Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Tóm tắt
Từ khóa
Tài liệu tham khảo
Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525–528 (2004).
Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949–951 (2004).
Tuzun, E. et al. Fine-scale structural variation of the human genome. Nat. Genet. 37, 727–732 (2005).
Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426 (2007).
Kidd, J.M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008).
Turner, D.J. et al. Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat. Genet. 40, 90–95 (2008).
Korbel, J.O. et al. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc. Natl. Acad. Sci. USA 106, 12031–12036 (2009).
Sharp, A.J. et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat. Genet. 38, 1038–1042 (2006).
McCarroll, S.A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat. Genet. 40, 1107–1112 (2008).
de Cid, R. et al. Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat. Genet. 41, 211–215 (2009).
Gonzalez, E. et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307, 1434–1440 (2005).
Aitman, T.J. et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439, 851–855 (2006).
Hastings, P.J., Lupski, J.R., Rosenberg, S.M. & Ira, G. Mechanisms of change in gene copy number. Nat. Rev. Genet. 10, 551–564 (2009).
Kim, P.M. et al. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res. 18, 1865–1874 (2008).
Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
Lee, J.A., Carvalho, C.M. & Lupski, J.R.A. DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235–1247 (2007).
Feuk, L., Carson, A.R. & Scherer, S.W. Structural variation in the human genome. Nat. Rev. Genet. 7, 85–97 (2006).
Korbel, J.O. et al. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 10, R23 (2009).
Wheeler, D.A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008).
Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008).
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).
Perry, G.H. et al. The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet. 82, 685–695 (2008).
Mills, R.E., Bennett, E.A., Iskow, R.C. & Devine, S.E. Which transposable elements are active in the human genome? Trends Genet. 23, 183–191 (2007).
Xing, J. et al. Mobile elements create structural variation: analysis of a complete human genome. Genome Res. 19, 1516–1526 (2009).
Myers, S., Bottolo, L., Freeman, C., McVean, G. & Donnelly, P. A fine-scale map of recombination rates and hotspots across the human genome. Science 310, 321–324 (2005).
Sharp, A.J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77, 78–88 (2005).
Meunier, J. & Duret, L. Recombination drives the evolution of GC-content in the human genome. Mol. Biol. Evol. 21, 984–990 (2004).
Breslauer, K.J., Frank, R., Blocker, H. & Marky, L.A. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83, 3746–3750 (1986).
Sarai, A., Mazur, J., Nussinov, R. & Jernigan, R.L. Sequence dependence of DNA conformational flexibility. Biochemistry 28, 7842–7849 (1989).
Bailey, J.A. & Eichler, E.E. Primate segmental duplications: crucibles of evolution, diversity and disease. Nat. Rev. Genet. 7, 552–564 (2006).
Bailey, T.L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202 (2009).
Myers, S., Freeman, C., Auton, A., Donnelly, P. & McVean, G. A common sequence motif associated with recombination hot spots and genome instability in humans. Nat. Genet. 40, 1124–1129 (2008).
Linardopoulou, E.V. et al. Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437, 94–100 (2005).
Lee, S., Cheran, E. & Brudno, M. A robust framework for detecting structural variations in a genome. Bioinformatics 24, i59–i67 (2008).
Campbell, P.J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40, 722–729 (2008).
Chiang, D.Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99–103 (2009).
Wang, L.Y., Abyzov, A., Korbel, J.O., Snyder, M. & Gerstein, M. MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Res. 19, 106–117 (2009).
Ye, K., Schulz, M.H., Long, Q., Apweiler, R. & Ning, Z. 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 (2009).
Paten, B. et al. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res. 18, 1829–1843 (2008).
Spencer, C.C. et al. The influence of recombination on human genetic diversity. PLoS Genet. 2, e148 (2006).
Mills, R.E. et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182–1190 (2006).
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W. & Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. USA 100, 11484–11489 (2003).
Zhang, Z. et al. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 22, 1437–1439 (2006).