reported here and the conclusions derived are the sole responsibility of the authors.
SEARCH: We thank the SEARCH team
SELECT: We thank the research and clinical staff at the sites that participated on SELECT study,
without whom the trial would not have been successful. We are also grateful to the 35,533 dedicated
men who participated in SELECT.
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
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37
WHI: The authors thank the WHI investigators and staff for their dedication, and the study
participants for making the program possible. A full listing of WHI investigators can be found at:
http://www.whi.org/researchers/Documents%20%20Write%20a%20Paper/WHI%20Investigator%20
Short%20List.pdf
Data availability statement
We obtained summary genetic association data on breast cancer risk from the Breast Cancer
Association Consortium (https://bcac.ccge.medschl.cam.ac.uk/), ovarian cancer risk from the Ovarian
Cancer Association Consortium (https://ocac.ccge.medschl.cam.ac.uk/), endometrial cancer risk from
the Endometrial Cancer Association Consortium
(https://www.ebi.ac.uk/gwas/publications/30093612#study_panel
), non-Hodgkin lymphoma risk from
Burrows et al. (10.5523/bris.aed0u12w0ede20olb0m77p4b9), and basal cell carcinoma risk from
Adolphe et al (https://www.ebi.ac.uk/gwas/publications/33549134#study_panel). Approval was
received to use restricted summary genetic association data from GECCO, INTEGRAL ILCCO, and
PRACTICAL consortia after submitting a proposal to access this data. Summary genetic association
data from these consortia can be accessed by contacting GECCO (
[email protected],
INTEGRAL ILCCO (
[email protected]) (https://ilcco.iarc.fr/), and PRACTICAL
(
[email protected]
). Approval was also received to use restricted summary genetic association data
on pancreatic cancer risk via dbGaP release phs000206.v5.p3. To enquire about gaining access to
summary genetic association data for renal and head and neck cancer risk, contact
[email protected]
.
To enquire about gaining access to summary genetic association data for bladder cancer risk, contact
[email protected].
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted May 5, 2023. ; https://doi.org/10.1101/2023.05.04.23289196doi: medRxiv preprint
38
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44
Table 1. Summary of studies included in GWAS meta-analysis of circulating inflammatory
markers.
Study N proteins Participants Units Adjustment Protein
assay
Karhunen et
al. [58]
47
inflammatory
proteins
840-13,365
Finnish
Inverse-normal rank
transformation
Age, sex, first 10
genetic principal
components
Bio-Rad
Bio-plex
assays,
custom
panel
Folkersen et
al. [55]
90 proteins 30,931
European
NPX values of
proteins (on the
log2 scale) were
rank-based inverse
normal transformed
and/or standardised
to unit variance
Variable across
studies
Olink
Gilly et al.
[56]
257 proteins 1,328
Greek
Inverse-normal
transformation of the
residuals
Age, age
2, sex,
plate number, per-
sample mean
NPX value across
all assays.
Adjustment for
season.
Olink
Hillary et al.
[57]
70
inflammatory
proteins
1,936
European
older adults
Standardised
residuals from these
regression models
were brought
forward for all
genetic-protein and
epigenetic-protein
analyses.
Age, sex, four
genetic principal
components of
ancestry, array
plate
Olink
Pietzner et
al. [59]
179 proteins 10,708
European
Rank-based inverse
normal
transformation
Age, sex, sample
collection site, 10
principal
components
SomaScan
Sun et al.
[60]
2,995
proteins
3,600
European
Rank-inverse
normalized
Age, sex, duration
between blood
draw and
processing, first
three principal
components of
ancestry from
multi-dimensional
scaling
SomaScan
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pQTL beta agreement
Instrument
Construction
Study QC and pre-processing
Map UniProt ID to platform-specific protein ID, drop problematic
probes, extract cis-window for data extraction, drop SNPs with
MAF 0.40
Extract SNPs at genome-wide significance (P < 5.0 x 10-8), drop
SNPs with evidence of heterogeneity (Phet<0.001), construct
instruments permitting LD r2 < 0.10 in PLINK
Check per-study beta agreement for each pQTL using
independent (r2<0.01) SNPs across two thresholds (P < 5.0 x
10-8, P < 5.0 x 10-4)
GWAS study selection
Meta-analysis
Instrument construction
Inverse-variance weighted fixed-effects meta-analysis in METAL
Validation analyses Discovery analyses
Mendelian randomization analysis
Wald ratio or inverse-variance weighted random-effects model
adjusted for LD between variants
Identification of GWAS with measured circulating
inflammatory markers
Sensitivity analyses
Colocalisation, iterative leave-one-out analysis, evaluation and
dropping of missense variants (or variants in high LD, r2>0.80) with
missense variants from instruments to prevent potential aptamer-
binding effects
Analysis
Test inflammatory marker-cancer pairs with Overall association
score ≥ 0.05 in Open Targets in Validation analyses. Test all
remaining inflammatory marker-cancer pairs in Discovery analyses
eQTL enrichment and multi-trait colocalisation
Examination of overlap of instruments with tissue-specific or immune
cell-specific gene expression quantitative trait loci (P < 5 x10-8), multi-
trait colocalisation to evaluate shared aetiology across traits
Drug repurposing assessment
Evaluation of approved, investigational, or experimental drugs targeting
inflammatory markers in DrugBank to identify potential drug repurposing
opportunities for cancer prevention
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TNFSF10 breast cancer
MIF bladder cancer
IL7R colon cancer
IL7R basal cell carcinoma
MIF breast cancer
CCL5 breast cancer
Chromosome
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ADM breast cancer
IL23R pancreatic cancer
F2 basal cell carcinoma
APCS low grade serous ovarian cancer
IL1RL1 triple-negative breast cancer HP colorectal cancer
Chromosome
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