RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference
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Local-ancestry inference is an important step in the genetic analysis of fully sequenced human genomes. Current methods can only detect continental-level ancestry (i.e., European versus African versus Asian) accurately even when using millions of markers. Here, we present RFMix, a powerful discriminative modeling approach that is faster (~30×) and more accurate than existing methods. We accomplish this by using a conditional random field parameterized by random forests trained on reference panels. RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians. Finally, we demonstrate that African Americans in HapMap contain modest (but nonzero) levels of Native American ancestry (~0.4%).
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More recent studies using high-density genotype data provide reliable individual ancestry estimates, illustrate large variability in African and European ancestry proportions at an individual level, and detect low proportions of Native American ancestry.
“More recent studies that utilized high-density genotype data provide reliable individual ancestry estimates, illustrate the large variability in African and European ancestry proportions at an individual level, and are able to detect low proportions of Native American ancestry.3–11”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [11]
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Cites
Breiman, L. (2001) · Machine Learning · doi:10.1023/a:1010933404324 · Cited by 133,538 · see citing works
The Elements of Statistical Learning
Hastie, T., Tibshirani, R., & Friedman, J. (2009) · Springer Series in Statistics · doi:10.1007/978-0-387-84858-7 · Cited by 25,970 · see citing works
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works
The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057 · see citing works
Nelson, M. R., Bryc, K., King, K. S., Indap, A., Boyko, A. R., Novembre, J., Briley, L. P., Maruyama, Y., Waterworth, D. M., Waeber, G., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.08.005 · Cited by 293 · see citing works
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Research works printed but not linked: 3
- [14]14. Gravel, S., Henn, B.M., Gutenkunst, R.N., Indap, A.R., Marth, G.T., Clark, A.G., Yu, F., Gibbs, R.A., and Bustamante, C.D.; 1000 Genomes Project. (2011). Demographic history and rare allele sharing among human populations. Proc. Natl. Acad. Sci. USA 108 , 11983-11988.
- [24]24. Ng, A.Y., and Jordan, M.I. (2001). On Discriminative vs. Generative Classifiers: A Comparison of Logistic Regression and Naive Bayes. In Advances in Neural Information Processing Systems 14, T.G. Dietterich, S. Becker, and Z. Ghahramani, eds. (Cambridge: MIT Press), pp. 841-848.
- [25]25. Lafferty, J., McCallum, A., and Pereira, F.C.N. (2001). Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data. Proceedings of the 18 th International Conference on Machine Learning, 282-289.
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Taliun, D., Harris, D. N., Kessler, M. D., Carlson, J., Szpiech, Z. A., Torres, R., Taliun, S. A. G., Corvelo, A., Gogarten, S. M., Kang, H. M., et al. (2021) · Nature · doi:10.1038/s41586-021-03205-y · Cited by 2,213 · see citing works
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Self-citationThe genetic ancestry of African Americans, Latinos, and European Americans across the United States
Bryc, K., Durand, E. Y., Macpherson, J. M., Reich, D., & Mountain, J. L. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.11.010 · Cited by 712 · see citing works
Improving polygenic prediction in ancestrally diverse populations
Ruan, Y., Lin, Y.-F., Feng, Y.-C. A., Chen, C.-Y., Lam, M., Guo, Z., Initiatives, S. G. A., Ahn, Y. M., Akiyama, K., Arai, M., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01054-7 · Cited by 707 · see citing works
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Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works
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Martin, A. R., Lin, M., Granka, J. M., Myrick, J. W., Liu, X., Sockell, A., Atkinson, E. G., Werely, C. J., Möller, M., Sandhu, M. S., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.015 · Cited by 156 · see citing works
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Ioannidis, A. G., Blanco-Portillo, J., Sandoval, K., Hagelberg, E., Barberena-Jonas, C., Hill, A. V. S., Rodríguez-Rodríguez, J. E., Fox, K., Robson, K., Haoa-Cardinali, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03902-8 · Cited by 124 · see citing works
Self-citationShriner, D. (2013) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg0123s76 · Cited by 111 · see citing works
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Perry, G. H., Foll, M., Grenier, J.-C., Patin, E., Nédélec, Y., Pacis, A., Barakatt, M., Gravel, S., Zhou, X., Nsobya, S. L., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1402875111 · Cited by 105 · see citing works
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Wang, H., Cade, B. E., Sofer, T., Sands, S. A., Chen, H., Browning, S. R., Stilp, A. M., Louie, T. L., Thornton, T. A., Johnson, W. C., et al. (2019) · Human Molecular Genetics · doi:10.1093/hmg/ddy387 · Cited by 56 · see citing works
Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03052-2 · Cited by 53 · see citing works
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Lyu, Y., Wang, F., Cheng, H., Han, J., Dang, R., Xia, X., Wang, H., Zhong, J., Lenstra, J. A., Zhang, H., et al. (2024) · Science Bulletin · doi:10.1016/j.scib.2024.05.030 · Cited by 50 · see citing works
Du, Z., Weinhold, N., Song, G. C., Rand, K. A., Van Den Berg, D. J., Hwang, A. E., Sheng, X., Hom, V., Ailawadhi, S., Nooka, A. K., et al. (2020) · Blood Advances · doi:10.1182/bloodadvances.2019000491 · Cited by 31 · see citing works
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Witt, K. E., Funk, A., Añorve-Garibay, V., Fang, L. L., & Huerta-Sánchez, E. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad066 · Cited by 29 · see citing works
“S1, Supplementary Material online), which used RFMix, a random forest-based ancestry inference method to identify haploid ancestry tracts (Maples et al. 2013).”
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“Through downsampling experiments of our data, we find that the average depth of coverage of that dataset (0.0004–0.0041×) does not yield enough power to carry out the specific statistical tests Colours correspond to the source populations from RFmix (Polynesian, Native American and European).”
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- Authors
- Maples, B. K., Gravel, S., Kenny, E. E., & Bustamante, C. D.
- Affiliations
- Stanford University (US)
- McGill University (CA)
- Corresponding author
- Bustamante, Carlos D.
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2013-08
- Volume
- 93
- Issue
- 2
- Pages
- 278-288
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC3738819
- OpenAlex
- W2128371599
- Cited by
- 900
- References
- 5
- Citations by year
- 2026: 90 · 2025: 111 · 2024: 94 · 2023: 106 · 2022: 88 · 2021: 108 · 2020: 88 · 2019: 66 · 2018: 45 · 2017: 35 · 2016: 21 · 2015: 19 · 2014: 26 · 2013: 3
- FWCI
- 15.26
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute (R01HG003229)
- U.S. National Library of Medicine (LM007033, T15LM007033)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Keywords
- local ancestry inference, conditional random fields, random forest, reference panel, admixture, African American ancestry, Native American ancestry, HapMap
- MeSH terms
- Black or African American, Computer Simulation, Genetic Testing, Haplotypes, Humans, Indians, North American, Models, Genetic, Genome, Human, Polymorphism, Single Nucleotide, Black People, White People, Asian People
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