Fast and accurate long-range phasing in a UK Biobank cohort
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Abstract
Recent work has leveraged the extensive genotyping of the Icelandic population to perform long-range phasing (LRP), enabling accurate imputation and association analysis of rare variants in target samples typed on genotyping arrays. Here we develop a fast and accurate LRP method, Eagle, that extends this paradigm to populations with much smaller proportions of genotyped samples by harnessing long (>4-cM) identical-by-descent (IBD) tracts shared among distantly related individuals. We applied Eagle to N ≈ 150,000 samples (0.2% of the British population) from the UK Biobank, and we determined that it is 1-2 orders of magnitude faster than existing methods while achieving similar or better phasing accuracy (switch error rate ≈ 0.3%, corresponding to perfect phase in a majority of 10-Mb segments). We also observed that, when used within an imputation pipeline, Eagle prephasing improved downstream imputation accuracy in comparison to prephasing in batches using existing methods, as necessary to achieve comparable computational cost.
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The capability to demultiplex and identify doublets using natural genetic variation reduces per-sample and per-cell library preparation cost, does not require synthetic barcodes or split-pool strategies, and captures biological variability among individual samples while limiting unwanted technical variability.
“The capability to demultiplex and identify doublets using natural genetic variation reduces the per-sample and per-cell library preparation cost of single-cell RNA-sequencing, does not require synthetic barcodes or split-pool strategies36–40, and captures biological variability among individual samples while limiting unwanted technical variability.”
From Multiplexed droplet single-cell RNA-sequencing using natural genetic variation (2018) · cites this paper as [39]
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- Authors
- Loh, P.-R., Palamara, P. F., & Price, A. L.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Loh, Po-Ru
- Price, Alkes L
- Venue
- Nature Genetics
- Published
- 2016-06-06
- Volume
- 48
- Issue
- 7
- Pages
- 811-816
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4925291
- OpenAlex
- W2413234541
- Cited by
- 342
- References
- 57
- Citations by year
- 2026: 11 · 2025: 29 · 2024: 40 · 2023: 39 · 2022: 39 · 2021: 65 · 2020: 50 · 2019: 31 · 2018: 22 · 2017: 10 · 2016: 6
- FWCI
- 18.56
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (480- 05-003)
- National Institutes of Health (1s10rr028832-01)
- National Institute of Mental Health (R01MH101244)
- National Human Genome Research Institute (R01HG006399, F32HG007805)
- National Center for Research Resources (S10 RR028832)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- eagle, outbred populations, UK Biobank, computational efficiency
- MeSH terms
- Algorithms, Genetics, Population, United Kingdom, Humans, Cohort Studies, Genome, Human, Sequence Analysis, DNA, Biological Specimen Banks, Computational Biology, Polymorphism, Single Nucleotide, Genomics, Inheritance Patterns, White People, High-Throughput Nucleotide Sequencing
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