Identifying the favored mutation in a positive selective sweep.
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Abstract
Most approaches that capture signatures of selective sweeps in population genomics data do not identify the specific mutation favored by selection. We present iSAFE (for "integrated selection of allele favored by evolution"), a method that enables researchers to accurately pinpoint the favored mutation in a large region (∼5 Mbp) by using a statistic derived solely from population genetics signals. iSAFE does not require knowledge of demography, the phenotype under selection, or functional annotations of mutations.
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iSAFE pinpointed several eQTLs (including rs1047626) among the most likely candidate mutations favored by selection along the region in both CEU and CHB.
“iSAFE [28] similarly pinpointed several eQTLs (including rs1047626) among the most likely candidate mutations favored by selection along the region (chr4: 41,853,671–42,153,671; GRCh37) in both CEU and CHB”
From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as [28]
The paper’s iSAFE evaluation discusses ranked candidate mutations at selected loci, but the passages in our copy do not identify rs1047626 or report several eQTLs as top candidates in the specified chromosome 4 region in both CEU and CHB. Searches for the variant, coordinates, and eQTL terminology found no passage addressing that specific result. (LLM, conf=0.73)
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References 72 · Cited by 95
- Authors
- Akbari, A., Vitti, J. J., Iranmehr, A., Bakhtiari, M., Sabeti, P. C., Mirarab, S., & Bafna, V.
- Affiliations
- University of California San Diego (US)
- Broad Institute (US)
- Corresponding author
- Akbari, Ali
- Bafna, Vineet
- Venue
- Nature Methods
- Published
- 2018-02-19
- Volume
- 15
- Issue
- 4
- Pages
- 279-282
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC6231406
- OpenAlex
- W2790130209
- Cited by
- 95
- References
- 72
- Citations by year
- 2026: 13 · 2025: 11 · 2024: 11 · 2023: 15 · 2022: 8 · 2021: 14 · 2020: 10 · 2019: 9 · 2018: 4
- FWCI
- 5.58
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (1458557, 1318386)
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM114362)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- positive selection, selective sweeps, population genomics, selection signatures
- MeSH terms
- Alleles, Biological Evolution, Haplotypes, Humans, Mutation, Nucleic Acid Hybridization, Nucleic Acid Amplification Techniques, Genomics
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