Detecting copy number variations from array cgh data based on a conditional random field model

Journal of Bioinformatics and Computational Biology

Volumn 8, Issue 2, 2010, Pages 295-314

  Yin, Xiao Lin ^a,b   Li, Jing ^a  

^a Case Western Reserve University   (United States)

^b NORTHEAST NORMAL UNIVERSITY   (China)

Author keywords

Array comparative genomic hybridization; Conditional random fields; Copy number variations

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; COPY NUMBER VARIATION; EVALUATION; HUMAN; NUCLEIC ACID DATABASE; PROBABILITY; STATISTICAL MODEL; STATISTICS;

ALGORITHMS; BAYES THEOREM; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DNA COPY NUMBER VARIATIONS; HUMANS; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL;

EID: 77951610981     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S021972001000480X     Document Type: Article

References (18)

1. Cho EK, Tchinda J, Freeman JL, Chung YJ, Cai WW, Lee C, Array-based comparative genomic hybridization and copy number variation in cancer research, Cytogenet Genome Res 115(3-4):262-272, 2006. (Pubitemid 44832029)
2. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C, Copy number variation: New insights in genome diversity, Genome Res 16(8):949-961, 2006. (Pubitemid 44162254)
3. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME, Global variation in copy number in the human genome, Nature 444(7118):444-454, 2006. (Pubitemid 44809057)
4. Carter NP, Methods and strategies for analyzing copy number variation using DNA microarrays, Nat Genet 39(7 Suppl):S16-21, 2007.
5. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J, Quantisnp: An objective Bayes Hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data, Nucleic Acids Res 35(6):2013-2025, 2007.
6. Hayes M, Li J, A linear-time algorithm for analyzing array CGH data using log ratio triangulation, Lecture Notes in Bioinformatics 5542, pp. 248-259, 2009.
7. Shah SP, Xuan X, DeLeeuw RJ, Khojasteh M, Lam WL, Ng R, Murphy KP, Integrating copy number polymorphisms into array cgh analysis using a robust hmm, Bioinformatics 22(14):E431-439, 2006.
8. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M, Penncnv: An integrated Hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data, Genome Res 17(11):1665-1674, 2007.
9. Chiang DY, Getz G, Jaffe DB, Kelly MJO, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES, High-resolution mapping of copy-number alterations with massively parallel sequencing, Nat Methods 6(1):99-103, 2009.
10. Sutton C, McCallum A, An introduction to conditional random fields for relational learning, in Getoor L, Taskar B (eds.), Introduction to Statistical Relational Learning, MIT Press, 2007.
11. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K, Law S, Myambo K, Palmer J, Ylstra B, Yue JP, Gray JW, Jain AN, Pinkel D, Albertson DG, Assembly of microarrays for genome-wide measurement of DNA copy number, Nat Genet 29(3):263-264, 2001.
12. Olshen AB, Venkatraman ES, Lucito R, Wigler M, Circular binary segmentation for the analysis of array-based DNA copy number data, Biostatistics 5(4):557-572, 2004.
13. Hupe P, Stransky N, Thiery JP, Radvanyi F, Barillot E, Analysis of array CGH data: From signal ratio to gain and loss of DNA regions, Bioinformatics 20(18):3413-3422, 2004.
14. Willenbrock H, Fridlyand J, A comparison study: Applying segmentation to array CGH data for downstream analyses, Bioinformatics 21(22):4084-4091, 2005.
15. Guha S, Li Y, Neuberg D, Bayesian hidden markov modeling of array CGH data, J Amer Statist Assoc 103(482):485-497, 2008.
16. Snyman JA, Practical Mathematical Optimization: An Introduction to Basic Optimization Theory and Classical and New Gradient-Based Algorithms, Springer, New York, 2005.
17. Lai WR, Johnson MD, Kucherlapati R, Park PJ, Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data, Bioinformatics 21(19):3763-3770, 2005.
18. Shen F, Huang J, Fitch KR, Truong VB, Kirby A, Chen W, Zhang J, Liu G, McCarroll SA, Jones KW, Shapero MH, Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes, BMC Genet 9(27):1471-2156, 2008.