Genotype Imputation for Rare Variants
Author Information
Author(s): Li Li, Li Yun, Browning Sharon R., Browning Brian L., Slater Andrew J., Kong Xiangyang, Aponte Jennifer L., Mooser Vincent E., Chissoe Stephanie L., Whittaker John C., Nelson Matthew R., Ehm Margaret Gelder
Primary Institution: Genetics, GlaxoSmithKline
Hypothesis
The performance of genotype imputation for rare variants has not been comprehensively studied.
Conclusion
Genotype imputation can effectively extend the assessment of common variants identified in humans via targeted exon resequencing into additional samples with GWAS data.
Supporting Evidence
- The study used 8865 human samples with high depth resequencing data.
- Imputation performance was evaluated using reference sets ranging from 100 to 3713 subjects.
- The proportion of well-imputed variants increased with the size of the reference panel.
Takeaway
This study looks at how well we can guess missing genetic information using data from many people, especially for rare genetic variants.
Methodology
The study utilized high depth resequencing data and GWAS data to evaluate the performance of genotype imputation for rare variants.
Limitations
Imputation of very rare variants (MAF≤0.005) will require reference panels with thousands of subjects.
Participant Demographics
The sample included 8865 individuals, primarily of European ancestry.
Digital Object Identifier (DOI)
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