The power of Trans-Omics for Precision Medicine (TOPMed) imputation for the discovery of Latino-enriched rare variants associated with type 2 diabetes
Authors' conclusion
Our results demonstrate the utility of TOPMed imputation for identifying low-frequency variants in understudied populations, leading to the discovery of novel disease associations and the improvement of polygenic scores.
Study context
- Population
- Latino individuals from six Latino cohorts; replication in six additional cohorts including All of Us whole-genome sequence data
- Participants
- 8,150 vs 10,735
- Comparison
- T2D cases vs controls; TOPMed vs 1000G imputation
- T2Dn = 8,150
- Controlsn = 10,735reference
- Outcome
- Genome-wide significant T2D signals
Methodological detailsimputation with TOPMed reference panel, replication in six additional cohorts
- Imputation with TOPMed reference panel
- Replication in six additional cohorts
Pooled result
As reported in the abstract
Genome-wide significant signals
26
Novel variant (minor allele frequency 1.7%)
OR 1.37
p=3.4 × 10-9
Further pooled results
Imputation performance: TOPMed vs 1000G
- TOPMed panel improved identification of rare and low-frequency variants vs 1000G
Latino-tailored polygenic score
- Improved prediction accuracy in a Latino target dataset; T2D risk variance explained up to
- 7.6%
Original publication
The power of TOPMed imputation for the discovery of Latino-enriched rare variants associated with type 2 diabetes. Diabetologia. Published 6 May 2023. doi:10.
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