Gene-based test results used for the analysis described in 'Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma'

The dataset deposited here contains the results of gene-based tests for 7 traits characterized in UK Biobank described in the following publication:

Y. Tanigawa, et al., Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma. bioRxiv (2019). doi:10.1101/677443


The 7 traits included in the datasets are:
- INI5255: Goldmann-correlated IOP (right)
- INI5263: Goldmann-correlated IOP (left)
- INI2005255: Goldmann-correlated IOP (median)
- INI5254: corneal-compensated IOP (right)
- INI5262: corneal-compensated IOP (left)
- INI2005254: corneal-compensated IOP (median)
- HC276: Glaucoma

Please read our preprint for more information regarding this dataset.

Abstract

Protein-altering variants that are protective against human disease provide in vivo validation of therapeutic targets. Here we use genotyping data from UK Biobank (n = 337,151 unrelated White British individuals) and FinnGen (n = 176,899) to conduct a search for protein-altering variants conferring lower intraocular pressure (IOP) and protection against glaucoma. Through rare protein-altering variant association analysis, we find a missense variant in ANGPTL7 in UK Biobank (rs28991009, MAF=0.8%, genotyped in 82,253 individuals with measured IOP and an independent set of 4,238 glaucoma patients and 250,660 controls) that significantly lowers IOP (β = -0.53 and -0.67 mmHg for heterozygotes, -3.40 and -2.37 mmHg for homozygotes, P = 5.96 x 10-9 and 1.07 x 10-13 for corneal compensated and Goldman-correlated IOP, respectively) and is associated with 34% reduced risk of glaucoma (P = 0.0062). In FinnGen, we identify an ANGPTL7 missense variant at a greater than 50-fold increased frequency in Finland compared with other populations (rs147660927, p.Arg220Cys, MAF Finland = 4.3%), which was genotyped in 6,537 glaucoma patients and 170,362 controls and is associated with a 29% lower glaucoma risk (P = 1.9 x 10-12 for all glaucoma types and also protection against its subtypes including exfoliation, primary open-angle, and primary angle-closure). We further find three rarer variants in UK Biobank, including a protein-truncating variant, which confer a strong composite lowering of IOP (P = 0.0012 and 0.24 for Goldman-correlated and corneal compensated IOP, respectively), suggesting the protective mechanism likely resides in the loss of an interaction or function. Our results support inhibition or down-regulation of ANGPTL7 as a therapeutic strategy for glaucoma.