InGAP-sv: A novel scheme to identify and visualize structural variation from paired end mapping data

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Qi, Ji ^a   Zhao, Fangqing ^b  

^a FUDAN UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; GENE CLUSTER; GENE INSERTION; GENE MAPPING; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC VARIABILITY; PRIORITY JOURNAL; SIMULATION; STRUCTURAL GENE;

CHROMOSOME ABERRATIONS; CHROMOSOME MAPPING; COMPUTER GRAPHICS; COMPUTER SIMULATION; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INDEL MUTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 79959965448     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr506     Document Type: Article

References (25)

1. Feuk, L., Carson, A.R. and Scherer, S.W. (2006) Structural variation in the human genome. Nat. Rev. Genet., 7, 85-97. (Pubitemid 43128895)
2. Sharp, A.J., Cheng, Z. and Eichler, E.E. (2006) Structural variation of the human genome. Annu. Rev. Genomics Hum. Genet., 7, 407-442. (Pubitemid 44641878)
3. Stankiewicz, P. and Lupski, J.R. (2010) Structural variation in the human genome and its role in disease. Annu. Rev. Med., 61, 437-455.
4. 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. (Pubitemid 41754889)
5. 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. (Pubitemid 47614521)
6. Medvedev, P., Stanciu, M. and Brudno, M. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6, S13-S20.
7. Chen, K., Wallis, J.W., McLellan, M.D., Larson, D.E., Kalicki, J.M., Pohl, C.S., McGrath, S.D., Wendl, M.C., Zhang, Q., Locke, D.P. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
8. Korbel, J.O., Abyzov, A., Mu, X.J., Carriero, N., Cayting, P., Zhang, Z., Snyder, M. and Gerstein, M.B. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10, R23.
9. Lee, S., Hormozdiari, F., Alkan, C. and Brudno, M. (2009) MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat. Methods, 6, 473-474.
10. 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.
11. 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.
12. Zeitouni, B., Boeva, V., Janoueix-Lerosey, I., Loeillet, S., Legoix-ne, P., Nicolas, A., Delattre, O. and Barillot, E. (2010) SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics, 26, 1895-1896.
13. Sindi, S., Helman, E., Bashir, A. and Raphael, B.J. (2009) A geometric approach for classification and comparison of structural variants. Bioinformatics, 25, i222-i230.
14. Campbell, P.J., Stephens, P.J., Pleasance, E.D., O'Meara, S., Li, H., Santarius, T., Stebbings, L.A., 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. (Pubitemid 351748860)
15. Ye, K., Schulz, M.H., Long, Q., Apweiler, R. and Ning, Z. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.
16. Abel, H.J., Duncavage, E.J., Becker, N., Armstrong, J.R., Magrini, V.J. and Pfeifer, J.D. (2010) SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data. Bioinformatics, 26, 2684-2688.
17. Wong, K., Keane, T.M., Stalker, J. and Adams, D.J. (2010) Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biol., 11, R128.
18. 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.
19. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
20. Qi, J., Zhao, F., Buboltz, A. and Schuster, S.C. (2010) inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics, 26, 127-129.
21. 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.
22. Mills, R.E., Walter, K., Stewart, C., Handsaker, R.E., Chen, K., Alkan, C., Abyzov, A., Yoon, S.C., Ye, K., Cheetham, R.K. et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-65.
23. 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.
24. McCarroll, S.A., Kuruvilla, F.G., Korn, J.M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M.H., de Bakker, P.I., Maller, J.B., Kirby, A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., 40, 1166-1174.
25. 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. (Pubitemid 351630326)