bio-causal-genomics-pleiotropy-detection

Version Compatibility

Reference examples tested with: MR-PRESSO 1.0+, TwoSampleMR 0.5+

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

• R: packageVersion("<pkg>") then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed

package and adapt the example to match the actual API rather than retrying.

Pleiotropy Detection

"Check my MR results for pleiotropic bias" → Detect and correct for horizontal pleiotropy using outlier removal (MR-PRESSO), directional pleiotropy testing (MR-Egger intercept), and variant directionality filtering (Steiger) to validate causal inference results.

• R: MRPRESSO::mr_presso() for global and distortion tests
• R: TwoSampleMR::mr_egger_regression() for Egger intercept test

Overview

Horizontal pleiotropy violates the exclusion restriction assumption of MR: instruments

affect the outcome through pathways other than the exposure. Detecting and correcting

for pleiotropy is essential for valid causal inference.

Types of pleiotropy:

• Vertical (mediated): Instrument -> exposure -> outcome (valid, not a problem)
• Horizontal (direct): Instrument -> outcome bypassing exposure (violates MR assumptions)
• Balanced: Pleiotropic effects cancel out (IVW still valid, Egger intercept ~0)
• Directional: Pleiotropic effects are systematic (biases IVW, Egger detects this)

MR-PRESSO

Goal: Detect and remove pleiotropic outlier instruments from an MR analysis.

Approach: Run MR-PRESSO to test for global pleiotropy, identify individual outlier SNPs, test whether their removal changes the causal estimate (distortion test), and obtain a corrected estimate.

# install.packages('remotes')
# remotes::install_github('rondolab/MR-PRESSO')
library(MRPRESSO)

# Input: harmonized data from TwoSampleMR
# Columns needed: beta.exposure, beta.outcome, se.exposure, se.outcome
presso_input <- data.frame(
  bx = dat$beta.exposure,
  by = dat$beta.outcome,
  bxse = dat$se.exposure,
  byse = dat$se.outcome
)

# --- Run MR-PRESSO ---
# NbDistribution: Number of simulations for null distribution (minimum 1000)
# SignifThreshold: P-value threshold for outlier detection (0.05 standard)
presso_result <- mr_presso(
  BetaOutcome = 'by', BetaExposure = 'bx',
  SdOutcome = 'byse', SdExposure = 'bxse',
  OUTLIERtest = TRUE, DISTORTIONtest = TRUE,
  data = presso_input,
  NbDistribution = 5000,
  SignifThreshold = 0.05
)

# --- Global test ---
# Tests whether there is any pleiotropy among instruments
# Significant p-value: Evidence of horizontal pleiotropy
global_p <- presso_result$`MR-PRESSO results`$`Global Test`$Pvalue
cat('Global test p-value:', global_p, '\n')

# --- Outlier test ---
# Identifies individual pleiotropic SNPs
outliers <- presso_result$`MR-PRESSO results`$`Outlier Test`
cat('\nOutlier test results:\n')
print(outliers)

# Outlier SNPs (p < 0.05)
outlier_indices <- which(outliers$Pvalue < 0.05)
cat('Outlier SNPs:', length(outlier_indices), '\n')

# --- Distortion test ---
# Tests whether removing outliers significantly changes the causal estimate
# Significant: Outliers were meaningfully biasing the estimate
distortion_p <- presso_result$`MR-PRESSO results`$`Distortion Test`$Pvalue
cat('Distortion test p-value:', distortion_p, '\n')

# --- Corrected estimate ---
# MR estimate after removing outlier SNPs
main_results <- presso_result$`Main MR results`
cat('\nRaw IVW estimate:', main_results$`Causal Estimate`[1], '\n')
cat('Corrected IVW estimate:', main_results$`Causal Estimate`[2], '\n')

MR-Egger Diagnostics

Goal: Test for directional pleiotropy and obtain a pleiotropy-adjusted causal estimate.

Approach: Fit MR-Egger regression where the intercept estimates average pleiotropic bias, and check I-squared for instrument strength under the NOME assumption.

library(TwoSampleMR)

# MR-Egger regression allows for a non-zero intercept
# The intercept estimates the average pleiotropic effect
egger <- mr_egger_regression(dat$beta.exposure, dat$beta.outcome,
                              dat$se.exposure, dat$se.outcome)

# --- Egger intercept ---
# Significant intercept (p < 0.05): Directional pleiotropy present
# Non-significant: No evidence (but low power with < 10 SNPs)
cat('Egger intercept:', round(egger$b_i, 5), '\n')
cat('Intercept SE:', round(egger$se_i, 5), '\n')
cat('Intercept p-value:', format.pval(egger$pval_i), '\n')

# --- Egger slope ---
# Valid causal estimate EVEN with directional pleiotropy (InSIDE assumption)
cat('\nEgger causal estimate:', round(egger$b, 4), '\n')
cat('Egger SE:', round(egger$se, 4), '\n')
cat('Egger p-value:', format.pval(egger$pval), '\n')

# --- I-squared for Egger ---
# I^2 measures instrument strength for MR-Egger specifically
# I^2 > 0.9: Egger estimate reliable
# I^2 < 0.6: Egger has low power, interpret with caution (NOME violation)
isq <- Isq(dat$beta.exposure, dat$se.exposure)
cat('\nI-squared:', round(isq, 3), '\n')
if (isq < 0.9) cat('Warning: I-squared < 0.9; Egger estimate may be unreliable (NOME violation)\n')

Steiger Filtering

Goal: Verify that instruments act in the correct causal direction (exposure -> outcome, not reverse).

