Large-scale plasma proteomics comparisons through genetics and disease associations
Publisher Copyright: © 2023, The Author(s). High-throughput proteomics platforms measuring thousands of proteins in plasma combined with genomic and phenotypic information have the power to bridge the gap between the genome and diseases. Here we performed association studies of Olink Explore 3072 da...
Published in: | Nature |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Format: | Article in Journal/Newspaper |
Language: | English |
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2023
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Online Access: | https://hdl.handle.net/20.500.11815/4547 https://doi.org/10.1038/s41586-023-06563-x |
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Opin vísindi (Iceland) |
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English |
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Gigtarlæknisfræði Africa/ethnology Asia Southern/ethnology Biological Specimen Banks Blood Proteins/analysis Datasets as Topic Disease Susceptibility Genome Human/genetics Genomics Genotype Humans Iceland/ethnology Ireland/ethnology Phenotype Plasma/chemistry Proteome/analysis Proteomics/methods Quantitative Trait Loci United Kingdom Multidisciplinary |
spellingShingle |
Gigtarlæknisfræði Africa/ethnology Asia Southern/ethnology Biological Specimen Banks Blood Proteins/analysis Datasets as Topic Disease Susceptibility Genome Human/genetics Genomics Genotype Humans Iceland/ethnology Ireland/ethnology Phenotype Plasma/chemistry Proteome/analysis Proteomics/methods Quantitative Trait Loci United Kingdom Multidisciplinary Eldjarn, Grimur Hjorleifsson Ferkingstad, Egil Lund, Sigrun H. Helgason, Hannes Magnusson, Olafur Th Gunnarsdottir, Kristbjorg Olafsdottir, Thorunn A. Halldorsson, Bjarni V. Olason, Pall I. Zink, Florian Gudjonsson, Sigurjon A. Sveinbjornsson, Gardar Magnusson, Magnus I. Helgason, Agnar Oddsson, Asmundur Halldorsson, Gisli H. Magnusson, Magnus K. Sævarsdóttir, Sædís Eiriksdottir, Thjodbjorg Masson, Gisli Stefansson, Hreinn Jonsdottir, Ingileif Holm, Hilma Rafnar, Thorunn Melsted, Pall Saemundsdottir, Jona Norddahl, Gudmundur L. Thorleifsson, Gudmar Ulfarsson, Magnus O. Gudbjartsson, Daniel F. Thorsteinsdottir, Unnur Sulem, Patrick Stefansson, Kari Large-scale plasma proteomics comparisons through genetics and disease associations |
topic_facet |
Gigtarlæknisfræði Africa/ethnology Asia Southern/ethnology Biological Specimen Banks Blood Proteins/analysis Datasets as Topic Disease Susceptibility Genome Human/genetics Genomics Genotype Humans Iceland/ethnology Ireland/ethnology Phenotype Plasma/chemistry Proteome/analysis Proteomics/methods Quantitative Trait Loci United Kingdom Multidisciplinary |
description |
Publisher Copyright: © 2023, The Author(s). High-throughput proteomics platforms measuring thousands of proteins in plasma combined with genomic and phenotypic information have the power to bridge the gap between the genome and diseases. Here we performed association studies of Olink Explore 3072 data generated by the UK Biobank Pharma Proteomics Project 1 on plasma samples from more than 50,000 UK Biobank participants with phenotypic and genotypic data, stratifying on British or Irish, African and South Asian ancestries. We compared the results with those of a SomaScan v4 study on plasma from 36,000 Icelandic people 2, for 1,514 of whom Olink data were also available. We found modest correlation between the two platforms. Although cis protein quantitative trait loci were detected for a similar absolute number of assays on the two platforms (2,101 on Olink versus 2,120 on SomaScan), the proportion of assays with such supporting evidence for assay performance was higher on the Olink platform (72% versus 43%). A considerable number of proteins had genomic associations that differed between the platforms. We provide examples where differences between platforms may influence conclusions drawn from the integration of protein levels with the study of diseases. We demonstrate how leveraging the diverse ancestries of participants in the UK Biobank helps to detect novel associations and refine genomic location. Our results show the value of the information provided by the two most commonly used high-throughput proteomics platforms and demonstrate the differences between them that at times provides useful complementarity. Peer reviewed |
