Proteomics in Proximity

Primary reference: Suhre K, Sarwath H, Engelke R, Sohail MU, Cho SJ, Whalen W, Alvarez-Mulett S, Krumsiek J, Choi AMK, Schmidt F. Identification of Robust Protein Associations With COVID-19 Disease Based on Five Clinical Studies. Front Immunol. 2022 12:781100. doi:10.3389/fimmu.2021.781100

Dr. Karsten Suhre’s Weill Cornell Medicine laboratory page: https://vivo.weill.cornell.edu/display/cwid-kas2049

Leukemia Inhibitory Factor reference: Loriot Y, Marabelle A, Guégan JP, et al. Plasma proteomics identifies leukemia inhibitory factor (LIF) as a novel predictive biomarker of immune-checkpoint blockade resistance. Ann Oncol. 2021 32(11):1381-1390. doi:10.1016/j.annonc.2021.08.1748

In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.

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To access Olink Insight free of charge, visit https://insight.olink.com 

The first two data stories, with Normal Range data and COVID-19 data, has been recently updated with the first Disease Atlas, with data characterizing 15 cancer types. This is available on Olink Insight here: https://insight.olink.com/data-stories/disease-atlas-cancer

To access the COVID-19 Data Story dataset itself, information about the study and how to access the data is available on our website here: https://olink.com/application/mgh-covid-19-study/

If you would like to contact Dale, Cindy or Sarantis feel free to email us at [email protected].

In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.

List of names and affiliations mentioned in the UK Biobank context: Mark McCarthy (Genentech), Slavé Petrovski (AstraZeneca), Chris Whelan (Johnson and Johnson), Erin Smith (Takeda Pharmaceuticals), Melissa Miller (Pfizer), Ben Sun (Biogen).

The ASHG announcement, honoring Sir Peter Donnelly, CEO of Genomics plc and Emeritus Professor of Statistical Science at the University of Oxford with the William Allan Award. 

A list of the many abstracts and plenary presentations at ASHG 2022 that mention Olink can be found here (PDF). 

The Ben Sun et al. preprint mentioned is titled “Genetic regulation of the human plasma proteome in 54,306 UK Biobank participants” and is available on BioRxiv here.

An overview published in 2013 of the STUCTURE software (one of the “most widely used population analysis tools”) is available here.

To join the All of Us research program, visit https://www.joinallofus.org/ and information about the Francis Collins asking for an African Moonshot on GenomeWeb is here.

If you would like to contact Dale, Cindy or Sarantis feel free to email us at [email protected].

In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.

One of the first publications using Olink technology came out by Enroth S and Gyllensten U et al. Nature Communications 2014 “Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs”. Link to the paper is here: DOI:10.1038/ncomms5684

To access the Olink Insight platform for protein biomarker data discovery free-of-charge with an email address, click here: https://insight.olink.com And be sure to check out the Publication Explorer!

A recent publication by the same group from the University of Uppsala is by Gyllensten U and Enroth S et al. Cancers 2022 “Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer”. Link to the paper is here: DOI:10.3390/cancers14071757

For the main Olink webpage that has over 900 publications as a single list (also classified by disease area and application type) you can access it here. 

If you would like to contact Dale, Cindy or Sarantis feel free to email us at [email protected].

In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.

The 2022 Science Advances paper, “Proteomic profiling platforms head to head: Leveraging genetics and clinical traits to compare aptamer- and antibody-based methods” by Daniel H Katz and Rob Gerszten et al. is available online here.

A highly informative Twitter thread by the first author Dr. Daniel Katz reviewing the figures of the paper is available here.

If you are interested in learning more about the use of proteomics in multiomic strategies, here’s link to the Olink website where examples of combinations of omics methods are combined.

If you would like to contact Dale, Cindy or Sarantis feel free to email us at [email protected].

In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.

Would you like to subscribe to the podcast on your favorite player or app? You can do so here: 

Apple Podcasts: https://apple.co/3T0YbSm
Spotify Podcasts: https://open.spotify.com/show/2sZ2wxOqI4b4vSngkajLs8?si=d957d55c8db046f7 Google Podcasts: https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy50cmFuc2lzdG9yLmZtL3Byb3Rlb21pY3MtaW4tcHJveGltaXR5
Amazon Music: https://music.amazon.com/podcasts/d97ace94-f02b-4b37-9532-799548ef2840
Podcast Addict: https://podcastaddict.com/podcast/4098296
Deezer: https://www.deezer.com/show/5178787
Player FM: https://player.fm/series/series-3396598

Show Notes for PiP Ep 02 “Empower Genomics with Proteomics”

For more information about the UK Biobank, an Olink to Science blog post called “Genetic Regulation of the Human Plasma Proteome in the UK Biobank” is available here. The preprint publication itself is available here on bioRxiv. 

If you’d like to see a great 15 minute presentation on what the goals are for the UK Biobank Pharma Proteomics Project, Dr. Chris Whelan (Biogen) presented this YouTube video at one of the UK Biobank’s scientific meetings that is worth watching.

A paper discussed by Folkersen et al., “Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals” was published in Nature Metabolism in late 2020, and is available here.

If you would like to contact Dale, Cindy or Sarantis feel free to email us at [email protected] and if you would like to learn more about our backgrounds, Cindy’s LinkedIn is here, Sarantis’ is here, and Dale’s is here.

In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.

In case you would like to learn more about our backgrounds, Cindy’s LinkedIn is here, Sarantis’ is here, and Dale’s is here.

For more information about the UK Biobank, an Olink to Science blog post called “Genetic Regulation of the Human Plasma Proteome in the UK Biobank” is available here. The preprint publication itself is available here on bioRxiv. If you’d like to see a great 15 minute presentation on what the goals are for the UK Biobank Pharma Proteomics Project, Dr. Chris Whelan (Biogen) presented this YouTube video at one of the UK Biobank’s scientific meetings that is worth watching.

If you would like to contact Dale, Cindy or Sarantis feel free to email us at [email protected]

In case you were wondering, Proteomics in Proximity refers to the principal underlying Olink Proteomics assay technology called the Proximity Extension Assay (PEA), and more information about the assay and how it works can be found here.

Co-hosts Dale Yuzuki, Cindy Lawley and Sarantis Chlamydas from Olink Proteomics talk about the intersection of proteomics with genomics for drug target discovery, the application of proteomics to reveal disease biomarkers, and current trends in using proteomics to unlock biological mechanisms.

In case you were wondering, "in Proximity" refers to Olink's underpinning technology called the Proximity Extension Assay, to allow highly multiplexed protein analysis from small sample volumes for pharmaceutical, clinical translation and academic research. More information about PEA can be found here on Olink's website.

If you have any questions or comments, feel free to email us at [email protected]. Thank you for listening!