This dataset represents associations on chromosome X in the female subset of the 70KforT2D GWAS dataset.
The 70KforT2D GWAS dataset includes cohorts that are also included in the DIAGRAM Transethnic meta-analysis dataset.
All samples except the non-European GERA samples are included in the "DIAMANTE (European) T2D GWAS" dataset.
Publications
Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes.
Bonàs-Guarch S, et al.
Nat Commun. 2018 Jan 22;9(1):321. doi: 10.1038/s41467-017-02380-9.
PMID: 29358691
Phenotypes
- type 2 diabetes
Project
The 70KforT2D project is a re-analysis of public type 2 diabetes (T2D) GWAS datasets for 70,127 subjects, using genotype imputation with two reference panels (1000 Genomes and UK10K). This study improved coverage of rare and low-frequency variants as well as small insertions and deletions (indels), which led to an improved fine-mapping over ∼15M variants as well as a comprehensive exploration of the role of X chromosome variation into the genetics of T2D.
Experiment summary
In this study, publicly available GWAS individual-level data were aggregated, harmonized, subjected to quality control and imputation, and re-analyzed for association with type 2 diabetes. This approach allowed the analysis of variants on the X chromosome, which had not been done previously. Because variants on the X chromosome may have different effects in males and females, results are provided for these variants in two subsets of these data: "70KforT2D GWAS: chrX, females" and "70KforT2D GWAS: chrX, males".
External Links to 70KforT2D GWAS data
dbGaP: phs000237.v1.p1, phs000100.v4.p1, phs000091.v2.p1, phs000674.v1.p1
EGA:EGAS00000000005 (EGAD00000000001 + EGAD00000000002 + EGAD00000000009)