The screening and ranking algorithm to detect DNA copy number variations

DOI10.1214/12-AOAS539zbMATH Open1401.92145arXiv1210.0345OpenAlexW2033695946MaRDI QIDQ714382FDOQ714382

Authors: Heping Zhang, Yue Selena Niu 

Publication date: 21 October 2012

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: DNA Copy number variation (CNV) has recently gained considerable interest as a source of genetic variation that likely influences phenotypic differences. Many statistical and computational methods have been proposed and applied to detect CNVs based on data that generated by genome analysis platforms. However, most algorithms are computationally intensive with complexity at least $O(n^2)$, where $n$ is the number of probes in the experiments. Moreover, the theoretical properties of those existing methods are not well understood. A faster and better characterized algorithm is desirable for the ultra high throughput data. In this study, we propose the Screening and Ranking algorithm (SaRa) which can detect CNVs fast and accurately with complexity down to O(n). In addition, we characterize theoretical properties and present numerical analysis for our algorithm.

Full work available at URL: https://arxiv.org/abs/1210.0345

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zbMATH Keywords

change-point detectionhigh dimensional datacopy number variationsscreening and ranking algorithm

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Statistical ranking and selection procedures (62F07) Genetics and epigenetics (92D10)

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Cited In (43)

• Detecting transcriptomic structural variants in heterogeneous contexts via the multiple compatible arrangements problem
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• Covariate assisted screening and estimation
• Authors' rejoinder on ``Birnbaum-Saunders distribution: a review of models, analysis, and applications
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• Moving Sum Procedure for Change Point Detection under Piecewise Linearity
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Uses Software

• PennCNV

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