The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Genotype Imputation with Millions of Reference Samples
Open accessAbstract
We present a genotype imputation method that scales to millions of reference samples. The imputation method, based on the Li and Stephens model and implemented in Beagle v.4.1, is parallelized and memory efficient, making it well suited to multi-core computer processors. It achieves fast, accurate, and memory-efficient genotype imputation by restricting the probability model to markers that are genotyped in the target samples and by performing linear interpolation to impute ungenotyped variants. We compare Beagle v.4.1 with Impute2 and Minimac3 by using 1000 Genomes Project data, UK10K Project data, and simulated data. All three methods have similar accuracy but different memory requirements and different computation times. When imputing 10 Mb of sequence data from 50,000 reference samples, Beagle's throughput was more than 100× greater than Impute2's throughput on our computer servers. When imputing 10 Mb of sequence data from 200,000 reference samples in VCF format, Minimac3 consumed 26× more memory per computational thread and 15× more CPU time than Beagle. We demonstrate that Beagle v.4.1 scales to much larger reference panels by performing imputation from a simulated reference panel having 5 million samples and a mean marker density of one marker per four base pairs.
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Cites
A tutorial on hidden Markov models and selected applications in speech recognition
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A global reference for human genetic variation
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Self-citationGenome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442
A map of human genome variation from population-scale sequencing.
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An integrated map of genetic variation from 1,092 human genomes
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A new multipoint method for genome-wide association studies by imputation of genotypes
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Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
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Cited by
Next-generation genotype imputation service and methods
Das, S., Forer, L., Schönherr, S., Sidore, C., Locke, A. E., Kwong, A., Vrieze, S. I., Chew, E. Y., Levy, S., McGue, M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3656 · Cited by 3,808
10 Years of GWAS Discovery: Biology, Function, and Translation
Visscher, P. M., Wray, N. R., Zhang, Q., Sklar, P., McCarthy, M. I., Brown, M. A., & Yang, J. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.06.005 · Cited by 3,719
A One-Penny Imputed Genome from Next-Generation Reference Panels
Browning, B. L., Zhou, Y., & Browning, S. R. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.07.015 · Cited by 2,092
Self-citationReference-based phasing using the Haplotype Reference Consortium panel
Loh, P.-R., Danecek, P., Palamara, P. F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G. R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3679 · Cited by 1,723
Mullins, N., Forstner, A. J., O’Connell, K. S., Coombes, B., Coleman, J. R. I., Qiao, Z., Als, T. D., Bigdeli, T. B., Børte, S., Bryois, J., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00857-4 · Cited by 1,517
Metadata
- Authors
- Browning, B. L., & Browning, S. R.
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2016-01
- Volume
- 98
- Issue
- 1
- Pages
- 116-126
- ISSN
- 0002-9297 (ISSN-L)
- OpenAlex
- W2230276206
- Cited by
- 1,146
- References
- 11
- FWCI
- 81.46
- Type
- journal article
- Language
- en
- Open access
- bronze
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