Large-scale integration of the plasma proteome with genetics and disease

The plasma proteome can help bridge the gap between the genome and diseases. Here we describe genome-wide association studies (GWASs) of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders. We found 18,084 associations between sequence variants and levels of proteins in plasma (p...

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Vydané v:Nature genetics Ročník 53; číslo 12; s. 1712 - 1721
Hlavní autori: Ferkingstad, Egil, Sulem, Patrick, Atlason, Bjarni A., Sveinbjornsson, Gardar, Magnusson, Magnus I., Styrmisdottir, Edda L., Gunnarsdottir, Kristbjorg, Helgason, Agnar, Oddsson, Asmundur, Halldorsson, Bjarni V., Jensson, Brynjar O., Zink, Florian, Halldorsson, Gisli H., Masson, Gisli, Arnadottir, Gudny A., Katrinardottir, Hildigunnur, Juliusson, Kristinn, Magnusson, Magnus K., Magnusson, Olafur Th, Fridriksdottir, Run, Saevarsdottir, Saedis, Gudjonsson, Sigurjon A., Stacey, Simon N., Rognvaldsson, Solvi, Eiriksdottir, Thjodbjorg, Olafsdottir, Thorunn A., Steinthorsdottir, Valgerdur, Tragante, Vinicius, Ulfarsson, Magnus O., Stefansson, Hreinn, Jonsdottir, Ingileif, Holm, Hilma, Rafnar, Thorunn, Melsted, Pall, Saemundsdottir, Jona, Norddahl, Gudmundur L., Lund, Sigrun H., Gudbjartsson, Daniel F., Thorsteinsdottir, Unnur, Stefansson, Kari
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: New York Nature Publishing Group US 01.12.2021
Nature Publishing Group
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ISSN:1061-4036, 1546-1718, 1546-1718
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Abstract The plasma proteome can help bridge the gap between the genome and diseases. Here we describe genome-wide association studies (GWASs) of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders. We found 18,084 associations between sequence variants and levels of proteins in plasma (protein quantitative trait loci; pQTL), of which 19% were with rare variants (minor allele frequency (MAF) < 1%). We tested plasma protein levels for association with 373 diseases and other traits and identified 257,490 associations. We integrated pQTL and genetic associations with diseases and other traits and found that 12% of 45,334 lead associations in the GWAS Catalog are with variants in high linkage disequilibrium with pQTL. We identified 938 genes encoding potential drug targets with variants that influence levels of possible biomarkers. Combining proteomics, genomics and transcriptomics, we provide a valuable resource that can be used to improve understanding of disease pathogenesis and to assist with drug discovery and development. A genome-wide association study of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders highlights links with over 370 disease endpoints and other traits.
AbstractList The plasma proteome can help bridge the gap between the genome and diseases. Here we describe genome-wide association studies (GWASs) of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders. We found 18,084 associations between sequence variants and levels of proteins in plasma (protein quantitative trait loci; pQTL), of which 19% were with rare variants (minor allele frequency (MAF) < 1%). We tested plasma protein levels for association with 373 diseases and other traits and identified 257,490 associations. We integrated pQTL and genetic associations with diseases and other traits and found that 12% of 45,334 lead associations in the GWAS Catalog are with variants in high linkage disequilibrium with pQTL. We identified 938 genes encoding potential drug targets with variants that influence levels of possible biomarkers. Combining proteomics, genomics and transcriptomics, we provide a valuable resource that can be used to improve understanding of disease pathogenesis and to assist with drug discovery and development. A genome-wide association study of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders highlights links with over 370 disease endpoints and other traits.
The proteome also introduces a new temporal quality: the levels of proteins may rise or fall as a function of time before or after an event or as disease progresses or regresses. [...]far, the largest pQTL study (n = 30,931) only assessed 90 proteins8, whereas the largest study with 200 or more proteins had less than 6,000 participants5. Here we report the analysis of the associations of 27.2 million sequence variants and 373 diseases and other traits with the levels of 4,907 plasma proteins measured in 35,559 Icelanders with SomaScan version 4 (Figs. 1 and 2). Accounting for multiple testing, the levels of 63% of the 4,907 proteins correlated positively with age and 18% correlated negatively with age (Supplementary Table 1). [...]levels of 33% of the proteins were higher in men and 23% were higher in women. Overall, the presence of PAVs in high LD, the absence of cis eQTL and lower protein levels associated with the alternative allele all increase the likelihood of an aptamer binding artifact (Fig. 4a,b and Extended Data Fig. 4).
