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Massively Parallel Sequencing Approaches for Characterization of Structural Variation

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Genomic Structural Variants

Part of the book series: Methods in Molecular Biology ((MIMB,volume 838))

Abstract

The emergence of next-generation sequencing (NGS) technologies offers an incredible opportunity to comprehensively study DNA sequence variation in human genomes. Commercially available platforms from Roche (454), Illumina (Genome Analyzer and Hiseq 2000), and Applied Biosystems (SOLiD) have the capability to completely sequence individual genomes to high levels of coverage. NGS data is particularly advantageous for the study of structural variation (SV) because it offers the sensitivity to detect variants of various sizes and types, as well as the precision to characterize their breakpoints at base pair resolution. In this chapter, we present methods and software algorithms that have been developed to detect SVs and copy number changes using massively parallel sequencing data. We describe visualization and de novo assembly strategies for characterizing SV breakpoints and removing false positives.

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References

  1. Mardis, E.R. (2008). The impact of next-generation sequencing technology on genetics. Trends Genet. 24(3): p. 133–41.

    Article  PubMed  CAS  Google Scholar 

  2. Ahn, S.M., T.H. Kim, S. Lee, et al. (2009). The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 19(9): p. 1622–9.

    Article  PubMed  CAS  Google Scholar 

  3. Bentley, D.R., S. Balasubramanian, H.P. Swerdlow, et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456(7218): p. 53–9.

    Article  PubMed  CAS  Google Scholar 

  4. Drmanac, R., A.B. Sparks, M.J. Callow, et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 327(5961): p. 78–81.

    Google Scholar 

  5. Kim, J.I., Y.S. Ju, H. Park, et al. (2009). A highly annotated whole-genome sequence of a Korean individual. Nature. 460(7258): p. 1011–5.

    PubMed  CAS  Google Scholar 

  6. McKernan, K.J., H.E. Peckham, G.L. Costa, 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(9): p. 1527–41.

    Article  PubMed  CAS  Google Scholar 

  7. Pushkarev, D., N.F. Neff, and S.R. Quake (2009). Single-molecule sequencing of an individual human genome. Nat Biotechnol. 27(9): p. 847–52.

    Article  PubMed  CAS  Google Scholar 

  8. Wang, J., W. Wang, R. Li, et al. (2008). The diploid genome sequence of an Asian individual. Nature. 456(7218): p. 60–5.

    Article  PubMed  CAS  Google Scholar 

  9. Wheeler, D.A., M. Srinivasan, M. Egholm, et al. (2008). The complete genome of an individual by massively parallel DNA sequencing. Nature. 452(7189): p. 872–6.

    Article  PubMed  CAS  Google Scholar 

  10. Volik, S., S. Zhao, K. Chin, et al. (2003). End-sequence profiling: sequence-based analysis of aberrant genomes. Proc Natl Acad Sci U S A. 100(13): p. 7696–701.

    Article  PubMed  Google Scholar 

  11. Raphael, B.J., S. Volik, C. Collins, et al. (2003). Reconstructing tumor genome architectures. Bioinformatics. 19 Suppl 2: p. ii162–71.

    Google Scholar 

  12. Tuzun, E., A.J. Sharp, J.A. Bailey, et al. (2005). Fine-scale structural variation of the human genome. Nat Genet. 37(7): p. 727–32.

    Article  PubMed  CAS  Google Scholar 

  13. Korbel, J.O., A.E. Urban, J.P. Affourtit, et al. (2007). Paired-end mapping reveals extensive structural variation in the human genome. Science. 318(5849): p. 420–6.

    Article  PubMed  CAS  Google Scholar 

  14. Campbell, P.J., P.J. Stephens, E.D. Pleasance, et al. (2008). Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 40(6): p. 722–9.

    Article  PubMed  CAS  Google Scholar 

  15. Stephens, P.J., D.J. McBride, M.L. Lin, et al. (2009). Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 462(7276): p. 1005–10.

    Article  PubMed  CAS  Google Scholar 

  16. Pleasance, E.D., P.J. Stephens, S. O’Meara, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature. 463(7278): p. 184–90.

    Google Scholar 

  17. Pleasance, E.D., R.K. Cheetham, P.J. Stephens, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 463(7278): p. 191–6.

    Google Scholar 

  18. Margulies, M., M. Egholm, W.E. Altman, et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437(7057): p. 376–80.

    PubMed  CAS  Google Scholar 

  19. Li, H. and N. Homer A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform.

    Google Scholar 

  20. Li, H., J. Ruan, and R. Durbin (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18(11): p. 1851–8.

    Article  PubMed  CAS  Google Scholar 

  21. Li, H. and R. Durbin (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25(14): p. 1754–60.

    Article  PubMed  CAS  Google Scholar 

  22. Langmead, B., C. Trapnell, M. Pop, et al. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10(3): p. R25.

    Google Scholar 

  23. Homer, N., B. Merriman, and S.F. Nelson (2009). BFAST: an alignment tool for large scale genome resequencing. PLoS One. 4(11): p. e7767.

    Google Scholar 

  24. Rumble, S.M., P. Lacroute, A.V. Dalca, et al. (2009). SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol. 5(5): p. e1000386.

