A fused lasso latent feature model for analyzing multi-sample aCGH data

Biostatistics

Volumn 12, Issue 4, 2011, Pages 776-791

  Nowak, Gen ^a   Hastie, Trevor ^b   Pollack, Jonathan R ^c   Tibshirani, Robert ^b  

^a HARVARD UNIVERSITY   (United States)

^b STANFORD UNIVERSITY   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cancer; DNA copy number; False discovery rate; Mutation

Indexed keywords

ARTICLE; BIOSTATISTICS; BREAST TUMOR; CHROMOSOME 17; CHROMOSOME 8; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; COPY NUMBER VARIATION; FEMALE; GENETICS; HUMAN; STATISTICAL ANALYSIS; STATISTICAL MODEL; STATISTICS;

BIOSTATISTICS; BREAST NEOPLASMS; CHROMOSOMES, HUMAN, PAIR 17; CHROMOSOMES, HUMAN, PAIR 8; COMPARATIVE GENOMIC HYBRIDIZATION; DATA INTERPRETATION, STATISTICAL; DNA COPY NUMBER VARIATIONS; FEMALE; HUMANS; MODELS, STATISTICAL;

EID: 80052701674     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxr012     Document Type: Article

References (27)

1. BENJAMINI, Y. AND HOCHBERG, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B (Methodological) 57, 289-300.
2. BEROUKHIM, R., GETZ, G., NGHIEMPHU, L., BARRETINA, J., HSUEH, T., LINHART, D., VIVANCO, I., LEE, J. C., HUANG, J. H., ALEXANDER, S. nd others (2007). Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proceedings f the National Academy of Sciences of the United States of America 104, 20007-20012.
3. BRÖET, P. AND RICHARDSON, S. (2006). Detection of gene copy number changes in CGH microarrays using a spatially correlated ixture model. Bioinformatics 22, 911-918.
4. DISKIN, S. J., ECK, T., GRESHOCK, J., MOSSE, Y. P., NAYLOR, T., STOECKERT, C. J., WEBER, B. L., MARIS, J. M. AND GRANT, G. R. (2006). TAC: a method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Research 6, 1149-1158. (Pubitemid 44320402)
5. EILERS, P. H. C. AND DE MENEZES, R. X. (2005). Quantile smoothing of array CGH data. Bioinformatics 21, 1146-1153. (Pubitemid 40467939)
6. ENGLER, D. A., MOHAPATRA, G., LOUIS, D. N. AND BETENSKY, R. A. (2006). A pseudolikelihood approach for simultaneous analysis of array comparative genomic hybridizations. Biostatistics 7, 399-421. (Pubitemid 43955049)
7. FRIDLYAND, J., SNIJDERS, A. M., PINKEL, D., ALBERTSON, D. G. AND JAIN, A. N. (2004). Hidden markov models approach to the analysis f array CGH data. Journal of Multivariate Analysis 90, 132-153. (Pubitemid 41137010)
8. FRIEDMAN, J., HASTIE, T., ḦOFLING, H. AND TIBSHIRANI, R. (2007). Pathwise coordinate optimization. The Annals of Applied Statistics 1, 302-332.
9. GUTTMAN, M., MIES, C., DUDYCZ-SULICZ, K., DISKIN, S. J., BALDWIN, D. A., STOECKERT, JR, C. J. AND GRANT, G. R. (2007). Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PLoS Genetics 3, 1464-1486. (Pubitemid 47358084)
10. HSU, L., SELF, S. G., GROVE, D., RANDOLPH, T., WANG, 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)
11. HUPÉ, P., STRANSKY, N., THIERY, J. P., 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)
12. LAI, T. L., XING, H. AND ZHANG, N. (2008). Stochastic segmentation models for array-based comparative genomic hybridization data analysis. Biostatistics 9, 290-307. (Pubitemid 351438554)
13. 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)
14. LI, Y. AND ZHU, J. (2007). Analysis of array CGH data for cancer studies using fused quantile regression. Bioinformatics 23, 2470-2476. (Pubitemid 47423846)
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. PICARD, F., ROBIN, S., LAVIELLE, M., VAISSE, C. AND DAUDIN, J. J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics 6, 27.
17. PINKEL, D. AND ALBERTSON, D. G. (2005). Array comparative genomic hybridization and its applications in cancer. Nature Genetics 37 (Suppl), 11-17.
18. PINKEL, D., SEGRAVES, R., SUDAR, D., CLARK, S., POOLE, I., KOWBEL, D., COLLINS, C., KUO, W.-L., CHEN, C., ZHAI, Y. and others (1998). High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics 20, 207-211. (Pubitemid 28455458)
19. POLLACK, J., SORLIE, T., PEROU, C., REES, C., JEFFREY, S., LONNING, P., TIBSHIRANI, R., BOTSTEIN, D., BORRESEN-DALE, A. AND BROWN, P. (2002). Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proceedings of the National Academy of Sciences of the United States of America 99, 12963-12968.
20. STJERNQVIST, S., RYDÉN, T., SK̈OLD, M. AND STAAF, J. (2007). Continuous-index hidden Markov modelling of array CGH copy number data. Bioinformatics 23, 1006-1014. (Pubitemid 47050588)
21. TIBSHIRANI, R., SAUNDERS, M., ROSSET, S., ZHU, J. AND KNIGHT, K. (2005). Sparsity and smoothness via the fused lasso. Journal of the Royal Statistical Society, Series B (Statistical Methodology) 67, 91-108. (Pubitemid 40167043)
22. TIBSHIRANI, R. AND WANG, P. (2008). Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics 9, 18-29. (Pubitemid 350274579)
23. TSENG, P. (1988). Coordinate ascent for maximizing nondifferentiable concave functions. Technical Report LIDS-P-1840. Cambridge, MA: Laboratory for Information and Decision Systems, Massachusetts Institute of Technology.
24. TSENG, P. (2001). Convergence of a block coordinate descent method for nondifferentiable minimization. Journal of Optimization Theory and Applications 109, 475-494.
25. 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)
26. WILLENBROCK, H. AND FRIDLYAND, J. (2005). A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics 21, 4084-4091. (Pubitemid 41672097)
27. WITTEN, D. M., TIBSHIRANI, R. AND HASTIE T. (2009). A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10, 515-534.