author2 |
Faculty of Physical Sciences Faculty of Sociology, Anthropology and Folkloristics Faculty of Industrial Engineering, Mechanical Engineering and Computer Science Faculty of Medicine Other departments Faculty of Electrical and Computer Engineering Health Sciences Reykjavik University |
format |
Article in Journal/Newspaper |
author |
Eldjarn, Grimur Hjorleifsson Ferkingstad, Egil Lund, Sigrun H. Helgason, Hannes Magnusson, Olafur Th Gunnarsdottir, Kristbjorg Olafsdottir, Thorunn A. Halldorsson, Bjarni V. Olason, Pall I. Zink, Florian Gudjonsson, Sigurjon A. Sveinbjornsson, Gardar Magnusson, Magnus I. Helgason, Agnar Oddsson, Asmundur Halldorsson, Gisli H. Magnusson, Magnus K. Sævarsdóttir, Sædís Eiriksdottir, Thjodbjorg Masson, Gisli Stefansson, Hreinn Jonsdottir, Ingileif Holm, Hilma Rafnar, Thorunn Melsted, Pall Saemundsdottir, Jona Norddahl, Gudmundur L. Thorleifsson, Gudmar Ulfarsson, Magnus O. Gudbjartsson, Daniel F. Thorsteinsdottir, Unnur Sulem, Patrick Stefansson, Kari |
author_facet |
Eldjarn, Grimur Hjorleifsson Ferkingstad, Egil Lund, Sigrun H. Helgason, Hannes Magnusson, Olafur Th Gunnarsdottir, Kristbjorg Olafsdottir, Thorunn A. Halldorsson, Bjarni V. Olason, Pall I. Zink, Florian Gudjonsson, Sigurjon A. Sveinbjornsson, Gardar Magnusson, Magnus I. Helgason, Agnar Oddsson, Asmundur Halldorsson, Gisli H. Magnusson, Magnus K. Sævarsdóttir, Sædís Eiriksdottir, Thjodbjorg Masson, Gisli Stefansson, Hreinn Jonsdottir, Ingileif Holm, Hilma Rafnar, Thorunn Melsted, Pall Saemundsdottir, Jona Norddahl, Gudmundur L. Thorleifsson, Gudmar Ulfarsson, Magnus O. Gudbjartsson, Daniel F. Thorsteinsdottir, Unnur Sulem, Patrick Stefansson, Kari |
author_sort |
Eldjarn, Grimur Hjorleifsson |
title |
Large-scale plasma proteomics comparisons through genetics and disease associations |
title_short |
Large-scale plasma proteomics comparisons through genetics and disease associations |
title_full |
Large-scale plasma proteomics comparisons through genetics and disease associations |
title_fullStr |
Large-scale plasma proteomics comparisons through genetics and disease associations |
title_full_unstemmed |
Large-scale plasma proteomics comparisons through genetics and disease associations |
title_sort |
large-scale plasma proteomics comparisons through genetics and disease associations |
publishDate |
2023 |
url |
https://hdl.handle.net/20.500.11815/4547 https://doi.org/10.1038/s41586-023-06563-x |
genre |
Iceland |
genre_facet |
Iceland |
op_relation |
Nature; 622(7982) https://doi.org/10.1038/s41586-023-06563-x http://www.scopus.com/inward/record.url?scp=85173272192&partnerID=8YFLogxK Eldjarn , G H , Ferkingstad , E , Lund , S H , Helgason , H , Magnusson , O T , Gunnarsdottir , K , Olafsdottir , T A , Halldorsson , B V , Olason , P I , Zink , F , Gudjonsson , S A , Sveinbjornsson , G , Magnusson , M I , Helgason , A , Oddsson , A , Halldorsson , G H , Magnusson , M K , Sævarsdóttir , S , Eiriksdottir , T , Masson , G , Stefansson , H , Jonsdottir , I , Holm , H , Rafnar , T , Melsted , P , Saemundsdottir , J , Norddahl , G L , Thorleifsson , G , Ulfarsson , M O , Gudbjartsson , D F , Thorsteinsdottir , U , Sulem , P & Stefansson , K 2023 , ' Large-scale plasma proteomics comparisons through genetics and disease associations ' , Nature , vol. 622 , no. 7982 , pp. 348-358 . https://doi.org/10.1038/s41586-023-06563-x 0028-0836 197043441 853d79a4-2768-4b45-88d7-805393f6c953 ORCID: /0000-0002-3806-2296/work/143584605 85173272192 unpaywall: 10.1038/s41586-023-06563-x 37794188 https://hdl.handle.net/20.500.11815/4547 doi:10.1038/s41586-023-06563-x |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/20.500.11815/454710.1038/s41586-023-06563-x |
container_title |
Nature |
container_volume |
622 |
container_issue |
7982 |
container_start_page |
348 |
op_container_end_page |
358 |
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1786206385496653824 |
spelling |
