Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

Bioinformatics

Volumn 28, Issue 1, 2012, Pages 40-47

  Gusnanto, Arief ^a   Wood, Henry M ^b   Pawitan, Yudi ^c   Rabbitts, Pamela ^b   Berri, Stefano ^b  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; COPY NUMBER VARIATION; DNA SEQUENCE; GENETICS; GENOME SIZE; HIGH THROUGHPUT SEQUENCING; HUMAN; LUNG TUMOR; NEOPLASM; TUMOR CELL LINE;

CELL LINE, TUMOR; COMPUTER SIMULATION; DNA COPY NUMBER VARIATIONS; GENOME SIZE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LUNG NEOPLASMS; NEOPLASMS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84855185866     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr593     Document Type: Article

References (23)

1. Bignell, G. et al. (2004) High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res., 14, 287-295.
2. Boeva, V. et al. (2011) Control-free calling of copy number alterations in deepsequencing data using GC-content normalization. Bioinformatics, 27, 268-269.
3. Castle, J. et al. (2010) DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing. BMC Genomics, 11, 244.
4. Chen, H-I. et al. (2008) A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. Bioinformatics, 24, 1749-1756.
5. Chiang, D.Y. et al. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99-103.
6. Greenman, C.D. et al. (2010) Picnic: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics, 11, 164-175.
7. Hartwell, L.H. and Kastan, M.B. (1994) Cell cycle control and cancer. Science, 266, 1821-1828
8. Huang, J. et al. (2007) Robust smooth segmentation approach for array CGH data analysis. Bioinformatics, 23, 2463-2469
9. Ivakhno, S. et al. (2010) CNAseg - a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics, 26, 3051-3058.
10. Kallioniemi, A. et al. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science, 258, 818-821.
11. Kim, T.M. et al. (2010) rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics, 11, 432.
12. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
13. McLachlan, G. and Krishnan, T. (1997) The EM Algorithm and Extensions. Wiley, New York.
14. Olshen, A.B. et al. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572.
15. Pawitan, Y. (2001) In All Likelihood: Statistical Modelling and Inference Using Likelihood. Oxford University Press, New York.
16. Pinkel, D. et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20, 207-211.
17. Pleasance, E.D. et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463, 191-196.
18. Staaf, J. et al. (2007) Normalization of array-CGH data: influence of copy number imbalances. BMC Genomics, 8, 382.
19. van Houte, B. et al. (2009) CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations. BMC Genomic, 10, 401.
20. Wood, H. et al. (2010) Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNAfrom formalinfixed paraffin-embedded specimens. Nucleic Acids Res., 38, e151.
21. Xie, C. and Tammi, M.T. (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing, BMC Bioinformatics, 10, 80.
22. Yau, C. et al. (2010) A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol., 11, R92.
23. Yoon, S. et al. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-1592.