Personalized copy number and segmental duplication maps using next-generation sequencing
Open accessAbstract
Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable owing to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. We estimate that, on average, 73-87 genes vary in copy number between any two individuals and find that these genic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology.
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Because read-pair and read-depth methods can detect structural variants in repetitive regions and interpret multi-mapping reads, the accessible genome fraction is higher for structural variants than for SNPs.
“owing to the abilities of RP and RD methods in detecting SVs in these regions and in interpreting reads with multiple mapping positions, the ‘accessible’ fraction of the genome is higher for SVs than for SNPs16.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [16]
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- Authors
- Alkan, C., Kidd, J. M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J. O., Baker, C., Malig, M., Mutlu, O., Sahinalp, S. C., Gibbs, R. A., & Eichler, E. E.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Washington (US)
- Simon Fraser University (CA)
- Carnegie Mellon University (US)
- Baylor College of Medicine (US)
- Corresponding author
- Eichler, Evan E
- ORCID
- Venue
- Nature Genetics
- Published
- 2009-08-30
- Volume
- 41
- Issue
- 10
- Pages
- 1061-1067
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC2875196
- OpenAlex
- W2139747296
- Cited by
- 748
- References
- 40
- Citations by year
- 2026: 10 · 2025: 9 · 2024: 29 · 2023: 15 · 2022: 17 · 2021: 30 · 2020: 29 · 2019: 37 · 2018: 40 · 2017: 41 · 2016: 45 · 2015: 71 · 2014: 70 · 2013: 74 · 2012: 73
- FWCI
- 44.02
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Funders
- National Science Foundation
- Howard Hughes Medical Institute
- National Human Genome Research Institute (P01HG004120, R01HG006004, 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 › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- copy number variation, segmental duplication, human genome, gene content variation, functional constraints, personalized genomics
- MeSH terms
- Algorithms, Chromosome Mapping, DNA, Humans, Polymorphism, Genetic, Genomic Library, Genome, Human, Sequence Analysis, DNA, Gene Dosage, Gene Duplication
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