Weischenfeldt, J., Symmons, O., Spitz, F. & Korbel, J. O. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat. Rev. Genet. 14, 125–138 (2013).
Lupski, J. R. Structural variation mutagenesis of the human genome: impact on disease and evolution. Environ. Mol. Mutagen. 56, 419–436 (2015).
Macintyre, G., Ylstra, B. & Brenton, J. D. Sequencing structural variants in cancer for precision therapeutics. Trends Genet. 32, 530–542 (2016).
Hedges, D. J. et al. Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci. Mol. Autism 3, 2 (2012).
Rovelet-Lecrux, A. et al. APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy. Nat. Genet. 38, 24–26 (2006).
Sudmant, P. H. et al. An integrated map of structural variation in 2,504 human genomes. Nature 526, 75–81 (2015).
Dennenmoser, S. et al. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. Mol. Ecol. 26, 4712–4724 (2017).
Jeffares, D. C. et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat. Commun. 8, 14061 (2017).
Zichner, T. et al. Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Genome Res. 23, 568–579 (2013).
Imprialou, M. et al. Genomic rearrangements in Arabidopsis considered as quantitative traits. Genetics 205, 1425–1441 (2017).
Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525–528 (2004).
Article PubMed CAS Google Scholar
Kadalayil, L. et al. Exome sequence read depth methods for identifying copy number changes. Brief. Bioinform. 16, 380–392 (2015).
Alkan, C., Coe, B. P. & Eichler, E. E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363–376 (2011).
Layer, R. M., Chiang, C., Quinlan, A. R. & Hall, I. M. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15, R84 (2014).
Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333–i339 (2012).
Chen, X. et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32, 1220–1222 (2016).
Huddleston, J. et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res. 27, 677–685 (2017).
English, A. C., Salerno, W. J. & Reid, J. G. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinformatics 15, 180 (2014).
Mills, R. E. et al. Mapping copy number variation by population-scale genome sequencing. Nature 470, 59–65 (2011).
Tattini, L., D’Aurizio, R. & Magi, A. Detection of genomic structural variants from next-generation sequencing data. Front. Bioeng. Biotechnol 3, 92 (2015).
Teo, S. M., Pawitan, Y., Ku, C. S., Chia, K. S. & Salim, A. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics 28, 2711–2718 (2012).
Lucas Lledó, J. I. & Cáceres, M. On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing. PLoS One 8, e61292 (2013).
Goodwin, S., McPherson, J. D. & McCombie, W. R. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17, 333–351 (2016).
Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome Res. 21, 487–493 (2011).
Chaisson, M. J. & Tesler, G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13, 238 (2012).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXivPreprint at https://arxiv.org/abs/1303.3997(2013).
Sović, I. et al. Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat. Commun. 7, 11307 (2016).
Xiao, C. L. et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat. Methods 14, 1072–1074 (2017).
Li, H. Minimap2: fast pairwise alignment for long nucleotide sequences. arXivPreprint at https://arxiv.org/abs/1708.01492 (2017).
Chaisson, M. J. et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 517, 608–611 (2015).
Sedlazeck, F. J., Rescheneder, P. & von Haeseler, A. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics 29, 2790–2791 (2013).
Carvalho, C. M. et al. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. Nat. Genet. 43, 1074–1081 (2011).
Shimojima, K. et al. Pelizaeus-Merzbacher disease caused by a duplication-inverted triplication-duplication in chromosomal segments including the PLP1 region. Eur. J. Med. Genet. 55, 400–403 (2012).
Carvalho, C. M. & Lupski, J. R. Mechanisms underlying structural variant formation in genomic disorders. Nat. Rev. Genet. 17, 224–238 (2016).
Mühle, C., Zenker, M., Chuzhanova, N. & Schneider, H. Recurrent inversion with concomitant deletion and insertion events in the coagulation factor VIII gene suggests a new mechanism for X-chromosomal rearrangements causing hemophilia A. Hum. Mutat. 28, 1045 (2007).
Gusfield, D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology (Cambridge Univ. Press, Cambridge, UK, 1997).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Chin, C. S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016).
Zook, J. M. et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci. Data 3, 160025 (2016).
Jain, M. et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol. 36, 338–345 (2018).
Zook, J. M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246–251 (2014).
Eberle, M. A. et al. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res. 27, 157–164 (2017).
Zimin, A. V., Smith, D. R., Sutton, G. & Yorke, J. A. Assembly reconciliation. Bioinformatics 24, 42–45 (2008).
Beri, S., Bonaglia, M. C. & Giorda, R. Low-copy repeats at the human VIPR2 gene predispose to recurrent and nonrecurrent rearrangements. Eur. J. Hum. Genet. 21, 757–761 (2013).
Nattestad, M. et al. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. bioRxiv Preprint athttps://www.biorxiv.org/content/early/2017/08/10/174938(2017).
Merker, J. D. et al. Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genet. Med. 20, 159–163 (2017).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Jeffares, D. C. et al. Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe. Nat. Commun. 8, 14061 (2017).