Bio Causal Genomics Proteome Mr Drug Target

Version Compatibility

Reference examples tested with: TwoSampleMR 0.5.11+, MendelianRandomization 0.10+, MR-PRESSO 1.0+, coloc 5.2.3+, susieR 0.12.35+, ieugwasr 1.0+, plink2 2.00a5+, R 4.4+.

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('') then ?function_name to verify parameters
• CLI: plink2 --version; VEP vep --help

If code throws OAuth or rate-limit errors from OpenGWAS, or a missing dataset$N from coloc, introspect the installed API and adapt the example rather than retrying. UKB-PPP, deCODE, and Fenland summary statistics changed file layouts between 2023 and 2025; verify column headers before passing into format_data().

Proteome-Wide Drug-Target Mendelian Randomization

"Does genetically lowering plasma protein X cause a change in disease Y, mimicking a drug?" -> Use cis-pQTLs in the gene window for protein X as instruments under the Schmidt 2020 framework (Nat Commun 11:3255), restrict the exclusion-restriction violation to the geometric neighbourhood of the encoding gene, triangulate with colocalization (3-tier PP.H4 ladder below) and cross-platform replication (Olink vs SomaScan), and flag protein-altering-variant (PAV) confounding. A single significant cis-MR estimate is necessary but not sufficient for a drug-target claim; the operational bar is MR + coloc + cross-platform agreement + PAV-excluded sensitivity.

PP.H4 Three-Tier Threshold Ladder

| Tier | PP.H4 | Use case | |------|-------|----------| | Suggestive | >= 0.7 | Open Targets / exploratory; consistent with shared-causal | | Standard publication | >= 0.8 | Wallace 2020 PLoS Genet 16:e1008720; most peer-reviewed pubs | | Industry / clinical | >= 0.95 | Drug-claim grade; pharma internal target-validation standard |

Operational rule: drug-target nomination requires PP.H4 >= 0.8 minimum; industry-grade clinical claim requires PP.H4 >= 0.95 plus the full triangulation panel.

• R (canonical): TwoSampleMR::mr() orchestrates the cis-IVW + Egger + median + Wald-ratio panel
• R (correlated cis-pQTLs in a window): MendelianRandomization::mr_ivw(model='default', correl=TRUE, correl.x=ld_matrix)
• R (triangulation): coloc::coloc.abf() or coloc::coloc.susie() on the same cis-window
• pheWAS: ieugwasr::associations() against the OpenGWAS catalogue, looped over outcomes
• VEP CLI: annotate every cis-pQTL with vep --species homo_sapiens --canonical --check_existing for PAV flagging

Data Source Taxonomy

| pQTL dataset | Platform | N | Proteins | Reference | Fails when | |--------------|----------|---|----------|-----------|------------| | UKB-PPP | Olink Explore 3072 (antibody PEA) | 54,219 | 2923 (54k primary cis-pQTLs across studies; 14,287 primary pQTLs across cis+trans) | Sun 2023 Nature 622:329 | Target not on Olink panel; ancestry mostly EUR; antibody epitope may miss isoforms | | deCODE | SomaScan v4 (aptamer SOMAmer) | 35,559 | 4907 | Ferkingstad 2021 Nat Genet 53:1712 | Population isolate; LD differs from outbred EUR; aptamers can be PAV-confounded | | Fenland | SomaScan v4 | 10,708 | 4775 | Pietzner 2021 Science 374:eabj1541 | UK Fenland-specific ascertainment; SomaScan caveats | | INTERVAL | SomaScan v3 (older) | 3301 | 3622 | Sun 2018 Nature 558:73 | Smaller N; older SomaScan version; useful only as replication | | ARIC | SomaScan v4 | ~7000 (multi-ancestry sub-cohorts) | 4877 | Zhang 2022 Nat Genet 54:593 | Stratify by ancestry; do not pool | | FinnGen-PPP | Olink Explore | ~12,000 | ~3000 | FinnGen DF12 (2024 release) | Finnish-specific allele frequencies; not always meta-analyse with UKB | | AGES-Reykjavik | SomaScan v4 | ~5400 | 4782 | Emilsson 2018 Science 361:769 | Elderly Icelandic cohort; ascertainment bias | | Olink Explore 1536 disease-specific cohorts (CARDIoGRAMplusC4D, etc) | Olink Explore subset | varies | varies | per-study | Lower N per cohort; use as replication |

Methodology evolves; check the UKB-PPP portal (ukb-ppp.gwas.eu), deCODE Genetics summary-stat releases, and the eQTL Catalogue / GTEx Portal for the current data version. UKB-PPP was substantially re-released in 2024 (extended ancestry meta-analyses); pin a download date in the methods.

