Resource abstract

Nature Methods 7, 365 - 371 (2010)
Published online: 18 April 2010 | doi:10.1038/nmeth.1451

Characterization of missing human genome sequences and copy-number polymorphic insertions

Jeffrey M Kidd1, Nick Sampas2, Francesca Antonacci1, Tina Graves3, Robert Fulton3, Hillary S Hayden1, Can Alkan1, Maika Malig1, Mario Ventura4, Giuliana Giannuzzi4, Joelle Kallicki3, Paige Anderson2, Anya Tsalenko2, N Alice Yamada2, Peter Tsang2, Rajinder Kaul1, Richard K Wilson3, Laurakay Bruhn2 & Evan E Eichler1,5

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.

  1. Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
  2. Agilent Laboratories, Santa Clara, California, USA.
  3. Washington University Genome Sequencing Center, School of Medicine, St. Louis, Missouri, USA.
  4. Department of Genetics and Microbiology, University of Bari, Bari, Italy.
  5. Howard Hughes Medical Institute, Seattle, Washington, USA.

Correspondence to: Evan E Eichler1,5 e-mail:


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