04 February 2019 by Stefan Gräf

Disentangling the missing heritability of pulmonary arterial hypertension

Background:

Most recently we identified ultra rare protein-coding mutations in novel causal genes, namely ATP13A3, AQP1 and SOX17, and provided independent validation of a critical role for GDF2 in PAH (Gräf et al., 2018, Nat Commun). In a complementary genome-wide association study we subsequently discovered common variation in two loci that reached genome-wide significance, one in a regulatory element upstream of SOX17 and another one in the HLA-DPA1/DPB1 region (Rhodes et al., 2018, Lancet Resp. Med). Although we increased the diagnostic yield to about one quarter of the patients, a large fraction of patients still remains unexplained at genomics level.

Objectives:

In order to disentangle the missing heritability in PAH we recognised that even larger cohorts are needed to increase statistical power for the identification of causal sequence variation with smaller effect size. And the GWAS study suggested that the non-coding, regulatory regions in the genome deserve particular attention.

Methods:

The expanded whole genome sequencing (WGS) cohort of the NIHR BioResource – Rare Diseases now comprised 13,037 individuals including 1148 subjects recruited to the PAH domain. We performed rare variant association analyses with BeviMed (Greene et al., 2017, AJHG) using selected endophenotypes to define subgroups. Furthermore, we have generated cell-type specific histone modification (H3K27ac) and open chromatin (ATAC) profiles with the aim to identify enhancer regions in the genome, within which we tested for an overrepresentation of variants in cases compared to controls.

Results:

The rare variant analysis reveals KDR, encoding the vascular endothelial growth factor receptor 2 (VEGFR2), as the next candidate PAH disease gene showing an overrepresentation of protein truncating variants in cases compared to controls with significantly reduced transfer coefficient (KCO). Further potentially pathogenic protein-coding and non-coding sequence variation will be discussed.

 

About the author


profile picture of Stefan Gräf

Stefan Gräf

Senior Research Associate

Department of Medicine, University of Cambridge

United Kingdom

Key Contributors

Stefan Gräf 1,2,3, Tobias Tilly 1, Emilia M. Swietlik 1, Nicholas W. Morrell 1,3 on behalf of the NIHR BioResource – Rare Diseases and the UK National Cohort Study of Idiopathic and Heritable PAH : 1.Department of Medicine, University of Cambridge, Cambridge, United Kingdom. 2.Department of Haematology, University of Cambridge, Cambridge, United Kingdom. 3.NIHR BioResource for Translational Research, Biomedical Campus, Cambridge, United Kingdom


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