Detecting copy number variation with mated short reads

Genome Research

Volumn 20, Issue 11, 2010, Pages 1613-1622

  Medvedev, Paul ^a   Fiume, Marc ^a   Dzamba, Misko ^a   Smith, Tim ^a   Brudno, Michael ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; DNA REPAIR; GENE CLUSTER; GENE MAPPING; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN GENOME; PRIORITY JOURNAL;

ALGORITHMS; BASE PAIRING; BASE SEQUENCE; CHROMOSOME BREAKAGE; CHROMOSOME MAPPING; DNA COPY NUMBER VARIATIONS; DNA MUTATIONAL ANALYSIS; DNA SHUFFLING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; REPRODUCIBILITY OF RESULTS;

EID: 78649309503     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.106344.110     Document Type: Article

References (40)

1. Ahuja RK, Magnanti TL, Orlin JB. 1993. Network flows: Theory, algorithms, and applications. Prentice-Hall, Upper Saddle River, NJ.
2. Alkan C, Kidd J, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, et al. 2009. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41: 1061-1067.
3. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
4. Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, et al. 2009. De novo transcriptome assembly with ABySS. Bioinformatics 25: 2872-2877.
5. Campbell P, Stephens P, Pleasance E, O'Meara S, Li H, Santarius T, Stebbings L, Leroy C, Edkins S, Hardy C, et al. 2008. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40: 722-729.
6. Carter N. 2007. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 39: S16-S21. (Pubitemid 47014471)
7. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, et al. 2009. BreakDancer: An algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6: 677-681.
8. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES. 2009. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6: 99-103.
9. Cooper GM, Zerr T, Kidd JM, Eichler EE, Nickerson DA. 2008. Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat Genet 40: 1199-1203.
10. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105. doi: 10.1092/nat/gkn425.
11. Fiume M, Williams V, Brook A, Brudno M. 2010. Savant: Genome browser for high throughput sequencing data. Bioinformatics 26: 1938-1944.
12. Gabow HN. 1983. An efficient reduction technique for degree-constrained subgraph and bidirected network flow problems. In Proceedings of the 15th Annual ACM Symposium on Theory of Computing, pp 448-456. ACM, New York.
13. Goldberg AV. 1997. An efficient implementation of a scalingminimum-cost flow algorithm. J Algorithms 22: 1-29. (Pubitemid 127451786)
14. Harismendy O, Ng P, Strausberg R, Wang X, Stockwell T, Beeson K, Schork N, Murray S, Topol E, Levy S, et al. 2009. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10: R32. doi: 10.1186/gb-2009-10-3-r32.
15. Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. 2009. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 19: 1270-1278.
16. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36: 949-951. (Pubitemid 39167488)
17. Kececioglu J. 1991. Exact and approximation algorithms for DNA sequence reconstruction. Technical Report 91-26. University of Arizona, Tuscon.
18. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, et al. 2008. Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64.
19. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, et al. 2007. Paired-end mapping reveals extensive structural variationin the human genome. Science 318: 420-426.
20. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
21. Lawler EL. 2001. Combinatorial Optimization: Networks and matroids. Dover Publications, Mineola, NY.
22. Lee S, Cheran E, Brudno M. 2008. A robust framework for detecting structural variations in a genome. Bioinformatics 24: i59-i67. (Pubitemid 351911658)
23. Lee S, Hormozdiari F, Alkan C, Brudno M. 2009. MoDIL: Detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods 6: 473-474.
24. Lewis DD, Gale WA. 1994. A sequential algorithm for training text classifiers. In Proceedings of the 17th annual international ACM SIGIR conference on research and development in information retrieval, pp 3-12. Springer-Verlag, New York.
25. Locke D, Archidiacono N, Misceo D, Cardone M, Deschamps S, Roe B, Rocchi M, Eichler E. 2003. Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. Genome Biol 4: R50. doi: 10.1186/gb-2003-4-8-r50.
26. McCarroll SA, Altshuler DM. 2007. Copy-number variation and association studies of human disease. Nat Genet 39: S37-S42. (Pubitemid 47014474)
27. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, et al. 2008. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
28. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, et al. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19: 1527-1541.
29. Medvedev P, Brudno M. 2009. Maximum likelihood genome assembly. J Comput Biol 16: 1-16.
30. Medvedev P, Stanciu M, Brudno M. 2009. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 6: S13-S20.
31. Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. 2008. Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res 18: 1814-1828.
32. Pevzner PA, Tang H, Tesler G. 2004. De novo repeat classification and fragment assembly. Genome Res 14: 1786-1796. (Pubitemid 39276437)
33. Raphael BJ, Volik S, Collins C, Pevzner PA. 2003. Reconstructing tumor genome architectures. Bioinformatics 19: 162-171.
34. Raphael B, Zhi D, Tang H, Pevzner P. 2004. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res 14: 2336-2346. (Pubitemid 39517341)
35. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. 2006. Global variation in copy number in the human genome. Nature 444: 444-454. (Pubitemid 44809057)
36. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, et al. 2004. Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
37. Simpson JT, McIntyre RE, Adams DJ, Durbin R. 2010. Copy number variant detection in inbred strains from short read sequence data. Bioinformatics 26: 565-567.
38. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, et al. 2005. Fine-scale structural variation of the human genome. Nat Genet 37: 727-732. (Pubitemid 41754889)
39. Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, Tao Q, Kowbel D, Huang G, Lapuk A, Kuo W, et al. 2003. End-sequence profiling: Sequence-based analysis of aberrant genomes. Proc Natl Acad Sci 100: 7696-7701.
40. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. 2009. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 19: 1586-1592.