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  Mapping copy number variation by population-scale genome sequencing

Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., et al. (2011). Mapping copy number variation by population-scale genome sequencing. Nature, 470(7332), 59-65. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/21293372 http://www.nature.com/nature/journal/v470/n7332/pdf/nature09708.pdf.

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Mills, R. E., Author
Walter, K., Author
Stewart, C., Author
Handsaker, R. E., Author
Chen, K., Author
Alkan, C., Author
Abyzov, A., Author
Yoon, S. C., Author
Ye, K., Author
Cheetham, R. K., Author
Chinwalla, A., Author
Conrad, D. F., Author
Fu, Y., Author
Grubert, F., Author
Hajirasouliha, I., Author
Hormozdiari, F., Author
Iakoucheva, L. M., Author
Iqbal, Z., Author
Kang, S., Author
Kidd, J. M., Author
Konkel, M. K., AuthorKorn, J., AuthorKhurana, E., AuthorKural, D., AuthorLam, H. Y., AuthorLeng, J., AuthorLi, R., AuthorLi, Y., AuthorLin, C. Y., AuthorLuo, R., AuthorMu, X. J., AuthorNemesh, J., AuthorPeckham, H. E., AuthorRausch, T.1, Author              Scally, A., AuthorShi, X., AuthorStromberg, M. P., AuthorStutz, A. M., AuthorUrban, A. E., AuthorWalker, J. A., AuthorWu, J., AuthorZhang, Y., AuthorZhang, Z. D., AuthorBatzer, M. A., AuthorDing, L., AuthorMarth, G. T., AuthorMcVean, G., AuthorSebat, J., AuthorSnyder, M., AuthorWang, J., AuthorEichler, E. E., AuthorGerstein, M. B., AuthorHurles, M. E., AuthorLee, C., AuthorMcCarroll, S. A., AuthorKorbel, J. O., Author more..
Affiliations:
1IMPRS for Computational Biology and Scientific Computing - IMPRS-CBSC (Kirsten Kelleher), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479666              

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Free keywords: DNA Copy Number Variations/*genetics; Gene Duplication/genetics; Genetic Predisposition to Disease/genetics; *Genetics, Population; Genome, Human/*genetics; *Genomics; Genotype; Humans; Mutagenesis, Insertional/genetics; Reproducibility of Results; Sequence Analysis, DNA; Sequence Deletion/genetics
 Abstract: Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.

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 Dates: 2011
 Publication Status: Published in print
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Title: Nature
Source Genre: Journal
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Pages: - Volume / Issue: 470 (7332) Sequence Number: - Start / End Page: 59 - 65 Identifier: ISSN: 1476-4687 (Electronic) 0028-0836 (Linking)