Platform and Cohort Versioning (2024-2026)

• UKB-PPP Phase 2 (2024) -- cross-ancestry meta-analyses; ~54k EUR plus multi-ancestry expansion; file layouts differ from Phase 1 (per-protein parquet vs flat TSV); the 14,287 primary pQTL count from Phase 1 shifts in Phase 2 results. Verify the freeze used.
• FinnGen-PPP -- Olink Explore platform; DF12 (2024) release is current; Finnish-specific allele frequencies require ancestry-aware downstream analysis.
• AoU pQTL (2024) -- All-of-Us proteomics; pre-symptomatic-cohort design strength for reverse-causation control and longitudinal follow-up.
• SomaScan v4 vs v5 -- v5 expands to ~11k SOMAmers (vs ~5k in v4); binding consistency for shared SOMAmers documented in deCODE / SomaLogic technical notes but not guaranteed; pin platform version.
• Olink Explore HT -- ~5,400 proteins (vs ~3,072 in Explore Expansion, ~1,536 in Explore 1536); UKB-PPP Phase 1 used Explore 3072 -- do not assume Explore HT coverage when reading Phase 1 papers.
• Pin specific platform version + release date in the methods section of every cis-MR drug-target manuscript.

Cis-MR Methodological Taxonomy

| Method | Cis-window assumption | Min cis-pQTLs | Strength | Fails when | |--------|------------------------|----------------|----------|------------| | Single cis-pQTL Wald ratio | Single sentinel SNP within +/-500 kb | 1 | Simplest, transparent point estimate beta_Y/beta_X and ratio SE | Confounded by LD-linked eQTL/pQTL of neighbour gene; no heterogeneity test | | Cis-IVW (clumped r2 0.1 inflates SE under independence assumption | | Cis-IVW with correlation correl=TRUE | Cis-pQTLs in moderate LD; supply LD matrix | 2 | Correct SE under correlated instruments (Burgess, Zuber, Valdes-Marquez, Sun, Hopewell 2017 Genet Epidemiol 41:714-725) | LD matrix mismatched to summary-stat ancestry | | Cis-MR-Egger | Directional pleiotropy across cis-pQTLs | 3+ (>=10 for power) | Sensitivity for in-window directional pleiotropy | Underpowered 50% invalid cis-pQTLs | | MR-PRESSO in cis-window | Outlier cis-pQTLs from LD-confounded neighbours | 4+ | Removes neighbour-eQTL-tagged cis-pQTLs; distortion test (Verbanck 2018) | T2D) | | On-target adverse-effect scan (already-marketed drug) | pheWAS cis-MR vs all FinnGen / OpenGWAS phenotypes | Bonferroni + coloc + clinical-event registry | Re-derives known and novel on-target effects | | Cross-platform replication required for clinical claim | Run independently on UKB-PPP (Olink) AND deCODE (SomaScan) | Direction agreement + magnitude within 2x | Single platform never sufficient for therapeutic decision | | Trans-pQTL "wants" to be an instrument | Refuse | -- | Trans = horizontal pleiotropy by definition; use only as confirmatory | | Target gene not on Olink panel | deCODE / Fenland SomaScan only | Cross-replicate across two SomaScan cohorts | Olink panel is gated; do not infer "untested" as null | | Target in cis-region with strong neighbour eQTL | coloc.susie + coloc to non-target gene's pQTL/eQTL | Drop cis-pQTLs that coloc with non-target | Mandatory: must rule out neighbour-gene mediation | | Sample overlap (UKB-PPP exposure + UKB phenotype outcome) | MR-RAPS with one-sample-equivalent correction OR independent outcome (FinnGen, BBJ) | Repeat in non-overlapping cohort | Pretending overlap is two-sample inflates effect estimates |

Per-Method Failure Modes

Olink vs SomaScan platform discordance

Trigger: A cis-pQTL effect size or even direction differs between UKB-PPP (Olink antibody) and deCODE/Fenland (SomaScan aptamer) for the same protein.

