A protocol for using human genetic data to identify circulating protein level changes that are the causal consequence of cancer processes

PRS will be calculated using the PRS continuous shrinkage approach (PRS-CS and PRS-CSx) for colorectal and lung cancer risk. This methodology utilises effect sizes from summary statistics from genome-wide association studies (GWAS) available for the cancers of interest to generate weights via the continuous shrinkage approach which incorporates the strengths of the GWAS associations into the shrinkage applied. This methodology both improves upon previous PRS methods in accuracy as well as improving cross-ancestry application in the PRS-CSx approach. GWAS summary statistics will be from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the International Lung Cancer Consortium (ILCCO). The association between the polygenic risk scores and 2923 proteins measured by the Olink platform in UK Biobank (UKB) participants with protein measures available will be assessed using linear regression under the assumption of linearity in the proteomic data. The proteins identified could represent several different scenarios of association such as forward causation (protein causes cancer), reverse causation (cancer genetic liability causes protein level change), or horizontal pleiotropy bias (no causal relationship exists between the protein and cancer). Forward and reverse Mendelian randomization sensitivity analyses, as well as colocalization analysis, will be performed in efforts to distinguish between these three scenarios. Protein changes identified as causally downstream of genetic liability to cancer could reflect processes occurring prior to, or after, cancer onset. Due to individuals in the UKB having proteins measures at only one timepoint, and because UKB contains a mix of incident and prevalent cases, some protein measures will have been made prior to a cancer diagnosis while others will have been made after a cancer diagnosis. We will explore the strength of association in relation to the time between protein measurement and prevalent or incident cancer diagnosis.