Biostatistics Vol. 5 No. 4 © Oxford University Press 2004; all rights reserved.
Circular binary segmentation for the analysis of array-based DNA copy number data
Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
olshena{at}mskcc.org
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
DNA sequence copy number is the number of copies of DNA at a region of a genome. Cancer progression often involves alterations in DNA copy number. Newly developed microarray technologies enable simultaneous measurement of copy number at thousands of sites in a genome. We have developed a modification of binary segmentation, which we call circular binary segmentation, to translate noisy intensity measurements into regions of equal copy number. The method is evaluated by simulation and is demonstrated on cell line data with known copy number alterations and on a breast cancer cell line data set.
Keywords: Array CGH; Binary segmentation; Change-point; ROMA
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|
|
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|
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 W. Lai, V. Choudhary, and P. J. Park CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms Bioinformatics, April 1, 2008; 24(7): 1014 - 1015. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
 A. Li, J. Walling, Y. Kotliarov, A. Center, M. E. Steed, S. J. Ahn, M. Rosenblum, T. Mikkelsen, J. C. Zenklusen, and H. A. Fine Genomic Changes and Gene Expression Profiles Reveal That Established Glioma Cell Lines Are Poorly Representative of Primary Human Gliomas Mol. Cancer Res., January 1, 2008; 6(1): 21 - 30. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 P. J. Park Integrated Analysis of Array-CGH and Expression Data Am. Assoc. Cancer Res. Educ. Book, April 14, 2007; 2007(1): 209 - 212. [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
E. S. Venkatraman and A. B. Olshen A faster circular binary segmentation algorithm for the analysis of array CGH data Bioinformatics, March 15, 2007; 23(6): 657 - 663. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
J. Hicks, A. Krasnitz, B. Lakshmi, N. E. Navin, M. Riggs, E. Leibu, D. Esposito, J. Alexander, J. Troge, V. Grubor, et al. Novel patterns of genome rearrangement and their association with survival in breast cancer Genome Res., December 1, 2006; 16(12): 1465 - 1479. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Fiegler, R. Redon, D. Andrews, C. Scott, R. Andrews, C. Carder, R. Clark, O. Dovey, P. Ellis, L. Feuk, et al. Accurate and reliable high-throughput detection of copy number variation in the human genome Genome Res., December 1, 2006; 16(12): 1566 - 1574. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Maher, C. Brennan, P. Y. Wen, L. Durso, K. L. Ligon, A. Richardson, D. Khatry, B. Feng, R. Sinha, D. N. Louis, et al. Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities Cancer Res., December 1, 2006; 66(23): 11502 - 11513. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Willenbrock, A. Petersen, C. Sekse, K. Kiil, Y. Wasteson, and D. W. Ussery Design of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling J. Bacteriol., November 15, 2006; 188(22): 7713 - 7721. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Liu, P. J. Park, W. Lai, E. Maher, A. Chakravarti, L. Durso, X. Jiang, Y. Yu, A. Brosius, M. Thomas, et al. A Genome-Wide Screen Reveals Functional Gene Clusters in the Cancer Genome and Identifies EphA2 as a Mitogen in Glioblastoma Cancer Res., November 15, 2006; 66(22): 10815 - 10823. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Trautmann, J. P. Terdiman, A. J. French, R. Roydasgupta, N. Sein, S. Kakar, J. Fridlyand, A. M. Snijders, D. G. Albertson, S. N. Thibodeau, et al. Chromosomal Instability in Microsatellite-Unstable and Stable Colon Cancer. Clin. Cancer Res., November 1, 2006; 12(21): 6379 - 6385. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Pejovic, J. E. Yates, H. Y. Liu, L. E. Hays, Y. Akkari, Y. Torimaru, W. Keeble, R. K. Rathbun, W. H. Rodgers, A. E. Bale, et al. Cytogenetic instability in ovarian epithelial cells from women at risk of ovarian cancer. Cancer Res., September 15, 2006; 66(18): 9017 - 9025. