Mapping and sequencing of structural variation from eight human genomes
Open accessAbstract
Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.
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High levels of structural variation, including copy-number variation, had previously been described for cell defense and sensory perception.
“High levels of structural variation, including copy-number variation, were previously described for both processes15,22,39.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [22]
Most high-frequency coding deletions occurred in regions annotated as segmental duplications, consistent with lessened evolutionary constraint in functionally redundant gene categories.
“Most of these occurred in regions annotated as segmental duplications, consistent with lessened evolutionary constraintin functionally redundant gene categories22.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [22]
Deletion discovery sensitivity was assessed against a gold standard assembled from four earlier surveys.
“We further assessed the sensitivity of deletion discovery methods by collating data from four earlier surveys1,13,22,28 into a gold standard”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [22]
Nucleotide-resolution breakpoint information enables inference of structural-variant formation mechanisms.
“Nucleotide resolution breakpoint information enables inference of SV formation mechanisms15,22.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [22]
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- Authors
- Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., Haugen, E., Zerr, T., Yamada, N. A., Tsang, P., Newman, T. L., Tüzün, E., Cheng, Z., Ebling, H. M., Tusneem, N., David, R., Gillett, W., Phelps, K. A., Weaver, M., Saranga, D., Brand, A., Tao, W., Gustafson, E., McKernan, K., Chen, L., Malig, M., Smith, J. D., Korn, J. M., McCarroll, S. A., Altshuler, D. A., Peiffer, D. A., Dorschner, M., Stamatoyannopoulos, J., Schwartz, D., Nickerson, D. A., Mullikin, J. C., Wilson, R. K., Bruhn, L., Olson, M. V., Kaul, R., Smith, D. R., & Eichler, E. E.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Washington (US)
- Agilent Technologies (United States) (US)
- Washington University in St. Louis (US)
- National Institutes of Health (US)
- University of Wisconsin–Madison (US)
- Broad Institute (US)
- Illumina (United States) (US)
- Corresponding author
- Eichler, Evan E.
- ORCID
- Kidd, Jeffrey M.
- Cooper, Gregory M.
- Hayden, Hillary S.
- Hansen, Nancy
- Teague, Brian
- Alkan, Can
- Antonacci, Francesca
- Haugen, Eric
- Tüzün, Eray
- Brand, Adrianne
- Tao, Wei
- Gustafson, Erik
- McKernan, Kevin
- Chen, Lin
- Malig, Maika
- Smith, Joshua D.
- Korn, Joshua M.
- McCarroll, Steven A.
- Altshuler, David A.
- Stamatoyannopoulos, John
- Schwartz, David
- Nickerson, Deborah A.
- Mullikin, James C.
- Bruhn, Laurakay
- Olson, Maynard V.
- Kaul, Rajinder
- Eichler, Evan E.
- Venue
- Nature
- Published
- 2008-05
- Volume
- 453
- Issue
- 7191
- Pages
- 56-64
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2424287
- OpenAlex
- W2032247293
- Cited by
- 1,119
- References
- 46
- Citations by year
- 2026: 7 · 2025: 8 · 2024: 12 · 2023: 20 · 2022: 23 · 2021: 28 · 2020: 34 · 2019: 35 · 2018: 25 · 2017: 38 · 2016: 43 · 2015: 61 · 2014: 68 · 2013: 89 · 2012: 115
- FWCI
- 95.82
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Funders
- National Science Foundation
- Howard Hughes Medical Institute
- Jane Coffin Childs Memorial Fund for Medical Research
- University of Washington
- National Institutes of Health (5u54hg002043-07)
- National Human Genome Research Institute (U54 HG002043, P01HG004120, 3 U54 HG002043, HG004120)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- structural variants, copy number variation, insertion, deletion, inversion, human genetic variation, non-allelic homologous recombination, mutational processes, reference genome
- MeSH terms
- Geography, Haplotypes, Humans, Chromosome Inversion, Genetic Variation, Reproducibility of Results, Genome, Human, Mutagenesis, Insertional, Gene Deletion, Sequence Analysis, DNA, Physical Chromosome Mapping, Polymorphism, Single Nucleotide, Euchromatin, Racial Groups
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