Mechanism: Olink uses paired antibody proximity-extension assay (PEA) binding distinct epitopes; SomaScan uses single-aptamer SOMAmer binding a folded epitope. A missense SNP that alters one epitope produces an apparent pQTL on that platform only (a pseudo-PAVQTL / aptamer-affinity QTL, AAVQTL). Splice/isoform differences also produce platform-specific signal. Pietzner 2021 and Sun 2023 reported ~15-30% protein-level discordance.

Symptom: Cis-MR significant on one platform, null on the other; or significant on both but opposite direction.

Fix: Replicate every cis-MR claim on at least one alternate platform; annotate cis-pQTLs with VEP and flag missense / nonsense / splice variants in the gene; consult Olink and SomaScan documentation for the protein's antibody / aptamer binding region; perform a PAV-excluded sensitivity analysis and report both estimates. If platforms disagree irreconcilably, report the protein as platform-discordant and do NOT advance for clinical claim.

Olink panel coverage pre-check: Olink Explore 3072 covers ~3,000 proteins; Explore Expansion ~3,000; Explore HT ~5,400. Always confirm the target is on the panel BEFORE running cis-MR: grep -i olink_panel_proteins.tsv (panel manifest from olink.com). Sun 2023 Nature supplementary Table S1 lists every UKB-PPP-covered protein explicitly; absence from Table S1 means the target was not measured in Phase 1 (regardless of biology) and the analysis must use SomaScan.

LD-based pleiotropy in the cis-window

Trigger: A cis-pQTL for target gene X is also a strong eQTL or pQTL for a neighbouring gene within +/-500 kb.

Mechanism: The instrument's effect on outcome may be mediated by the neighbour gene's protein, not by target X. Cis-window proximity does NOT guarantee specificity.

Symptom: Colocalization with the non-target gene's pQTL or eQTL returns PP.H4 >= 0.7; cis-MR using only "clean" cis-pQTLs (those not coloc'd with neighbours) gives a substantially different estimate.

Fix: For every cis-pQTL, run colocalization against all eQTL/pQTL signals within +/-500 kb in the relevant tissue; drop cis-pQTLs that coloc (PP.H4 >= 0.5) with any non-target gene; coloc.susie is preferred when multiple credible sets exist in the window. Reports must list which cis-pQTLs were retained and the rationale.

Reverse causation from disease state on plasma protein

Trigger: The outcome trait elevates the protein as a downstream consequence (e.g. CRP elevated in coronary disease patients; TNF in autoimmune disease).

Mechanism: Plasma proteomes measured in observational cohorts (including UKB-PPP) include people who have or will develop the outcome; the observed protein-disease association may be downstream not upstream.

Symptom: Observational protein-disease association is large; cis-MR estimate is much smaller, null, or in the opposite direction.

Fix: Apply Steiger filtering on each cis-pQTL (steiger_filtering()); restrict to pre-symptomatic samples where possible (pediatric or early-adult cohorts); replicate in longitudinal cohorts measuring protein years before disease onset. Note: Steiger has its own caveat under unmeasured confounding (Hemani Tilling 2022 Wellcome Open Res 7:14); cross-validate via bidirectional cis-MR.

library(TwoSampleMR)
dat = 0.8** between cis-pQTL and outcome GWAS at the gene locus -- standard publication tier; >= 0.95 for industry-grade claim (cross-reference causal-genomics/colocalization-analysis)
3. **Cross-platform replication** -- significant on both Olink (UKB-PPP) AND SomaScan (deCODE or Fenland); direction agreement is mandatory, magnitude within 2x is acceptable
4. **Cross-cohort replication** (ideal but not strictly required) -- UKB-PPP -> deCODE -> FinnGen-PPP step-up
5. **PAV-excluded sensitivity** -- the cis-MR survives when missense / nonsense / splice / aptamer-binding-region SNPs are dropped
6. **No neighbour-gene coloc** -- no cis-pQTL in the instrument set coloc-shares a causal variant with any non-target gene's eQTL or pQTL within +/-500 kb
7. **Open Targets L2G concordance** -- Open Targets Platform locus-to-gene score for the target gene >= 0.5 at the disease GWAS lead (cross-reference causal-genomics/effector-gene-prioritization)

Operational claim ladder: cis-MR significant alone = exploratory; +coloc PP.H4 >= 0.7 = consistent with shared-causal; +cross-platform = consistent across detection chemistries; +PAV-excluded + neighbour-clear = publication-grade target nomination; +cohort replication + Open Targets L2G >= 0.5 = clinical-pharmacology-grade. Clinical-pharmacology claims require ALL 6 original criteria PLUS L2G concordance.

