title: A novel approach to DNA copy number data segmentation.
abstract: DNA copy number (DCN) is the number of copies of DNA at a region of a genome. The alterations of DCN are highly associated with the development of different tumors. Recently, microarray technologies are being employed to detect DCN changes at many loci at the same time in tumor samples. The resulting DCN data are often very noisy, and the tumor sample is often contaminated by normal cells. The goal of computational analysis of array-based DCN data is to infer the underlying DCNs from raw DCN data. Previous methods for this task do not model the tumor/normal cell mixture ratio explicitly and they cannot output segments with DCN annotations. We developed a novel model-based method using the minimum description length (MDL) principle for DCN data segmentation. Our new method can output underlying DCN for each chromosomal segment, and at the same time, infer the underlying tumor proportion in the test samples. Empirical results show that our method achieves better accuracies on average as compared to three previous methods, namely Circular Binary Segmentation, Hidden Markov Model and Ultrasome.
authors.affiliation: Department of Computer Science and Engineering, Southern Methodist University, Dallas, Texas 75205, USA. silingw@smu.edu
authors.forename: Siling
authors.initials: S
authors.lastname: Wang
authors.forename: Yuhang
authors.initials: Y
authors.lastname: Wang
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.forename: Guanghua
authors.initials: G
authors.lastname: Xiao
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D056915:DNA Copy Number Variations; D004273:DNA, Neoplasm / Q000235:genetics; D003627:Data Interpretation, Statistical; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D006801:Humans; D008390:Markov Chains; D015233:Models, Statistical; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D012984:Software
chemical_list: D004273:DNA, Neoplasm