Identifying Recent Adaptations in Large-Scale Genomic Data
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SUMMARY While several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from the 1000 Genomes Project (1000G) and the Composite of Multiple Signals (CMS) test, we investigated 412 candidate signals and leveraged functional annotation, protein structure modeling, epigenetics, and association studies to identify and extensively annotate candidate causal variants. The resulting catalog provides a tractable list for experimental follow-up; it includes thirty-five high-scoring non-synonymous variants, fifty-nine variants associated with expression levels of a nearby coding gene or lincRNA, and numerous variants associated with susceptibility to infectious disease and other phenotypes. We experimentally characterized one candidate non-synonymous variant in TLR5, and show that it leads to altered NF-κB signaling in response to bacterial flagellin.
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SLC30A9 encodes ZnT9, a ubiquitously expressed zinc transporter, and has been repeatedly reported as a top candidate region for positive selection in humans, mostly in East Asian populations.
“The SLC30A9 gene (chr4: 41,990,502–42,090,461; GRCh38) has been repeatedly reported as a top candidate region for positive selection in several genome-wide scans of selection, mostly in East Asian populations [14,16–20].”
From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as [17]
The Results section, “412 Fine-mapped Signals of Selection” (page unavailable), describes candidate regions and the populations studied, but does not identify SLC30A9 as one of those regions. Searches for SLC30A9, zinc transporter, and East Asian selection found no passage establishing that this gene was repeatedly reported as a top candidate, mostly in East Asians. (LLM, conf=0.70)
Experimental — accuracy not yet measuredPrevious studies detected strong signatures of positive selection in the SLC30A9 region.
“The motivation for this study was the previous detection of strong signatures of positive selection in the SLC30A9 region [13,14,16,17,20,25].”
From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as [17]
The Results section (‘412 Fine-mapped Signals of Selection’; page unavailable) reports candidate regions under selection, but the retrieved passages do not identify SLC30A9 as one of them. Searches for SLC30A9 and zinc-transporter terminology found no passage connecting that region to a selection signal. (LLM, conf=0.73)
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- Authors
- Grossman, S. R., Andersen, K. G., Shlyakhter, I., Tabrizi, S., Winnicki, S., Yen, A., Park, D. J., Griesemer, D., Karlsson, E. K., Wong, S. H., Cabili, M., Adegbola, R. A., Bamezai, R. N. K., Hill, A. V. S., Vannberg, F. O., Rinn, J. L., Lander, E. S., Schaffner, S. F., & Sabeti, P. C.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- Centre for Human Genetics (GB)
- Georgia Institute of Technology (US)
- Corresponding author
- Grossman, Sharon R.
- Sabeti, Pardis C.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-02
- Volume
- 152
- Issue
- 4
- Pages
- 703-713
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3674781
- OpenAlex
- W2041825325
- Semantic Scholar
- 4c9e770760294713a0e8d5515c7c615b16031a8f
- Cited by
- 368
- References
- 75
- Citations by year
- 2026: 7 · 2025: 13 · 2024: 8 · 2023: 19 · 2022: 10 · 2021: 25 · 2020: 24 · 2019: 25 · 2018: 23 · 2017: 51 · 2016: 30 · 2015: 50 · 2014: 44 · 2013: 39
- FWCI
- 36.05
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- David and Lucile Packard Foundation
- American Cancer Society
- Burroughs Wellcome Fund
- Wellcome Trust (090532)
- Broad Institute
- National Institute for Health and Care Research
- Research Councils UK
- Scheme for Promotion of Academic and Research Collaboration
- National Institutes of Health (1dp2od006514-01)
- Medical Research Council
- National Human Genome Research Institute (T32HG002295)
- National Institute of General Medical Sciences (T32GM007753)
- National Institute of Allergy and Infectious Diseases (R01AI114855, AI2009061)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- positive selection, candidate causal variants, non-synonymous mutations, TLR5, NF-κB signaling, flagellin, infection susceptibility, expression quantitative trait loci, long intergenic non-coding RNA, 1000 Genomes Project
- MeSH terms
- Animals, Bacteria, Flagellin, Genetic Techniques, Humans, Mutation, Signal Transduction, Genome, Human, NF-kappa B, Quantitative Trait Loci, Regulatory Elements, Transcriptional, Toll-Like Receptor 5, Genome-Wide Association Study, HapMap Project
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