A Bayesian segmentation approach to ascertain copy number variations at the population level

Bioinformatics

Volumn 25, Issue 13, 2009, Pages 1669-1679

  Wu, Long Yang ^a   Chipman, Hugh A ^b   Bull, Shelley B ^c,d   Briollais, Laurent ^d   Wang, Kesheng ^e  

^a UNIVERSITY OF WATERLOO   (Canada)

^b ACADIA UNIVERSITY   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d MOUNT SINAI HOSPITAL   (Canada)

^e EAST TENNESSEE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; BAYES THEOREM; GENETIC DATABASE; GENETIC VARIABILITY; HAPLOTYPE MAP; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; POPULATION GENETICS; POPULATION RESEARCH; PRIORITY JOURNAL; SIMULATION;

BAYES THEOREM; COMPUTATIONAL BIOLOGY; GENE DOSAGE; GENE EXPRESSION PROFILING; GENETIC VARIATION; GENETICS, POPULATION; HUMANS;

EID: 67649199562     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp270     Document Type: Article

References (38)

1. Beroukhim,R. et al. (2007) Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma. Proc. Natl Acad. Sci. USA, 104, 20007-20012.
2. Broet,P. and Richardson,S. (2006) Detection of gene copy number changes in CGH microarray using a spatially correlated mixture model. Bioinformatics, 22, 911-918.
3. Cahan,P. et al. (2008) wuHMM: A robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data. Nucleic Acids Res., 36, e41.
4. Colella,S. et al. (2007) QuantiSNP: An objective Bayes hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res., 35, 2013-2025.
5. Conrad,D.F. and Hurles,M.E. (2007) The population genetics of structural variation. Nat. Genet., 39, S30.
6. Daruwala,R. et al. (2004) Aversatile statistical analysis algorithm to detect genome copy number variation. Proc. Natl Acad. Sci. USA, 101, 16292-16297.
7. Diskin,S. et al. (2006) STAC: A method for testing the significance of DNA copy number aberrations across mulitple array-CGH experiments. Genome Res., 16, 1149-1158.
8. Diskin,S. et al. (2008) Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res., 36, e126.
9. Estivill,X. and Armengol,L. (2007) Copy number variants and common disorders: Filling the gaps and exploring complexity in genome-wide association studies. PLoS Genet., 3, e190.
10. Feuk,L. et al. (2006) Structural variation in the human genome. Nat. Rev. Genet., 7, 85-97.
11. Fiegler,H. et al. (2006) Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res. 16, 1566-1574.
12. Friedman,J. and Fisher,N. (1999) Bump hunting in high-dimensional data. Stat. Comput., 9, 1-20.
13. Fridlyand,J. et al. (2004) A hidden Markov models approach to the analysis of array CGH data. J. Multivar. Anal., 90, 132-1153.
14. Hupe,P. et al. (2004) Analysis of array CGH data: From signal ratio to gain and loss of DNA regions. Bionformatics 20, 3413-3422.
15. Jin,D. et al. (2007) CD38 is critical for social behaviour by regulating oxytocin secretion. Nature, 446, 41-45.
16. Kass,R.E. and Raftery,A.E. (1995) Bayes factors. J. Am. Stat. Assoc. 90, 773-795.
17. Klijn,C. et al. (2008) Identification of cancer genes using a statistical framework for multi-experiment analysis of non-discretized array CGH data. Nucleic Acids Res., 36, e13.
18. Korbel,J. et al. (2007) Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc. Natl Acad. Sci. USA, 104, 10110-10115.
19. Korn,J.M. et al. (2008) Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet., 40, 1253-1260.
20. Kraft,P. et al. (2005) Accounting for haplotype uncertainty in matched association studies: A comparison of simple and flexible techniques. Genet. Epidemiol., 28, 261-272.
21. Lai,W.R. et al. (2005) Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics, 19, 3763-3770.
22. Marioni,J.C. et al. (2007) Breaking the waves: Improved detection of copy number variation form microarray comparative genomic hybridization. Genome Biol., 8, R228.
23. Marioni,J.C. et al. (2008) Hidden copy number variation in the HapMap population. Proc. Natl Acad. Sci. USA, 105, 10067-10072.
24. McCarroll,S.A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., 40, 1166-1174.
25. Morgan,R.O. et al. (1999) Novel human and mouse annexin A10 are linked to the genome duplications during early chordate evolution. Gemomics, 60, 40-49.
26. Olshen,A.B. et al. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Bioinformatics, 5 557-572.
27. Perry,G.H. et al. (2008) The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet., 82, 685-695.
28. Pique-Regi,R. et al. (2008) Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics, 24, 309-318.
29. Redon,R. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454.
30. Rouveirol,C. et al. (2006) Computation of recurrent minimal genomic alterations from array-CGH data. Bioinformatics, 22, 849-856.
31. Rueda,O.M. and Diaz-Uriarte,R. (2007) Flexible and accurate detection of genomic copy-number changes from acgh. PLoS Comput. Biol., 3 e122.
32. Shah,S.P. et al. (2006) Integrating copy number polymorphisms into arry cgh analysis using a robust HMM. Bioinformatcs, 22, e431-e439.
33. Shah,S.P. et al. (2007) Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics, 23, 450-458.
34. Sharp,A.J. et al. (2007) Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet., 77, 78-88.
35. Yuk,F.L. and Cavalieri,D. (2003) Fundamentals of cDNA microarray data analysis. Trends Genet., 19, 649-659.
36. Wang,K. et al. (2007) PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res., 17, 1665-1674.
37. Weir,B. (1996) Genetic Data Anaysis II. Sinauer Associates, Inc., Sunderland, MA, USA.
38. Willenbrock,H. and Fridlyand,J. (2005) A comparison study: Applying segmentation to array CGH data for downstream analyses. Bioinformatics, 21, 4084-4091.