Abstract
The extent of human genomic structural variation suggests that there must be portions of the genome yet to be discovered, annotated and characterized at the sequence level. We present a resource and analysis of 2,363 new insertion sequences corresponding to 720 genomic loci. We found that a substantial fraction of these sequences are either missing, fragmented or misassigned when compared to recent de novo sequence assemblies from short-read next-generation sequence data. We determined that 18–37% of these new insertions are copy-number polymorphic, including loci that show extensive population stratification among Europeans, Asians and Africans. Complete sequencing of 156 of these insertions identified new exons and conserved noncoding sequences not yet represented in the reference genome. We developed a method to accurately genotype these new insertions by mapping next-generation sequencing datasets to the breakpoint, thereby providing a means to characterize copy-number status for regions previously inaccessible to single-nucleotide polymorphism microarrays.
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Acknowledgements
We thank C. Campbell, G. Cooper, T. Marques-Bonet for thoughtful discussion, P. Sudmant for assistance with Illumina sequence data and members of the University of Washington and Washington University Genomes Centers for assistance with data generation. J.M.K. is supported by a US National Science Foundation Graduate Research Fellowship. This work was supported by the US National Institutes of Health grant HG004120 to E.E.E. E.E.E. receives funds as an Investigator of the Howard Hughes Medical Institute.
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J.M.K., N.S., F.A., A.T., R.K. and E.E.E. analyzed data. N.S., P.A., A.T., N.A.Y., P.T. and L.B. performed array CGH and copy-number analysis. F.A., M.V. and G.G. performed FISH experiments. C.A. assembled contigs. T.G., R.F., H.S.H., M.M., J.K., R.K. and R.K.W. performed clone characterization and sequencing. J.M.K., R.K., L.B. and E.E.E. designed the study. J.M.K. and E.E.E. wrote the paper with contributions from the other authors.
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N.S., P.A., A.T., N.A.Y., P.T. and L.B. are employees of Agilent Technologies. E.E.E. is a scientific advisory board member for Pacific Biosciences.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–7 and Supplementary Tables 2,3,5,9,11,12, Supplementary Note (PDF 10023 kb)
Supplementary Table 1
Contig information (XLS 795 kb)
Supplementary Table 4
Summary of unassembled OEA sequences (XLS 3949 kb)
Supplementary Table 6
Assigned copy-number genotypes (XLS 151 kb)
Supplementary Table 7
Insertion allele frequencies (XLS 76 kb)
Supplementary Table 8
Novel insertions with high FST (XLS 21 kb)
Supplementary Table 10
Sequenced fosmid clones (XLS 64 kb)
Supplementary Table 13
Exons within insertion sequences (XLS 19 kb)
Supplementary Table 14
Breakpoint k-mer genotyping results (XLS 20 kb)
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Kidd, J., Sampas, N., Antonacci, F. et al. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods 7, 365–371 (2010). https://doi.org/10.1038/nmeth.1451
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DOI: https://doi.org/10.1038/nmeth.1451
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