Recurrent mutation in the ancestry of a rare variant Article Swipe
John Wakeley
,
Wai-Tong Louis Fan
,
Evan Koch
,
Shamil Sunyaev
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/2022.08.18.504427
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/2022.08.18.504427
Recurrent mutation produces multiple copies of the same allele which may be co-segregating in a population. Yet most analyses of allele-frequency or site-frequency spectra assume that all observed copies of an allele trace back to a single mutation. We develop a sampling theory for the number of latent mutations in the ancestry of a rare variant, specifically a variant observed in relatively small count in a large sample. Our results follow from the statistical independence of low-count mutations, which we show to hold for the standard neutral coalescent or diffusion model of population genetics as well as for more general coalescent trees. For populations of constant size, these counts are given by the Ewens sampling formula. We develop a Poisson sampling model for populations of varying size, and illustrate it using new results for site-frequency spectra in an exponentially growing population. We apply our model to a large data set of human SNPs and use it to explain dramatic differences in site-frequency spectra across the range of mutation rates in the human genome.
Related Topics
Concepts
Coalescent theory
Mutation
Genetics
Allele frequency
Biology
Population
Poisson distribution
Mutation rate
Allele
Sampling (signal processing)
Statistics
Mathematics
Demography
Gene
Physics
Optics
Phylogenetic tree
Detector
Sociology
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2022.08.18.504427
- https://www.biorxiv.org/content/biorxiv/early/2022/08/18/2022.08.18.504427.full.pdf
- OA Status
- green
- References
- 104
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4292978263
All OpenAlex metadata
Raw OpenAlex JSON
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- DOI
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https://doi.org/10.1101/2022.08.18.504427Digital Object Identifier
- Title
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Recurrent mutation in the ancestry of a rare variantWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-08-18Full publication date if available
- Authors
-
John Wakeley, Wai-Tong Louis Fan, Evan Koch, Shamil SunyaevList of authors in order
- Landing page
-
https://doi.org/10.1101/2022.08.18.504427Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2022/08/18/2022.08.18.504427.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2022/08/18/2022.08.18.504427.full.pdfDirect OA link when available
- Concepts
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Coalescent theory, Mutation, Genetics, Allele frequency, Biology, Population, Poisson distribution, Mutation rate, Allele, Sampling (signal processing), Statistics, Mathematics, Demography, Gene, Physics, Optics, Phylogenetic tree, Detector, SociologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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104Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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