Cited by 1,630Genomic variations and chromosomal abnormalitiesGenome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

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Genome structural variation discovery and genotyping

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Alkan, Can, Coe, Bradley P., Eichler, Evan E.·2011·Nature Reviews Genetics

DOI 10.1038/nrg2958PMC PMC4108431

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Abstract

Comparisons of human genomes show that more base pairs are altered as a result of structural variation - including copy number variation - than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the discovery of smaller structural-variation events. Some global discovery biases remain, but the integration of experimental and computational approaches is proving fruitful for accurate characterization of the copy, content and structure of variable regions. We argue that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation.

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Global variation in copy number in the human genome
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Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
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Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892
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Authors: Alkan, C., Coe, B. P., & Eichler, E. E.
Affiliations: University of Washington (US)
Howard Hughes Medical Institute (US)
Corresponding author: Eichler, Evan E.
ORCID: Alkan, Can
Coe, Bradley P.
Eichler, Evan E.
Venue: Nature Reviews Genetics
Publisher: Springer Science and Business Media LLC
Published: 2011-03-01
Volume: 12
Issue: 5
Pages: 363-376
ISSN: 1471-0056 (ISSN-L)
1471-0064
DOI: 10.1038/nrg2958
PMC: PMC4108431
OpenAlex: W2083870688
Cited by: 1,630
References: 121
Citations by year: 2026: 67 · 2025: 129 · 2024: 100 · 2023: 81 · 2022: 94 · 2021: 104 · 2020: 148 · 2019: 122 · 2018: 132 · 2017: 102 · 2016: 93 · 2015: 108 · 2014: 107 · 2013: 108 · 2012: 89
FWCI: 11.82
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature Reviews Genetics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: Howard Hughes Medical Institute
Wellcome Trust
Canadian Institutes of Health Research
National Human Genome Research Institute (P01HG004120)
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 › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: structural variants, copy number variation, structural variant genotyping, structural variant calling, next-generation sequencing, de novo genome assembly, human genome, complex traits
MeSH terms: Genotype, Humans, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, DNA Copy Number Variations, High-Throughput Nucleotide Sequencing

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