A high-throughput computational framework for identifying significant copy number aberrations from array comparative genomic hybridisation data

Advances in Bioinformatics

Volumn 2012, Issue , 2012, Pages

  Roberts, Ian ^a   Carter, Stephanie A ^a   Scarpini, Cinzia G ^a   Karagavriilidou, Konstantina ^a   Barna, Jenny C J ^a   Calleja, Mark ^b   Coleman, Nicholas ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84867380026     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2012/876976     Document Type: Article

References (15)

1. Kallioniemi A., CGH microarrays and cancer. Current Opinion in Biotechnology 2008 19 1 36 40 2-s2.0-39149090682 10.1016/j.copbio.2007.11.004
2. Aguirre A. J., Brennan C., Bailey G., Sinha R., Feng B., Leo C., Zhang Y., Zhang J., Gans J. D., Bardeesy N., Cauwels C., Cordon-Cardo C., Redston M. S., DePinho R. A., Chin L., High-resolution characterization of the pancreatic adenocarcinoma genome. Proceedings of the National Academy of Sciences of the United States of America 2004 101 24 9067 9072 2-s2.0-2942643922 10.1073/pnas.0402932101 (Pubitemid 38781612)
3. Wiedemeyer R., Brennan C., Heffernan T. P., Xiao Y., Mahoney J., Protopopov A., Zheng H., Bignell G., Furnari F., Cavenee W. K., Hahn W. C., Ichimura K., Collins V. P., Chu G. C., Stratton M. R., Ligon K. L., Futreal P. A., Chin L., Feedback circuit among INK4 tumor suppressors constrains human glioblastoma development. Cancer Cell 2008 13 4 355 364 2-s2.0-41449108880 10.1016/j.ccr.2008.02.010 (Pubitemid 351454058)
4. Beroukhim R., Getz G., Nghiemphu L., Barretina J., Hsueh T., Linhart D., Vivanco I., Lee J. C., Huang J. H., Alexander S., Du J., Kau T., Thomas R. K., Shah K., Soto H., Perner S., Prensner J., Debiasi R. M., Demichelis F., Hatton C., Rubin M. A., Garraway L. A., Nelson S. F., Liau L., Mischel P. S., Cloughesy T. F., Meyerson M., Golub T. A., Lander E. S., Mellinghoff I. K., Sellers W. R., Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proceedings of the National Academy of Sciences of the United States of America 2007 104 50 20007 20012 2-s2.0-38049100456 10.1073/pnas.0710052104
5. Sanchez-Garcia F., Akavia U. D., Mozes E., Pe'er D., JISTIC: identification of significant targets in cancer. BMC Bioinformatics 2010 11 189 2-s2.0-77953330045 10.1186/1471-2105-11-189
6. Chari R., Lockwood W. W., Lam W. L., Computational methods for the analysis of array comparative genomic hybridization. Cancer Informatics 2006 2 48 58 2-s2.0-33744953369 (Pubitemid 43854387)
7. Pinkel D., Albertson D. G., Comparative genomic hybridization. Annual Review of Genomics and Human Genetics 2005 6 331 354 2-s2.0-25844449738 10.1146/annurev.genom.6.080604.162140 (Pubitemid 41397087)
8. Gentleman R. C., Carey V. J., Bates D. M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A. J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J. Y., Zhang J., Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 2004 5 10 R80 2-s2.0-28744458859
9. Olshen A. B., Venkatraman E. S., Lucito R., Wigler M., Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004 5 4 557 572 2-s2.0-3543105225 10.1093/biostatistics/kxh008 (Pubitemid 41180205)
10. Venkatraman E. S., Olshen A. B., A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007 23 6 657 663 2-s2.0-34147104969 10.1093/bioinformatics/btl646 (Pubitemid 46554715)
11. Hupé P., Stransky N., Thiery J. P., Radvanyi F., Barillot E., Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics 2004 20 18 3413 3422 2-s2.0-12344259648 10.1093/bioinformatics/ bth418 (Pubitemid 40136776)
12. Fridlyand J., Snijders A. M., Pinkel D., Albertson D. G., Jain A. N., Hidden Markov models approach to the analysis of array CGH data. Journal of Multivariate Analysis 2004 90 1 132 153 2-s2.0-9244229940 10.1016/j.jmva.2004. 02.008 (Pubitemid 41137010)
13. Marioni J. C., Thorne N. P., Tavaré S., BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics 2006 22 9 1144 1146 2-s2.0-33646163019 10.1093/bioinformatics/btl089
14. Thain D., Tannenbaum T., Livny M., Distributed computing in practice: the Condor experience. Concurrency Computation Practice and Experience 2005 17 24 323 356 2-s2.0-14244258507 10.1002/cpe.938 (Pubitemid 40285781)
15. van Houte B. P. P., Binsl T. W., Hettling H., Pirovano W., Heringa J., CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations. BMC Genomics 2009 10 401 2-s2.0-70349653773 10.1186/1471-2164-10-401