SCALLOP - genetic regulation of the proteome

SCALLOP genetics of the proteome


The SCALLOP consortium is a collaborative framework for discovery and follow-up of genetic associations, with proteins on the Olink Proteomics platform. To date, 25 PIs from 20 research institutions have joined the effort, which now comprises summary level data on SNP to protein level associations for more than 65,000 patients or controls. SCALLOP welcomes new members.


For more information please contact Anders Mälarstig.

For the latest news about SCALLOP view this news page,

or read more in our flyer.



Introduction from Anders Mälarstig






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 whereas trans-pQTLs are distal regulation of proteins via an often unknown path.
  • Trans-pQTLs can provide unique insights of molecular connections in human biology.

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. The SCALLOP consortium is currently underway with mapping novel pQTLs for several 100s of proteins in unprecedented sample sizes, something which will yield much deeper insights into the trans-regulation of plasma proteins than what has been possible to date.




Identify causal protein biomarkers






Operations


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.

The leadership for subprojects within the SCALLOP consortium rotates and members can take new ideas and suggestions for additional subprojects to the monthly steering committee meetings.

SCALLOP uses a dedicated server for sharing of data. The server is set up under the Danish node of the TRYGGVE server structure. TRYGGVE allows sharing of sensitive data thanks to 2-step authorization procedures and high data security. Thanks to this structure SCALLOP is set up to move to individual-level data should the consortium wish to do so.




Repository browser


Acronym Design Sample size Olink panels
Aristotle Atrial fibrillation 1500 3
ASAP Aortic valve surgery 573 5
BioFinder Dementia 1550 4
COSM-C Population based 4500 3
DIRECT Diabetes 3000 5
EpiHealth Prospective observational 2500 3
Estonian Biobank Population based 500 4
FENLAND Population based 500 15
Framingham Population based 520 5
HELIC MANOLIS Population isolate 1475 6
HELIC POMAK Population isolate 1500 5
IMPROVE Prospective, metabolic syndrome 3403 1
INTERVAL Blood donors 5000 4
Kadoorie biobank Pancreatic cancer 1400 1
KARMA Incident breast cancer 1820 2
KORA F4 Population based 1050 1
LBC1936 Population aged 72 750 1
LifeLines Deep Population based 1200 1
Pfizer/ MadCam_ph2 Inflammatory bowel disease 200 3
MPP-RES Heart failure 1000 1
NSPHS Population isolate 1000 6
ORCADES Population isolate 1000 15
PIVUS Prospective observational 933 1
PRIDE Dementia 1500 14
PROCARDIS Coronary artery disease 900 1
PURE Epidemiological cohort 8000 15
Qmdiab Diabetes 320 2
RECOMBINE Rheumatoid arthritis 800 1
RISC Prospective observational 1000 9
Rotterdam Population based 250 1
Rotterdam Study-III cohort Population based 3500 2
SMCC/ SIMPLER Population based, women 5000 3
STABILITY Acute coronary syndrome 3000 2
STANLEY Bipolar disorder, depression 681 4
SWHS/ SMHS/ SCCS Population based 300 14
ULSAM Prospective observational 1000 9
VIS Population isolate 1000 3
WHI Clinical trial, mixed population, women 1400 5




pQTL publications and data from SCALLOP members


Folkersen L, Gustafsson S, Wang Q, et al, Genomic evaluation of circulating proteins for drug target characterisation and precision medicine. bioRxiv 2020.04.03.023804. Αrticle link


Folkersen L, Fauman E, Sabater-Lleal M, Strawbridge R, Frånberg M, Sennblad B, Baldassarre D, Veglia F, Humphries S, Rauramaa R, de Faire U, Smit A, Giral P, Kurl S, Mannarino E, Enroth S, Johansson A, Bosdotter Enroth S, Gustafsson S, Lind L, Lindgren C, Morris A, Giedraitis V, Silveira A, Franco-Cereceda A, Tremoli E, IMPROVE study group , Gyllensten U, Ingelsson E, Brunak S, Eriksson P, Ziemek D, Hamsten A and Mälarstig A. Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease. (2017) PLOS Genetics 13(4), doi.org/10.1371/journal.pgen.1006706. Αrticle link


Enroth S, Johansson A, Bosdotter Enroth S and Ulf Gyllensten U. Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs. Nature Commun. (2014) Aug 22;5:4684. doi: 10.1038/ncomms5684. PubMed link