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Fast and accurate long-range phasing in a UK Biobank cohort
- Source :
- Nature genetics
- Publication Year :
- 2016
-
Abstract
- Recent work has leveraged the unique genealogical structure and extensive genotyping (>30%) 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 outbred populations by harnessing long (>4cM) identical-by-descent (IBD) tracts shared among distantly related individuals. We applied Eagle to N=150K 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 exquisite phasing accuracy (switch error rate ≈0.3%, corresponding to perfect phase at the scale of >10Mb). Moreover, we observed that Eagle imputed masked genotypes with accuracy R2>0.75 down to a minor allele frequency of 0.1%. Compared to computationally tractable alternatives, Eagle attained large improvements in phasing and imputation accuracy at N=150K and smaller improvements at smaller sample sizes, illustrating the advantages that LRP-based imputation will yield as very large reference panels become available.
- Subjects :
- 0301 basic medicine
Eagle
Computer science
Population
Inheritance Patterns
Polymorphism, Single Nucleotide
White People
Article
Cohort Studies
03 medical and health sciences
0302 clinical medicine
biology.animal
Statistics
Genetics
Range (statistics)
Humans
Imputation (statistics)
education
Genotyping
Biological Specimen Banks
030304 developmental biology
Genetic association
0303 health sciences
education.field_of_study
biology
Genome, Human
Computational Biology
High-Throughput Nucleotide Sequencing
Genomics
Sequence Analysis, DNA
Phaser
Biobank
United Kingdom
Minor allele frequency
Genetics, Population
030104 developmental biology
Sample size determination
Cohort
Cartography
Algorithms
030217 neurology & neurosurgery
Imputation (genetics)
Subjects
Details
- ISSN :
- 15461718 and 10614036
- Volume :
- 48
- Issue :
- 7
- Database :
- OpenAIRE
- Journal :
- Nature Genetics
- Accession number :
- edsair.doi.dedup.....15a241bef2c4b3aa5ac2ae4d76d4e49a