ftopinvisindi:oai:opinvisindi.is:20.500.11815/4547 2023-12-24T10:17:56+01:00 Large-scale plasma proteomics comparisons through genetics and disease associations Eldjarn, Grimur Hjorleifsson Ferkingstad, Egil Lund, Sigrun H. Helgason, Hannes Magnusson, Olafur Th Gunnarsdottir, Kristbjorg Olafsdottir, Thorunn A. Halldorsson, Bjarni V. Olason, Pall I. Zink, Florian Gudjonsson, Sigurjon A. Sveinbjornsson, Gardar Magnusson, Magnus I. Helgason, Agnar Oddsson, Asmundur Halldorsson, Gisli H. Magnusson, Magnus K. Sævarsdóttir, Sædís Eiriksdottir, Thjodbjorg Masson, Gisli Stefansson, Hreinn Jonsdottir, Ingileif Holm, Hilma Rafnar, Thorunn Melsted, Pall Saemundsdottir, Jona Norddahl, Gudmundur L. Thorleifsson, Gudmar Ulfarsson, Magnus O. Gudbjartsson, Daniel F. Thorsteinsdottir, Unnur Sulem, Patrick Stefansson, Kari Faculty of Physical Sciences Faculty of Sociology, Anthropology and Folkloristics Faculty of Industrial Engineering, Mechanical Engineering and Computer Science Faculty of Medicine Other departments Faculty of Electrical and Computer Engineering Health Sciences Reykjavik University 2023-10-04 11 18846445 348-358 https://hdl.handle.net/20.500.11815/4547 https://doi.org/10.1038/s41586-023-06563-x en eng Nature; 622(7982) https://doi.org/10.1038/s41586-023-06563-x http://www.scopus.com/inward/record.url?scp=85173272192&partnerID=8YFLogxK Eldjarn , G H , Ferkingstad , E , Lund , S H , Helgason , H , Magnusson , O T , Gunnarsdottir , K , Olafsdottir , T A , Halldorsson , B V , Olason , P I , Zink , F , Gudjonsson , S A , Sveinbjornsson , G , Magnusson , M I , Helgason , A , Oddsson , A , Halldorsson , G H , Magnusson , M K , Sævarsdóttir , S , Eiriksdottir , T , Masson , G , Stefansson , H , Jonsdottir , I , Holm , H , Rafnar , T , Melsted , P , Saemundsdottir , J , Norddahl , G L , Thorleifsson , G , Ulfarsson , M O , Gudbjartsson , D F , Thorsteinsdottir , U , Sulem , P & Stefansson , K 2023 , ' Large-scale plasma proteomics comparisons through genetics and disease associations ' , Nature , vol. 622 , no. 7982 , pp. 348-358 . https://doi.org/10.1038/s41586-023-06563-x 0028-0836 197043441 853d79a4-2768-4b45-88d7-805393f6c953 ORCID: /0000-0002-3806-2296/work/143584605 85173272192 unpaywall: 10.1038/s41586-023-06563-x 37794188 https://hdl.handle.net/20.500.11815/4547 doi:10.1038/s41586-023-06563-x info:eu-repo/semantics/openAccess Gigtarlæknisfræði Africa/ethnology Asia Southern/ethnology Biological Specimen Banks Blood Proteins/analysis Datasets as Topic Disease Susceptibility Genome Human/genetics Genomics Genotype Humans Iceland/ethnology Ireland/ethnology Phenotype Plasma/chemistry Proteome/analysis Proteomics/methods Quantitative Trait Loci United Kingdom Multidisciplinary /dk/atira/pure/researchoutput/researchoutputtypes/contributiontojournal/article 2023 ftopinvisindi https://doi.org/20.500.11815/454710.1038/s41586-023-06563-x 2023-11-29T23:55:20Z Publisher Copyright: © 2023, The Author(s). High-throughput proteomics platforms measuring thousands of proteins in plasma combined with genomic and phenotypic information have the power to bridge the gap between the genome and diseases. Here we performed association studies of Olink Explore 3072 data generated by the UK Biobank Pharma Proteomics Project 1 on plasma samples from more than 50,000 UK Biobank participants with phenotypic and genotypic data, stratifying on British or Irish, African and South Asian ancestries. We compared the results with those of a SomaScan v4 study on plasma from 36,000 Icelandic people 2, for 1,514 of whom Olink data were also available. We found modest correlation between the two platforms. Although cis protein quantitative trait loci were detected for a similar absolute number of assays on the two platforms (2,101 on Olink versus 2,120 on SomaScan), the proportion of assays with such supporting evidence for assay performance was higher on the Olink platform (72% versus 43%). A considerable number of proteins had genomic associations that differed between the platforms. We provide examples where differences between platforms may influence conclusions drawn from the integration of protein levels with the study of diseases. We demonstrate how leveraging the diverse ancestries of participants in the UK Biobank helps to detect novel associations and refine genomic location. Our results show the value of the information provided by the two most commonly used high-throughput proteomics platforms and demonstrate the differences between them that at times provides useful complementarity. Peer reviewed Article in Journal/Newspaper Iceland Opin vísindi (Iceland) Nature 622 7982 348 358 |