SCALLOP
The SCALLOP consortium (Systematic and Combined AnaLysis of Olink Proteins) is a collaborative framework for discovering and following up on genetic associations with proteins on Olink’s PEA platform. It consists of two components: the research arm and the clinical trial arm.
SCALLOP Research Arm comprises numerous PIs from various research institutions that have joined the effort, contributing to a wealth of summary-level data from over 70,000 patients and controls across more than 45 cohort studies.
SCALLOP Clinical Trial Arm was introduced after the research arm, and is dedicated to establishing a pre-competitive repository for proteomics data in longitudinal samples to investigate dynamic proteomics changes in healthy volunteers and placebo/standard of care response across disease indications.
As the research arm database expands and the clinical trial arm develops, SCALLOP welcomes new members to join this collaborative endeavor.
For more information, please contact Anders Mälarstig (SCALLOP project chair).
Current work
Each SCALLOP member works on human study collections from the general population, clinical trials or patients with certain diseases such as coronary artery disease, rheumatoid arthritis, bipolar disease, heart failure, dementias or metabolic syndrome.
The aim of the SCALLOP consortium is to identify novel molecular connections and protein biomarkers that are causal in diseases.
This work starts with identification of so called protein quantitative trait loci, pQTLs, which are robust connections between a gene variant and the levels of a protein.
There are two types of pQTLs:
- Cis-pQTLs are variants that are proximal to the gene encoding the protein under study. Cis-pQTLs are strong instruments for determining if a protein biomarker for disease is causing disease or elevated or suppressed as a consequence of it.
- Trans-pQTLs are involved in the distal regulation of proteins via an often unknown path. Trans-pQTLs can provide unique insights into molecular connections in human biology.
The SCALLOP consortium is currently underway with mapping novel pQTLs for several hundreds of proteins in unprecedented sample sizes, something which will yield much deeper insights into the trans-regulation of plasma proteins than has been possible to date.
Identify causal protein biomarkers
Operations
SCALLOP Research Arm
To be a member of the SCALLOP consortium you have to be the PI of a study collection with Olink proteomics and genome-wide genotyping data. We also expect members to sign up to the Consortium Agreement, which manages conduct and authorships. Download the Consortium Agreement here [link].
The leadership for subprojects within the SCALLOP consortium rotates. Members can take new ideas and suggestions for additional subprojects to the bi-monthly steering committee meetings.
SCALLOP Clinical Trial Arm
Companies and academic parties with at least 500 longitudinal samples or with existing data of the proposed scale (along with 8-16 samples for data bridging) can participate. The highlights of the collaboration include:
- Remote access to a harmonized data repository with longitudinal clinical information and deep targeted proteomics that is comparable with major resources such as the Human Disease Atlas.
- Access to a long-lasting standard to bridge data with internal studies.
- Discounts for data generation.
Data storage and handling
SCALLOP uses the compute and storage resources at the National Academic infrastructure for Supercomputing in Sweden (NAISS) for storage, processing, and sharing of data. The servers are GDPR-compliant and provide high data security. SCALLOP offers central support for data harmonization and normalization. Analysts can securely access the joint database remotely.
| Documents | Type | File |
|---|---|---|
| SCALLOP repository | Data resource | Download CSV |
Selected SCALLOP publications
Here are selected publications from SCALLOP. For a full list, browse our Publication library and search for ‘SCALLOP’ to see peer-reviewed publications from consortium members as well from other scientists utilizing published SCALLOP data.
