reference Deletions and amplifications of the human genomic sample are differentially labelled with dyes, typically Cy3 DNA copy number are the causes of numerous diseases.