## Phenome-Wide Drug-Target MR

**Goal:** For a single drug target (single protein), test causal effect across hundreds of outcomes to discover on-target adverse effects.

**Approach:** Hold cis-pQTL instrument set fixed; loop outcome over OpenGWAS catalogue or FinnGen DF12; multi-test correct over outcomes.

```r
library(TwoSampleMR); library(ieugwasr)

target_pqtl = 50000 & population == 'European')

results  T2D signal (Schmidt 2017 Lancet Diabetes Endocrinol 5:97) was discovered exactly via curated-endpoint pheWAS: cis-MR of LDL-lowering instruments revealed on-target T2D risk before clinical trials confirmed it. Drug-target pheWAS is the canonical use case.

## Cis-MR Standard Workflow

**Goal:** Produce a defensible cis-MR estimate with triangulation, given a target gene and an outcome.

**Approach:** Extract cis-pQTLs in +/-500 kb of the gene -> compute F per instrument from exposure -> clump within window at r2  harmonise with outcome -> run TwoSampleMR -> run coloc.abf on the same window -> PAV-annotate via VEP -> report panel.

```r
library(TwoSampleMR); library(coloc); library(ieugwasr)

cis_window_kb  (gene_start - cis_window_kb * 1000) &
    POS = 10)  # Staiger-Stock 1997 weak-IV floor

exposure_dat  cis_pqtls.vcf
vep --species homo_sapiens --assembly GRCh38 --canonical --check_existing \
    --input_file cis_pqtls.vcf --output_file pqtl_vep.tsv --tab --force_overwrite

PAV consequences to flag (drop in sensitivity analysis): missense_variant, stop_gained, stop_lost, frameshift_variant, splice_acceptor_variant, splice_donor_variant, start_lost, protein_altering_variant. For aptamer panels, additionally consider synonymous_variant within the SOMAmer-binding region (rare but documented).

Cis-Window Width: 500 kb vs 1 Mb Decision

• Default ±500 kb (Schmidt 2020 Nat Commun 11:3255 standard) -- balances cis-specificity against power; matches Open Targets Genetics defaults
• Widen to ±1 Mb when: (a) target gene has a documented distal regulatory element in ENCODE-rE2G or ABC enhancer-gene maps; (b) 500 kb itself, e.g. DMD, RBFOX1)
• Narrow to ±250 kb when high-density cis-eQTL background causes multi-gene pleiotropy concerns (e.g. HLA region; gene-dense pericentromeric loci)

Pre-specify the window in the methods section; window-width sensitivity is a recognized peer-review pushback (see Anticipated Reviewer Pushback below).

Quantitative Thresholds

| Threshold | Source | Rationale | |-----------|--------|-----------| | Bonferroni for cis-MR pheWAS | Standard | `P = 0.7 (suggestive) | Open Targets Genetics; Mountjoy 2021 Nat Genet 53:1527 | Exploratory; consistent with shared-causal | | Coloc PP.H4 >= 0.8 (publication) | Wallace 2020 PLoS Genet 16:e1008720 | Standard peer-reviewed publication bar | | Coloc PP.H4 >= 0.95 (industry) | Pharma internal target-validation standard | Drug-claim grade; clinical-pharmacology bar | | Cis-pQTL F >= 10 | Staiger & Stock 1997; Burgess 2011 | Weak-instrument floor | | Cis-window +/-500 kb | Schmidt 2020 Nat Commun 11:3255 | Standard cis definition; some pipelines use 1 Mb | | r2 = 2 pQTL datasets in agreement | Best-practice (UKB-PPP + deCODE) | Cross-platform replication mandatory for clinical claim | | PAV-excluded sensitivity | Sun 2023 supplementary | Required for clinical claim; Olink/SomaScan vulnerable to PAV artifact | | Neighbour-gene coloc PP.H4 0.05 (correct direction) | Hemani 2017 PLoS Genet 13:e1007081 | Directionality check; subject to

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Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: GPTomics
• Source: GPTomics/bioSkills
• License: MIT

Install and usage instructions live in the source repository linked above.