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Ng, J. Huang, I. Roberts, and N. Coleman Defining Ploidy-Specific Thresholds in Array Comparative Genomic Hybridization to Improve the Sensitivity of Detection of Single Copy Alterations in Cell Lines J. Mol. Diagn., September 1, 2006; 8(4): 449 - 458. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. L. Rosa, E. Viara, P. Hupe, G. Pierron, S. Liva, P. Neuvial, I. Brito, S. Lair, N. Servant, N. Robine, et al. VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles Bioinformatics, September 1, 2006; 22(17): 2066 - 2073. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. N. van Wieringen, J. A. M. Belien, S. J. Vosse, E. M. Achame, and B. Ylstra ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data Bioinformatics, August 1, 2006; 22(15): 1919 - 1920. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Zhang, J. Huang, N. Yang, J. Greshock, M. S. Megraw, A. Giannakakis, S. Liang, T. L. Naylor, A. Barchetti, M. R. Ward, et al. microRNAs exhibit high frequency genomic alterations in human cancer PNAS, June 13, 2006; 103(24): 9136 - 9141. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Strefford, F. W. van Delft, H. M. Robinson, H. Worley, O. Yiannikouris, R. Selzer, T. Richmond, I. Hann, T. Bellotti, M. Raghavan, et al. Complex genomic alterations and gene expression in acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21 PNAS, May 23, 2006; 103(21): 8167 - 8172. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Mohapatra, R. A. Betensky, E. R. Miller, B. Carey, L. D. Gaumont, D. A. Engler, and D. N. Louis Glioma Test Array for Use with Formalin-Fixed, Paraffin-Embedded Tissue: Array Comparative Genomic Hybridization Correlates with Loss of Heterozygosity and Fluorescence in Situ Hybridization J. Mol. Diagn., May 1, 2006; 8(2): 268 - 276. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Marioni, N. P. Thorne, and S. Tavare BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data Bioinformatics, May 1, 2006; 22(9): 1144 - 1146. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Yao, S. Weremowicz, B. Feng, R. C. Gentleman, J. R. Marks, R. Gelman, C. Brennan, and K. Polyak Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression. Cancer Res., April 15, 2006; 66(8): 4065 - 4078. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Chen, J. Houldsworth, A. B. Olshen, G. Nanjangud, S. Chaganti, E. S. Venkatraman, J. Halaas, J. Teruya-Feldstein, A. D. Zelenetz, and R. S. K. Chaganti Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas Blood, March 15, 2006; 107(6): 2477 - 2485. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Willenbrock and J. Fridlyand A comparison study: applying segmentation to array CGH data for downstream analyses Bioinformatics, November 15, 2005; 21(22): 4084 - 4091. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Huang, B. Wu, P. Lizardi, and H. Zhao Detection of DNA copy number alterations using penalized least squares regression Bioinformatics, October 15, 2005; 21(20): 3811 - 3817. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. R. Lai, M. D. Johnson, R. Kucherlapati, and P. J. Park Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data Bioinformatics, October 1, 2005; 21(19): 3763 - 3770. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. van de Wiel, S. J. Smeets, R. H. Brakenhoff, and B. Ylstra CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data Bioinformatics, July 15, 2005; 21(14): 3193 - 3194. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Zhao, B. A. Weir, T. LaFramboise, M. Lin, R. Beroukhim, L. Garraway, J. Beheshti, J. C. Lee, K. Naoki, W. G. Richards, et al. Homozygous Deletions and Chromosome Amplifications in Human Lung Carcinomas Revealed by Single Nucleotide Polymorphism Array Analysis Cancer Res., July 1, 2005; 65(13): 5561 - 5570. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. S. Price, R. Regan, R. Mott, A. Hedman, B. Honey, R. J. Daniels, L. Smith, A. Greenfield, A. Tiganescu, V. Buckle, et al. SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data Nucleic Acids Res., June 16, 2005; 33(11): 3455 - 3464. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. H. C. Eilers and R. X. de Menezes Quantile smoothing of array CGH data Bioinformatics, April 1, 2005; 21(7): 1146 - 1153. [Abstract] [Full Text] [PDF]
|
|