The plasma proteome can help bridge the gap between the genome and diseases. Here we describe genome-wide association studies (GWASs) of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders. We found 18,084 associations between sequence variants and levels of proteins in plasma (protein quantitative trait loci; pQTL), of which 19% were with rare variants (minor allele frequency (MAF) < 1%). We tested plasma protein levels for association with 373 diseases and other traits and identified 257,490 associations. We integrated pQTL and genetic associations with diseases and other traits and found that 12% of 45,334 lead associations in the GWAS Catalog are with variants in high linkage disequilibrium with pQTL. We identified 938 genes encoding potential drug targets with variants that influence levels of possible biomarkers. Combining proteomics, genomics and transcriptomics, we provide a valuable resource that can be used to improve understanding of disease pathogenesis and to assist with drug discovery and development.
The plasma proteome can help bridge the gap between the genome and diseases. Here we describe genome-wide association studies (GWASs) of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders. We found 18,084 associations between sequence variants and levels of proteins in plasma (protein quantitative trait loci; pQTL), of which 19% were with rare variants (minor allele frequency (MAF) < 1%). We tested plasma protein levels for association with 373 diseases and other traits and identified 257,490 associations. We integrated pQTL and genetic associations with diseases and other traits and found that 12% of 45,334 lead associations in the GWAS Catalog are with variants in high linkage disequilibrium with pQTL. We identified 938 genes encoding potential drug targets with variants that influence levels of possible biomarkers. Combining proteomics, genomics and transcriptomics, we provide a valuable resource that can be used to improve understanding of disease pathogenesis and to assist with drug discovery and development.The plasma proteome can help bridge the gap between the genome and diseases. Here we describe genome-wide association studies (GWASs) of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders. We found 18,084 associations between sequence variants and levels of proteins in plasma (protein quantitative trait loci; pQTL), of which 19% were with rare variants (minor allele frequency (MAF) < 1%). We tested plasma protein levels for association with 373 diseases and other traits and identified 257,490 associations. We integrated pQTL and genetic associations with diseases and other traits and found that 12% of 45,334 lead associations in the GWAS Catalog are with variants in high linkage disequilibrium with pQTL. We identified 938 genes encoding potential drug targets with variants that influence levels of possible biomarkers. Combining proteomics, genomics and transcriptomics, we provide a valuable resource that can be used to improve understanding of disease pathogenesis and to assist with drug discovery and development.
Author Oddsson, Asmundur
Masson, Gisli
Fridriksdottir, Run
Norddahl, Gudmundur L.
Rognvaldsson, Solvi
Melsted, Pall
Halldorsson, Bjarni V.
Olafsdottir, Thorunn A.
Atlason, Bjarni A.
Sveinbjornsson, Gardar
Gunnarsdottir, Kristbjorg
Thorsteinsdottir, Unnur
Saevarsdottir, Saedis
Halldorsson, Gisli H.
Steinthorsdottir, Valgerdur
Rafnar, Thorunn
Eiriksdottir, Thjodbjorg
Holm, Hilma
Lund, Sigrun H.
Ferkingstad, Egil
Styrmisdottir, Edda L.
Gudbjartsson, Daniel F.
Tragante, Vinicius
Jensson, Brynjar O.
Helgason, Agnar
Stefansson, Kari
Sulem, Patrick
Jonsdottir, Ingileif
Arnadottir, Gudny A.
Katrinardottir, Hildigunnur
Saemundsdottir, Jona
Magnusson, Magnus I.
Zink, Florian
Magnusson, Magnus K.
Gudjonsson, Sigurjon A.
Stacey, Simon N.
Ulfarsson, Magnus O.
Juliusson, Kristinn
Stefansson, Hreinn
Magnusson, Olafur Th
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/34857953$$D View this record in MEDLINE/PubMed
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Copyright The Author(s), under exclusive licence to Springer Nature America, Inc. 2021
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Snippet The plasma proteome can help bridge the gap between the genome and diseases. Here we describe genome-wide association studies (GWASs) of plasma protein levels...
The proteome also introduces a new temporal quality: the levels of proteins may rise or fall as a function of time before or after an event or as disease...
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SubjectTerms 45/23
45/43
45/91
631/114/2784
631/208/205/2138
692/308/2056
82/47
82/79
82/80
Agriculture
Animal Genetics and Genomics
Aptamers
Biomarkers
Biomarkers - blood
Biomedical and Life Sciences
Biomedicine
Blood Proteins - genetics
Blood Proteins - metabolism
Cancer Research
Disease
Disease - genetics
Female
Gene expression
Gene Frequency
Gene Function
Genetic Variation
Genetics
Genome-Wide Association Study
Genomes
Genomics
Human Genetics
Humans
Male
Middle Aged
Pathogenesis
Plasma
Plasma proteins
Proteins
Proteome - genetics
Proteomes
Quantitative Trait Loci
Title Large-scale integration of the plasma proteome with genetics and disease
URI https://link.springer.com/article/10.1038/s41588-021-00978-w
https://www.ncbi.nlm.nih.gov/pubmed/34857953
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Volume 53
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