The Annals of Applied Statistics

The screening and ranking algorithm to detect DNA copy number variations

Yue S. Niu and Heping Zhang

Full-text: Open access

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.

Article information

Source
Ann. Appl. Stat., Volume 6, Number 3 (2012), 1306-1326.

Dates
First available in Project Euclid: 31 August 2012

Permanent link to this document
https://projecteuclid.org/euclid.aoas/1346418584

Digital Object Identifier
doi:10.1214/12-AOAS539

Mathematical Reviews number (MathSciNet)
MR3012531

Zentralblatt MATH identifier
06096532

Keywords
Change-point detection copy number variations high dimensional data screening and ranking algorithm

Citation

Niu, Yue S.; Zhang, Heping. The screening and ranking algorithm to detect DNA copy number variations. Ann. Appl. Stat. 6 (2012), no. 3, 1306--1326. doi:10.1214/12-AOAS539. https://projecteuclid.org/euclid.aoas/1346418584


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Supplemental materials

  • Supplementary material: A description of general weight functions and technical proofs. The pdf file contains a description of general weight functions and the proof of Theorem 1.