An all-statistics, high-speed algorithm for the analysis of copy number variation in genomes

Nucleic Acids Research

Volumn 39, Issue 13, 2011, Pages

  Chen, Chih Hao ^a,b   Lee, Hsing Chung ^a,c   Ling, Qingdong ^a,b   Chen, Hsiao Rong ^a,e   Ko, Yi An ^a,f   Tsou, Tsong Shan ^a,b   Wang, Sun Chong ^a   Wu, Li Ching ^a   Lee, H C ^a,b,d  

^a NATIONAL CENTRAL UNIVERSITY   (Taiwan)

^b Cathay Medical Research Institute   (Taiwan)

^c CATHAY GENERAL HOSPITAL   (Taiwan)

^d NATIONAL CENTER FOR THEORETICAL SCIENCES   (Taiwan)

^e BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CHROMOSOME ANALYSIS; COMPUTER INTERFACE; COMPUTER MEMORY; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE CLUSTER; GENE CONSTRUCT; GENETIC ALGORITHM; HUMAN; HUMAN CELL; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; STATISTICAL ANALYSIS;

ALGORITHMS; CLUSTER ANALYSIS; DATA INTERPRETATION, STATISTICAL; DNA COPY NUMBER VARIATIONS; GENOME; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS;

EID: 80052237138     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr137     Document Type: Article

References (25)

1. Pollack, J.R., Perou, C.M., Alizadeh, A.A., Eisen, M.B., Pergamenschikov, A., Williams, C.F., Jeffrey, S.S., Botstein, D. and Brown, P.O. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet., 23, 41-46. (Pubitemid 29418785)
2. Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Maner, S., Massa, H., Walker, M., Chi, M. et al. (2004) Large-Scale copy number polymorphism in the human genome. Science, 305, 525-528. (Pubitemid 38971344)
3. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., Fiegler, H., Shapero, M.H., Carson, A.R., Chen, W. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454. (Pubitemid 44809057)
4. Barnes, C., Plagnol, V., Fitzgerald, T., Redon, R., Marchini, J., Clayton, D. and Hurles, M.E. (2008) A robust statistical method for case-control association testing with copy number variation. Nat. Genet., 40, 1245-1252.
5. Solinas-Toldo, S., Lampel, S., Stilgenbauer, S., Nickolenko, J., Benner, A., Dohner, H., Cremer, T. and Lichter, P. (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Gene Chromosome. Canc., 20, 399-407. (Pubitemid 27520090)
6. Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.L., Chen, C., Zhai, Y. et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20, 207-211. (Pubitemid 28455458)
7. Pinkel, D. and Albertson, D.G. (2005) Array comparative genomic hybridization and its applications in cancer. Nat. Genet., 37(Suppl.), 11-17.
8. Brennan, C., Zhang, Y., Leo, C., Feng, B., Cauwels, C., Aguirre, A.J., Kim, M., Protopopov, A. and Chin, L. (2004) High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res., 64, 4744-4748. (Pubitemid 38924516)
9. Lucito, R., Healy, J., Alexander, J., Reiner, A., Esposito, D., Chi, M., Rodgers, L., Brady, A., Sebat, J., Troge, J. et al. (2003) Representational oligonucleotide microarray analysis: a highresolution method to detect genome copy number variation. Genome Res., 13, 2291-2305. (Pubitemid 37265995)
10. Ishkanian, A.S., Malloff, C.A., Watson, S.K., deLeeuw, R.J., Chi, B., Coe, B.P., Snijders, A., Albertson, D.G., Pinkel, D., Marra, M.A. et al. (2004) A tiling resolution DNAmicroarray with complete coverage of the human genome. Nat. Genet., 36, 299-303. (Pubitemid 38282757)
11. Lai, W.R., Johnson, M.D., Kucherlapati, R. and Park, P.J. (2005) Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics, 21, 3763-3770. (Pubitemid 41535525)
12. Hsu, L., Self, S.G., Grove, D., Randolph, T., Want, K., Delrow, J.J., Loo, L. and Porter, P. (2005) Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics, 6, 211-226. (Pubitemid 41240354)
13. Eilers, P.H.C. and de Menezes, R.X. (2005) Quantile smoothing of array CGH data. Bioinformatics, 21, 1146-1153. (Pubitemid 40467939)
14. Picard, F., Robin, S., Lavielle, M., Vaisse, C. and Daudin, J. (2005) A statistical approach for array CGH data analysis. BMC Bioinforma., 6, 27.
15. Olshen, A.B., Venkatraman, E.S., Lucito, R. and Wigler, M. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572. (Pubitemid 41180205)
16. Myers, C.L., Dunham, M.J., Kung, S.Y. and Troyanskaya, O.G. (2004) Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics, 20, 3533-3543. (Pubitemid 40136789)
17. Lingjde, O.C., Baumbusch, L.O., Liest, K., Glad, I.K. and Bresen-Dale, A. (2005) CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics, 21, 821-822. (Pubitemid 40439420)
18. Fridlyand, J., Snijders, A.M., Pinkel, D., Albertson, D.G. and Jain, A.N. (2004) Hidden Markov models approach to the analysis of array CGH data. J. Multivariate Anal., 90, 132-153. (Pubitemid 41137010)
19. Hupe, P., Stransky, N., Thiery, J., Radvanyi, F. and Barillot, E. (2004) Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics, 20, 3413-3422. (Pubitemid 40136776)
20. Jong, K., Marchiori, E., van der Vaart, A., Ylstra, B., Weiss, M. and Meijer, G. (2003) Chromosomal breakpoint detection in human cancer. In Lecture Notes in Computer Science. Springer, Berlin, pp. 54-65.
21. Wang, P., Kim, Y., Pollack, J., Narasimhan, B. and Tibshirani, R. (2005) A method for calling gains and losses in array CGH data. Biostatistics, 6, 45-58. (Pubitemid 41240369)
22. Fiegler, H., Redon, R., Andrews, D., Scott, C., Andrews, R., Carder, C., Clark, R., Dovey, O., Ellis, P., Feuk, L. et al. (2006) Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res., 16, 1566-1574. (Pubitemid 44878495)
23. Price, T.S., Regan, R., Mott, R., Hedman.A, Honey, B., Daniels, R.J., Smith, L., Gerrnfield, A., Tiganescu, A., Buckle, Vl. et al. (2005) 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., 33, 3455-3464. (Pubitemid 41430569)
24. Venkatraman, E.S. and Olshen, A.B. (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 23, 657-663. (Pubitemid 46554715)
25. Snijders, A.M., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A.K., Huey, B., Kimura, K. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet., 29, 263-264. (Pubitemid 33096449)