A faster circular binary segmentation algorithm for the analysis of array CGH data | Zendy

E. S. Venkatraman | Zendy; Adam B. Olshen | Zendy

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A faster circular binary segmentation algorithm for the analysis of array CGH data

Author(s) -

E. S. Venkatraman,

Adam B. Olshen

Publication year - 2007

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btl646

Subject(s) - permutation (music) , algorithm , computer science , statistic , binary number , computation , bioconductor , test statistic , mathematics , statistical hypothesis testing , statistics , arithmetic , biochemistry , physics , chemistry , acoustics , gene

Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number. The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding P-value. The number of computations required for the maximal test statistic is O(N2), where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm.

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