Baseline: Assessment ⏵ Genomics ⏵ Genetic risk scores ⏵ Adiposity
Description
This category contains genetic risk scores (GRSs) for adiposity, used in Publication 30.GRSs for BMI, hip circumference, waist circumference and %body fat with transancestry weights from Fairhurst et. al.-see additional information provided in Resource 107. Any variants not available in MCPS (for which no good proxy was found) or palindromic variants that could not be harmonised were dropped. Palindromic variants were harmonised on the forward strand using the 1000Genomes as the reference VCF and the sumstat-harmoniser workflow from Open Targets (https://github.com/opentargets/genetics-sumstat-harmoniser). Since not all SNPs were available, when proxies were used, the weights of the original SNPs were used by matching the alleles based on the minor allele frequencies (SNPs with MAF>0.42 were not matched and were dropped).
Overall and sex-specific GRSs for BMI from the GIANT consortium based on the study by Pulit et. al 2018. A list of variants is provided in Resource 108. The initial scores included 766 genetic variants and were based on a pruning r2 threshold of 0.2 as done by Pulit et al. We further applied a more stringent threshold for clumping at r2>0.001 and these scores included 612 genetic variants. Note that these scores were generated with a previous version of our MR workflow that did not handle palindromic variants.
