CNVeM: Copy number variation detection using uncertainty of read mapping

Journal of Computational Biology

Volumn 20, Issue 3, 2013, Pages 224-236

  Wang, Zhanyong ^a   Hormozdiari, Farhad ^a   Yang, Wen Yun ^a   Halperin, Eran ^b,c   Eskin, Eleazar ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

^c INTERNATIONAL COMPUTER SCIENCE INSTITUTE   (United States)

Author keywords

algorithms; next generation sequencing; statistical models; structural genomics

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; CHROMOSOME; COMPUTER SIMULATION; COPY NUMBER VARIATION; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; MOUSE; NUCLEIC ACID DATABASE; STATISTICAL MODEL; TIME; UNCERTAINTY;

ALGORITHMS; ANIMALS; CHROMOSOMES, MAMMALIAN; COMPUTER SIMULATION; DATABASES, NUCLEIC ACID; DNA COPY NUMBER VARIATIONS; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; MODELS, STATISTICAL; TIME FACTORS; UNCERTAINTY;

EID: 84874746879     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0258     Document Type: Article

References (22)

1. Abyzov, A., Urban, A.E., Snyder, M., and Gerstein, M. 2011. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974-984.
2. Alkan, C., Kidd, J.M., Marques-Bonet, T., et al. 2009. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet. 41, 1061-1067.
3. Cappuzzo, F., Hirsch, F.R., Rossi, E., et al. 2005. Epidermal growth factor receptor gene and protein and gefitinib sensitivity in non-small-cell lung cancer. J. Natl. Cancer Inst. 97, 643-655.
4. Carter, N.P. 2007. Methods and strategies for analyzing copy number variation using dna microarrays. Nat. Genet. 39, S16-S21.
5. Chen, P.-A., Liu, H.-F., and Chao, K.-M. 2008. CNVDetector: locating copy number variations using array CGH data. Bioinformatics 24, 2773-2775.
6. Chiang, D.Y., Getz, G., Jaffe, D.B., 2009. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99-103.
7. Comaniciu, D., and Meer, P., 2002. Mean shift: A robust approach toward feature space analysis. IEEE Trans. Pattern Anal. Mach. Intell. 24, 603-619.
8. Hach, F., Hormozdiari, F., Alkan, C., et al. 2010. mrsfast: a cache-oblivious algorithm for short-read mapping. Nat. Methods 7, 576-577.
9. Halperin, E., and Hazan, E. 2006. HAPLOFREQ-estimating haplotype frequencies efficiently. J. Comput. Biol. 13, 481-500.
10. He, D., Furlotte, N., and Eskin, E. 2010. Detection and reconstruction of tandemly organized de novo copy number variations. BMC Bioinf.
11. He, D., Hormozdiari, F., Furlotte, N., and Eskin, E. 2011. Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions. Bioinformatics 27, 1513-1520.
12. Hormozdiari, F., Alkan, C., Eichler, E.E., and Sahinalp, S.C. 2009. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res. 19, 1270-1278.
13. Iafrate, A.J., Feuk, L., Rivera, M.N., et al. 2004. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949-951.
14. Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.
15. Medvedev, P., Fiume, M., Dzamba, M., et al. 2010. Detecting copy number variation with mated short reads. Genome Res. 20, 1613-1622.
16. Redon, R., Ishikawa, S., Fitch, K.R., et al. Global variation in copy number in the human genome. Nature 444, 444- 454.
17. Sebat, J., Lakshmi, B., Malhotra, D., et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449.
18. Simpson, J.T., McIntyre, R.E., Adams, D.J., and Durbin, R. 2010. Copy number variant detection in inbred strains from short read sequence data. Bioinformatics 26, 565-567.
19. Sudbery, I., Stalker, J., Simpson, J.T., et al. 2009. Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biol. 10, R112.
20. Sudmant, P.H., Kitzman, J.O., Antonacci, F., et al. 2010. Diversity of human copy number variation and multicopy genes. Science 330, 641-646.
21. Tuzun, E., Sharp, A.J., Bailey, J.A., 2005. Fine-scale structural variation of the human genome. Nat. Genet. 37, 727- 732.
22. Yoon, S., Xuan, Z., Makarov, V., et al. 2009. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19, 1586-1592.