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Accurate haplotype imputation with individualized ancestry-adjusted reference panels
- Source :
- Genomics. 110:329-335
- Publication Year :
- 2018
- Publisher :
- Elsevier BV, 2018.
-
Abstract
- Accurate data imputation requires ethnicity-matched reference panels. However, recent admixtures have created mosaic human genomes, different chromosomal segments have different ethnic backgrounds, so it is impossible for a single-ethnicity reference panel to be the matched for data imputation. In this study, we explored a novel strategy for imputation. We created individualized mosaic reference panel for each person according to his/her ethnic backgrounds at each genomic locus. We examined on datasets with 70% missing values on haplotypes and 50% missing values on genotypes. Results showed that the imputation with mosaic references steadily yielded high imputation accuracy and outperforms the other strategies. With the mosaic reference panels, the imputation accuracy was 98.8 ± 0.1% (CEU), 98.7 ± 0.1% (YRI), 98.5 ± 0.1% (CHB), 98.6 ± 0.1% (ASW), 97.3 ± 0.1% (MKK) and 98.2 ± 0.1% (MXL). Mosaic reference panel will be one option for future missing value imputation in big data era.
- Subjects :
- 0301 basic medicine
African american
Genome, Human
Haplotype
Black People
Biology
Missing data
Chromosomes
03 medical and health sciences
030104 developmental biology
Haplotypes
Reference Values
Statistics
Genetics
Missing value imputation
Humans
Imputation (genetics)
Genome-Wide Association Study
Subjects
Details
- ISSN :
- 08887543
- Volume :
- 110
- Database :
- OpenAIRE
- Journal :
- Genomics
- Accession number :
- edsair.doi.dedup.....8453be1dfae77aa965624ba642fa20d1