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Genome structural variation discovery and genotyping
Open accessAbstract
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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“Determination of the length, weight and relative GC content of genome is subjected to the accuracy of the genome assembly and to the variability existing among individuals [41].”
From On the length, weight and GC content of the human genome (2019) · cites this paper as [41]
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“However, the human genetic diversity ranges from the single-nucleotide variation to large chromosomal events [41, 42].”
From On the length, weight and GC content of the human genome (2019) · cites this paper as [41]
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“Current genotyping platforms and CNV discovery algorithms enable the genotyping of ~1000 common copy number polymorphisms (CNPs) and the discovery of additional “novel” CNVs, including mutations that are rare or unique to an individual (Alkan et al., 2011).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Alkan et al., 2011
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Metadata
- Authors
- Alkan, C., Coe, B. P., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E.
- Venue
- Nature Reviews Genetics
- Published
- 2011-03-01
- Volume
- 12
- Issue
- 5
- Pages
- 363-376
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- 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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