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Thareja G, Belkadi A, Arnold M, Albagha OME, Graumann J, Schmidt F, Grallert H, Peters A, Gieger C, Consortium TQGPR, Suhre K. Differences and commonalities in the genetic architecture of protein quantitative trait loci in European and Arab populations. Hum Mol Genet 2023; 32:907-916. [PMID: 36168886 PMCID: PMC9990988 DOI: 10.1093/hmg/ddac243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/12/2022] Open
Abstract
Polygenic scores (PGS) can identify individuals at risk of adverse health events and guide genetics-based personalized medicine. However, it is not clear how well PGS translate between different populations, limiting their application to well-studied ethnicities. Proteins are intermediate traits linking genetic predisposition and environmental factors to disease, with numerous blood circulating protein levels representing functional readouts of disease-related processes. We hypothesized that studying the genetic architecture of a comprehensive set of blood-circulating proteins between a European and an Arab population could shed fresh light on the translatability of PGS to understudied populations. We therefore conducted a genome-wide association study with whole-genome sequencing data using 1301 proteins measured on the SOMAscan aptamer-based affinity proteomics platform in 2935 samples of Qatar Biobank and evaluated the replication of protein quantitative traits (pQTLs) from European studies in an Arab population. Then, we investigated the colocalization of shared pQTL signals between the two populations. Finally, we compared the performance of protein PGS derived from a Caucasian population in a European and an Arab cohort. We found that the majority of shared pQTL signals (81.8%) colocalized between both populations. About one-third of the genetic protein heritability was explained by protein PGS derived from a European cohort, with protein PGS performing ~20% better in Europeans when compared to Arabs. Our results are relevant for the translation of PGS to non-Caucasian populations, as well as for future efforts to extend genetic research to understudied populations.
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Affiliation(s)
- Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, NY 10065, New York, USA
| | - Aziz Belkadi
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, NY 10065, New York, USA
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.,Department of Psychiatry and Behavioral Sciences, Duke University, NC 27710, USA
| | - Omar M E Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, 34110 Doha, Qatar.,Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, EH4 2XU, Edinburgh, UK
| | - Johannes Graumann
- Institute of Translational Proteomics, Department of Medicine, Philipps-Universität Marburg, Marburg, Germany
| | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, Neuherberg 85764, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.,Department of Epidemiology, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| | | | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, NY 10065, New York, USA
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Belkadi A, Thareja G, Abbaszadeh F, Badii R, Fauman E, Albagha OM, Suhre K. Identification of PCSK9-like human gene knockouts using metabolomics, proteomics, and whole-genome sequencing in a consanguineous population. Cell Genom 2022; 3:100218. [PMID: 36777185 PMCID: PMC9903797 DOI: 10.1016/j.xgen.2022.100218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/16/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
Natural human knockouts of genes associated with desirable outcomes, such as PCSK9 with low levels of LDL-cholesterol, can lead to the discovery of new drug targets and treatments. Rare loss-of-function variants are more likely to be found in the homozygous state in consanguineous populations, and deep molecular phenotyping of blood samples from homozygous carriers can help to discriminate between silent and functional variants. Here, we combined whole-genome sequencing with proteomics and metabolomics for 2,935 individuals from the Qatar Biobank (QBB) to evaluate the power of this approach for finding genes of clinical and pharmaceutical interest. As proof-of-concept, we identified a homozygous carrier of a very rare PCSK9 variant with extremely low circulating PCSK9 levels and low LDL. Our study demonstrates that the chances of finding such variants are about 168 times higher in QBB compared with GnomAD and emphasizes the potential of consanguineous populations for drug discovery.
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Affiliation(s)
- Aziz Belkadi
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA
| | - Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Omar M.E. Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar,Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA,Corresponding author
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