TOPMed T2D Latin American GWAS meta-analysis (2022)

We meta-analyzed 6 type 2 diabetes GWAS of Latin American ancestry, comprising 8,150 cases and 10,735 controls. Individuals were from hospital and population-based studies. Genotyping was done using several commercially available genome-wide arrays, and for a subset of samples, whole-exome sequencing was integrated. We applied pre-imputation quality control to each dataset separately, and all cohorts were imputed to the TOPMed freeze 8 reference panel. Type 2 diabetes association analyses were performed in each cohort with SNPTEST using the expectation maximization method and we included only the variants where the count of the minor allele was at least 5. Models were adjusted for sex, age, body mass index and 10 PCs to account for population structure. Variants with an imputation quality of r2>=0.5 were meta-analyzed using the inverse of the corresponding squared standard errors in METAL. Autosomes as well as the sexual chromosome X were analyzed. For chromosome X, we imputed and performed the association analyses in females and males, separately.

The file contains summary statistics of the TOPMed T2D Latin American GWAS meta-analysis, including the following information:

chromosome(b38): chromosome number
position(b38): Position in b38
chrposID: markername in chr:pos:a1:a2 format
effect_allele: Effect allele
other_allele: Other allele
effect_allele_frequency: Effect allele frequency
Fixed-effects_beta: Effect estimate
Fixed-effects_SE: Standard error of the effect estimate
Fixed-effects_p-value: p-value
Effect_direction: Direction of the effect estimate by study
Heterogeneity_p-value: study heterogeneity p-value

Please refer any queries to Alicia Huerta (ahuerta@broadinstitute.org) or Josep Mercader (mercader@broadinstitute.org)