Outlier reset CUSUM for the exploration of copy number alteration data
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Yinglei Lai
und
Joseph L. Gastwirth
Abstract
Copy number alteration (CNA) data have been collected to study disease related chromosomal amplifications and deletions. The CUSUM procedure and related plots have been used to explore CNA data. In practice, it is possible to observe outliers. Then, modifications of the CUSUM procedure may be required. An outlier reset modification of the CUSUM (ORCUSUM) procedure is developed in this paper. The threshold value for detecting outliers or significant CUSUMs can be derived using results for sums of independent truncated normal random variables. Bartel’s non-parametric test for autocorrelation is also introduced to the analysis of copy number variation data. Our simulation results indicate that the ORCUSUM procedure can still be used even in the situation where the degree of autocorrelation level is low. Furthermore, the results show the outlier’s impact on the traditional CUSUM’s performance and illustrate the advantage of the ORCUSUM’s outlier reset feature. Additionally, we discuss how the ORCUSUM can be applied to examine CNA data with a simulated data set. To illustrate the procedure, recently collected single nucleotide polymorphism (SNP) based CNA data from The Cancer Genome Atlas (TCGA) Research Network is analyzed. The method is applied to a data set collected in an ovarian cancer study. Three cytogenetic bands (cytobands) are considered to illustrate the method. The cytobands 11q13 and 9p21 have been shown to be related to ovarian cancer. They are presented as positive examples. The cytoband 3q22, which is less likely to be disease related, is presented as a negative example. These results illustrate the usefulness of the ORCUSUM procedure as an exploratory tool for the analysis of SNP based CNA data.
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©2015 by De Gruyter
Artikel in diesem Heft
- Frontmatter
- Research Articles
- Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions
- Outlier reset CUSUM for the exploration of copy number alteration data
- Simultaneous Bayesian analysis of contingency tables in genetic association studies
- Modeling the next generation sequencing read count data for DNA copy number variant study
- Synonymous and nonsynonymous distances help untangle convergent evolution and recombination
- Node sampling for protein complex estimation in bait-prey graphs
Artikel in diesem Heft
- Frontmatter
- Research Articles
- Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions
- Outlier reset CUSUM for the exploration of copy number alteration data
- Simultaneous Bayesian analysis of contingency tables in genetic association studies
- Modeling the next generation sequencing read count data for DNA copy number variant study
- Synonymous and nonsynonymous distances help untangle convergent evolution and recombination
- Node sampling for protein complex estimation in bait-prey graphs
