Reprever: Resolving low-copy duplicated sequences using template driven assembly

Nucleic Acids Research

Volumn 41, Issue 12, 2013, Pages

  Kim, Sangwoo ^a   Medvedev, Paul ^a   Paton, Tara A ^b   Bafna, Vineet ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; AUTOANALYZER; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE DOSAGE; GENE DUPLICATION; GENE IDENTIFICATION; GENE INSERTION; GENE LOCATION; GENE MAPPING; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; HIDDEN MARKOV MODEL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEGMENTAL DUPLICATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VALIDATION PROCESS;

ALGORITHMS; DNA COPY NUMBER VARIATIONS; GENOME, HUMAN; HUMANS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SOFTWARE; TEMPLATES, GENETIC;

EID: 84880211563     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt339     Document Type: Article

References (38)

1. Tuzun, E., Sharp, A.J., Bailey, J.A., Kaul, R., Morrison, V.A., Pertz, L.M., Haugen, E., Hayden, H., Albertson, D., Pinkel, D. et al. (2005) Fine-scale structural variation of the human genome. Nat. Genet., 37, 727-732.
2. Korbel, J.O., Urban, A.E., Affourtit, J.P., Godwin, B., Grubert, F., Simons, J.F., Kim, P.M., Palejev, D., Carriero, N.J., Du, L. et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science, 318, 420-426.
3. Bashir, A., Volik, S., Collins, C., Bafna, V. and Raphael, B.J. (2008) Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput. Biol., 4, e1000051.
4. Medvedev, P., Fiume, M., Dzamba, M., Smith, T. and Brudno, M. (2010) Detecting copy number variation with mated short reads. Genome Res., 20, 1613-1622.
5. Chiang, D.Y., Getz, G., Jaffe, D.B., O'Kelly, M.J., Zhao, X., Carter, S.L., Russ, C., Nusbaum, C., Meyerson, M. and Lander, E.S. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99-103.
6. Alkan, C., Kidd, J.M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J.O., 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.
7. Mills, R.E., Luttig, C.T., Larkins, C.E., Beauchamp, A., Tsui, C., Pittard, W.S. and Devine, S.E. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res., 16, 1182-1190.
8. Ye, K., Schulz, M.H., Long, Q., Apweiler, R. and Ning, Z. (2009) Pindel: a pattern growth approach to detect breakpoints of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.
9. Jiang, Y., Wang, Y. and Brudno, M. (2012) PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics, 28, 2576-2583.
10. Chaisson, M.J. and Pevzner, P.A. (2008) Short read fragment assembly of bacterial genomes. Genome Res., 18, 324-330.
11. Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
12. Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J. and Birol, I. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
13. Quinlan, A.R., Clark, R.A., Sokolova, S., Leibowitz, M.L., Zhang, Y., Hurles, M.E., Mell, J.C. and Hall, I.M. (2010) Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res., 20, 623-635.
14. Stewart, C., Kural, D., Stromberg, M.P., Walker, J.A., Konkel, M.K., Stutz, A.M., Urban, A.E., Grubert, F., Lam, H.Y., Lee, W.P. et al. (2011) A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet., 7, e1002236.
15. Hajirasouliha, I., Hormozdiari, F., Alkan, C., Kidd, J.M., Birol, I., Eichler, E.E. and Sahinalp, S.C. (2010) Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics, 26, 1277-1283.
16. Parrish, N., Hormozdiari, F. and Eskin, E. (2011) Assembly of non-unique insertion content using next-generation sequencing. BMC Bioinformatics, 12(Suppl. 6), S3.
17. Bargmann, C.I., Hung, M.C. and Weinberg, R.A. (1986) Multiple independent activations of the neu oncogene by a point mutation altering the transmembrane domain of p185. Cell, 45, 649-657.
18. Barroso, G., Bois, F. and Labarere, J. (2001) Duplication of a truncated paralog of the family B DNA polymerase gene Aa-polB in the Agrocybe aegerita mitochondrial genome. Appl. Environ. Microbiol., 67, 1739-1743.
19. Presgraves, D.C. (2007) Does genetic conflict drive rapid molecular evolution of nuclear transport genes in Drosophila? Bioessays, 29, 386-391.
20. Zakov, S., Kinsella, M. and Bafna, V. (2013) An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proc. Natl Acad. Sci. USA, 110, 5546-5551.
21. Stephens, P.J., Greenman, C.D., Fu, B., Yang, F., Bignell, G.R., Mudie, L.J., Pleasance, E.D., Lau, K.W., Beare, D., Stebbings, L.A. et al. (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell, 144, 27-40.
22. Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L.J., Lohr, J.G., Harris, C.C., Ding, L., Wilson, R.K. et al. (2012) Landscape of Somatic Retrotransposition in Human Cancers. Science, 337, 967-971.
23. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
24. Yoon, S., Xuan, Z., Makarov, V., Ye, K. and Sebat, J. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-1592.
25. Conrad, D.F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T.D., Barnes, C., Campbell, P. et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature, 464, 704-712.
26. Kidd, J.M., Cooper, G.M., Donahue, W.F., Hayden, H.S., 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.
27. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
28. Kidd, J.M., Graves, T., Newman, T.L., Fulton, R., Hayden, H.S., Malig, M., Kallicki, J., Kaul, R., Wilson, R.K. and Eichler, E.E. (2010) A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell, 143, 837-847.
29. Larkin, M., Blackshields, G., Brown, N., Chenna, R., McGettigan, P., McWilliam, H., Valentin, F., Wallace, I., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
30. Diskin, S.J., Hou, C., Glessner, J.T., Attiyeh, E.F., Laudenslager, M., Bosse, K., Cole, K., Mosse, Y.P., Wood, A., Lynch, J.E. et al. (2009) Copy number variation at 1q21.1 associated with neuroblastoma. Nature, 459, 987-991.
31. Levy, S., Sutton, G., Ng, P.C., Feuk, L., Halpern, A.L., Walenz, B.P., Axelrod, N., Huang, J., Kirkness, E.F., Denisov, G. et al. (2007) The diploid genome sequence of an individual human. PLoS Biol., 5, e254.
32. Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J. and Marra, M.A. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639-1645.
33. Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., Hall, K.P., Evers, D.J., Barnes, C.L., Bignell, H.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
34. McKernan, K.J., Peckham, H.E., Costa, G.L., McLaughlin, S.F., Fu, Y., Tsung, E.F., Clouser, C.R., Duncan, C., Ichikawa, J.K., Lee, C.C. 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.
35. Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O. and Walichiewicz, J. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res., 110, 462-467.
36. Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
37. Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J. and Eichler, E.E. (2001) Segmental duplications: organization and impact within the current human genome project assembly. Genome Res., 11, 1005-1017.
38. Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.