A linear-time algorithm for analyzing array CGH data using log ratio triangulation

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5542, Issue , 2009, Pages 248-259

  Hayes, Matthew ^a   Li, Jing ^a  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMIC METHODS; CHANGE-POINT; COMPARATIVE GENOMIC HYBRIDIZATIONS; COPY NUMBER; DATA SETS; GENETIC ABNORMALITY; LINEAR-TIME ALGORITHMS; NOISE LEVELS; TRIANGULATION METHOD;

CLUSTERING ALGORITHMS; DNA; GENES; NUCLEIC ACIDS; RESEARCH; TRIANGULATION;

BIOINFORMATICS;

EID: 67650189399     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-01551-9_25     Document Type: Conference Paper

References (18)

1. Veltman, J.A., Fridlyand, J., Pejavar, S., Olshen, A., Korkola, J., DeVries, S., Carroll, P., Kuo, W., Pinkel, D., Albertson, D., Cordon-Cardo, C., Jain, A., Waldman, F.: Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res. 63, 2872-2880 (2003) (Pubitemid 36667159)
2. Whang-Peng, J., Kao-Shan, C., Lee, E., Bunn, P., Carney, D., Gadzar, A., Minna, J.: Specific chromosome defect associated with human small cell lung cancer; deletion 3p(14-23). Science 215, 181-182 (1982) (Pubitemid 12178106)
3. de Leeuw, R.,Davies, J., Rosenwald, A., Bebb, G., Gascoyne, D., Dyer,M., Staudt, L., Martinez-Climent, J., Lam, W.: Comprehensive whole genome array cgh profiling of mantle cell lymphoma model genomes. Hum. Mol. Genet. 13(17), 1827-1837 (2004) (Pubitemid 39214331)
4. Fridlyand, J., Snijders, A., Ylstra, B., Li, H., Olshen, A., Segraves, R., Dairkee, Shanaz, Tokuasu, T., Ljung, B., Jain, A., McLenna, J., Ziegler, J., Chin, K., De-Vries, S., Feiler, H., Gray, J., Waldman, F., Pinkel, D., Albertson, D.: Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 6, 96 (2006)
5. Wang, Y., Makedon, F., Pearlman, J.: Tumor classification based on DNA copy number aberrations determined using SNP arrays. Oncology Reports 15, 1057-1061 (2006)
6. Pinkel, D., Albertson, D.G.: Array comparative genomic hybridization and its applications in cancer. Nat. Genet. 37, suppl. S11-S17 (2005)
7. Snijders, A., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A.,Huey, B., Kimura, K., Law, S., Myambo, K., Palmer, J., Ylstra, B., Yue, J., Gray, J., Jain, A., Pinkel, D., Albertson, D.: Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet. 3, 263-264 (2001) (Pubitemid 33096449)
8. Olshen, A., Venkatraman, E.: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557-572 (2004) (Pubitemid 41180205)
9. Willenbrock, H., Fridlyand, J.: A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics 21(22), 4084-4091 (2005) (Pubitemid 41672097)
10. Lai, W., Johnson, M., Kucherlapati, R., Park, P.: Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 21, 3763-3770 (2005) (Pubitemid 41535525)
11. Venkatraman, E., Olshen, A.: A Faster Circular Binary Segmentation Algorithm for the Analysis of Array CGH Data. Bioinformatics 23(6), 657-663 (2007) (Pubitemid 46554715)
12. Guha, S., Li, Y., Neuberg, D.: Bayesian Hidden Markov Modeling of Array CGH Data. Harvard University Biostatistics Working Paper Series. Working Paper 24 (2006)
13. Fridlyand, J., Snijders, A., Pinkel, D., Albertson, D., Jain, A.: Hidden Markov models approach to the analysis of array CGH data. J. Multivar. Anal. 90, 132
14. Durbin, R., et al.: Biological Sequence Analysis. Cambridge University Press, Cambridge (1999)
15. Daruwala, R., Rudra, A., Ostrer, H., Lucito, R., Wigler, M., Mishra, B.: A versatile statistical analysis algorithm to detect genome copy number variation. Proc. Natl. Acad. Sci. 101(46), 16292-16297 (2004) (Pubitemid 39552838)
16. 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., Cho, E.K., Dallaire, S., Freeman, J.L., Gonzalez, J.R., Gratacos, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J.R., Marshall, C.R., Mei, R., Montgomery, L., Nishimura, K., Okamura, K., Shen, F., Somerville, M.J., Tchinda, J., Valsesia, A., Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Armengol, L., Conrad, D.F., Estivill, X., Tyler-Smith, C., Carter, N.P., Aburatani, H., Lee, C., Jones, K.W., Scherer, S.W., Hurles, M.E.: Global variation in copy number in the human genome. Nature 444(7118), 444-454 (2006) (Pubitemid 44809057)
17. Carter, N.P.: Methods and strategies for analyzing copy number variation using dna microarrays. Nat. Genet. 39(suppl. 7), S16-S21 (2007)
18. Chiang, D.Y., Getz, G., Jaffe, D.B., O'Kelly, M.J., Zhao, X., Carter, S.L., Russ, C., Nusbaum, C., Meyerson, M., Lander, E.S.: High-resolution mapping of copynumber alterations with massively parallel sequencing. Nat. Methods 6(1), 99-103 (2009)