    Google Scholar 

  25. Ning, Z., A.J. Cox, and J.C. Mullikin (2001). SSAHA: a fast search method for large DNA databases. Genome Res. 11(10): p. 1725–9.

    Article  PubMed  CAS  Google Scholar 

  26. Li, H. and R. Durbin Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 26(5): p. 589–95.

    Google Scholar 

  27. Li, H., B. Handsaker, A. Wysoker, et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics. 25(16): p. 2078–9.

    Article  PubMed  Google Scholar 

  28. Kidd, J.M., G.M. Cooper, W.F. Donahue, et al. (2008). Mapping and sequencing of structural variation from eight human genomes. Nature. 453(7191): p. 56–64.

    Article  PubMed  CAS  Google Scholar 

  29. Yoon, S., Z. Xuan, V. Makarov, et al. (2009). Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19(9): p. 1586–92.

    Article  PubMed  CAS  Google Scholar 

  30. Chiang, D.Y., G. Getz, D.B. Jaffe, et al. (2009). High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods. 6(1): p. 99–103.

    Article  PubMed  CAS  Google Scholar 

  31. Alkan, C., J.M. Kidd, T. Marques-Bonet, et al. (2009). Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet. 41(10): p. 1061–7.

    Article  PubMed  CAS  Google Scholar 

  32. Koboldt, D.C. (2009). Short Read Aligners. MassGenomics. http://www.massgenomics.org/short-read-aligners.

  33. Hormozdiari, F., C. Alkan, E.E. Eichler, et al. (2009). Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res. 19(7): p. 1270–8.

    Article  PubMed  CAS  Google Scholar 

  34. Sindi, S., E. Helman, A. Bashir, et al. (2009). A geometric approach for classification and comparison of structural variants. Bioinformatics. 25(12): p. i222–30.

    Article  PubMed  CAS  Google Scholar 

  35. Ye, K., M.H. Schulz, Q. Long, et al. (2009). Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 25(21): p. 2865–71.

    Article  PubMed  CAS  Google Scholar 

  36. Chen, K., J.W. Wallis, M.D. McLellan, et al. (2009). BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 6(9): p. 677–81.

    Article  PubMed  CAS  Google Scholar 

  37. Futreal, P.A., L. Coin, M. Marshall, et al. (2004). A census of human cancer genes. Nat Rev Cancer. 4(3): p. 177–83.

    Article  PubMed  CAS  Google Scholar 

  38. Maher, C.A., C. Kumar-Sinha, X. Cao, et al. (2009). Transcriptome sequencing to detect gene fusions in cancer. Nature. 458(7234): p. 97–101.

    Article  PubMed  CAS  Google Scholar 

  39. Levin, J.Z., M.F. Berger, X. Adiconis, et al. (2009). Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol. 10(10): p. R115.

    Google Scholar 

  40. Fiume, M., V. Williams, A. Brook, et al. Savant: genome browser for high-throughput sequencing data. Bioinformatics. 26(16): p. 1938–44.

    Google Scholar 

  41. Manske, H.M. and D.P. Kwiatkowski (2009). LookSeq: a browser-based viewer for deep sequencing data. Genome Res. 19(11): p. 2125–32.

    Article  PubMed  CAS  Google Scholar 

  42. Krzywinski, M., J. Schein, I. Birol, et al. (2009). Circos: an information aesthetic for comparative genomics. Genome Res. 19(9): p. 1639–45.

    Article  PubMed  CAS  Google Scholar 

  43. Bashir, A., S. Volik, C. Collins, et al. (2008). Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol. 4(4): p. e1000051.

    Google Scholar 

  44. Eichler, E.E., D.A. Nickerson, D. Altshuler, et al. (2007). Completing the map of human genetic variation. Nature. 447(7141): p. 161–5.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We thank John Wallis for insightful discussions on structural variant analysis. We are also grateful for the support of the medical genomics, analysis pipeline, and technology development groups of the Genome Institute at Washington University in St. Louis.

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Authors and Affiliations

  1. The Genome Institute at Washington University School of Medicine, St. Louis, MO, USA

    Daniel C. Koboldt, David E. Larson, Ken Chen, Li Ding & Richard K. Wilson

Authors
  1. Daniel C. Koboldt
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  2. David E. Larson
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  3. Ken Chen
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  4. Li Ding
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  5. Richard K. Wilson
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Corresponding author

Correspondence to Richard K. Wilson .

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Editors and Affiliations

  1. Dept. Immunology, Genetics & Pathology, Uppsala University, Dag Hammarskjölds väg 20, Uppsala, 751 85, Sweden

    Lars Feuk

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Koboldt, D.C., Larson, D.E., Chen, K., Ding, L., Wilson, R.K. (2012). Massively Parallel Sequencing Approaches for Characterization of Structural Variation. In: Feuk, L. (eds) Genomic Structural Variants. Methods in Molecular Biology, vol 838. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-507-7_18

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  • DOI: https://doi.org/10.1007/978-1-61779-507-7_18

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-506-0

  • Online ISBN: 978-1-61779-507-7

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