Development of an Improved Segmentation Method Based on Circular Binary Segmentation for Array Comparative Genomic Hybridization
Date Issued
2007
Date
2007
Author(s)
Hsu, Fang-Han
DOI
en-US
Abstract
Chromosomal aberration in the form of DNA copy number changes correlates with numerous disease including cancer. aCGH is a novel technique to detect the DNA copy number changes. For a given genomic profile, the initial computational process in aCGH data analysis is commonly referred to as “segmentation”. DNAcopy, one of the most popular segmentation methods, has good sensitivity and False Discovery Rate (FDR) for breakpoint detection. However, the time-consuming process of computation prohibits the method from analyzing large dataset. Based on DNAcopy, we proposed an improved segmentation method, called Faster Circular Binary Segmentation (FCBS). The approximation of the p-value of t-test by using Student’s t-distribution is applied to speed up the algorithm and a delayed decision is introduced for further improvement. We show through simulation that our method has minimal effect on accuracy. Finally, two aCGH datasets were analyzed and the time consumption of DNAcopy and FCBS was compared and studied.
Subjects
比較基因體雜合
去氧核醣核酸拷貝數
分割法
循環二元分割法
aCGH
DNA copy numbers
segmentation
DNAcopy
FCBS
SDGs
Type
thesis
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