Approach: Apply the Steiger test to each instrument, remove those explaining more outcome variance than exposure variance, and re-run MR on filtered instruments.

library(TwoSampleMR)

# Steiger test: Verify each instrument explains more variance in
# the exposure than the outcome. Instruments failing this test
# may act through a reverse causal pathway.

steiger <- steiger_filtering(dat)

# Keep only correctly oriented instruments
dat_steiger <- steiger[steiger$steiger_dir == TRUE, ]
cat('Instruments passing Steiger filter:', nrow(dat_steiger), 'of', nrow(steiger), '\n')

# Re-run MR with filtered instruments
results_steiger <- mr(dat_steiger)
print(results_steiger[, c('method', 'nsnp', 'b', 'se', 'pval')])

# Directionality test (aggregate)
direction <- directionality_test(dat)
cat('\nCorrect causal direction:', direction$correct_causal_direction, '\n')
cat('Steiger p-value:', format.pval(direction$steiger_pval), '\n')

Additional Sensitivity Methods

library(TwoSampleMR)

# --- Contamination mixture ---
# Assumes some instruments are valid, others are not
# Does not require majority valid assumption
mr_conmix <- mr(dat, method_list = 'mr_raps')

# --- MR-RAPS ---
# NOTE: MRAPS CRAN package was archived March 2025.
# Use the MendelianRandomization package instead, or install from GitHub:
# remotes::install_github('qingyuanzhao/mr.raps')
library(MendelianRandomization)

mr_input <- mr_input(
  bx = dat$beta.exposure, bxse = dat$se.exposure,
  by = dat$beta.outcome, byse = dat$se.outcome
)

raps_result <- mr_raps(mr_input)
cat('MR-RAPS estimate:', raps_result$Estimate, '\n')
cat('MR-RAPS p-value:', raps_result$Pvalue, '\n')

# --- Multivariable MR ---
# Controls for pleiotropy by including multiple exposures simultaneously
# e.g., adjust for BMI when estimating effect of lipids on CHD
exposure1 <- extract_instruments('ieu-a-300')  # LDL
exposure2 <- extract_instruments('ieu-a-302')  # HDL

# Combine and perform multivariable MR
# (See TwoSampleMR vignette for full multivariable workflow)

Comprehensive Sensitivity Framework

Goal: Run a complete battery of MR sensitivity analyses to validate causal findings.

Approach: Apply IVW, MR-Egger, weighted median, weighted mode, heterogeneity, Egger intercept, leave-one-out, and MR-PRESSO in a single function and summarize results.

library(TwoSampleMR)
library(MRPRESSO)

run_sensitivity <- function(dat) {
  results <- list()

  # 1. IVW (primary)
  results$ivw <- mr(dat, method_list = 'mr_ivw')

  # 2. MR-Egger
  results$egger <- mr(dat, method_list = 'mr_egger_regression')

  # 3. Weighted median (robust to 50% invalid instruments)
  results$median <- mr(dat, method_list = 'mr_weighted_median')

  # 4. Weighted mode
  results$mode <- mr(dat, method_list = 'mr_weighted_mode')

  # 5. Heterogeneity
  results$het <- mr_heterogeneity(dat)

  # 6. Egger intercept
  results$pleio <- mr_pleiotropy_test(dat)

  # 7. Leave-one-out
  results$loo <- mr_leaveoneout(dat)

  # 8. MR-PRESSO
  presso_input <- data.frame(
    bx = dat$beta.exposure, by = dat$beta.outcome,
    bxse = dat$se.exposure, byse = dat$se.outcome
  )
  results$presso <- mr_presso(
    BetaOutcome = 'by', BetaExposure = 'bx',
    SdOutcome = 'byse', SdExposure = 'bxse',
    OUTLIERtest = TRUE, DISTORTIONtest = TRUE,
    data = presso_input, NbDistribution = 5000, SignifThreshold = 0.05
  )

  results
}

summarize_sensitivity <- function(sens) {
  cat('=== MR Sensitivity Analysis Summary ===\n\n')

  # Method comparison
  all_mr <- rbind(sens$ivw, sens$egger, sens$median, sens$mode)
  cat('Method comparison:\n')
  print(all_mr[, c('method', 'b', 'se', 'pval')])

  # Heterogeneity
  cat('\nHeterogeneity (Cochran Q):\n')
  cat('  Q p-value (IVW):', sens$het$Q_pval[sens$het$method == 'Inverse variance weighted'], '\n')

  # Egger intercept
  cat('\nEgger intercept:\n')
  cat('  Intercept:', sens$pleio$egger_intercept, '\n')
  cat('  P-value:', sens$pleio$pval, '\n')

  # MR-PRESSO global test
  cat('\nMR-PRESSO global test p-value:',
      sens$presso$`MR-PRESSO results`$`Global Test`$Pvalue, '\n')

  cat('\n--- Interpretation ---\n')
  cat('Consistent estimates across methods: Evidence strengthened\n')
  cat('Significant Egger intercept: Directional pleiotropy present\n')
  cat('Significant MR-PRESSO global: Horizontal pleiotropy detected\n')
  cat('Significant heterogeneity: Instruments may be invalid\n')
}

STROBE-MR Reporting

When reporting MR analyses, follow STROBE-MR guidelines:

1. Report all MR methods tested (not just the most significant)
2. Report heterogeneity Q-statistic and p-value
3. Report Egger intercept with p-value
4. Report MR-PRESSO global test and number of outliers removed
5. Report F-statistics for instrument strength
6. Report Steiger directionality test
7. State whether results are consistent across sensitivity analyses
8. Acknowledge limitations of the MR assumptions

Related Skills

• mendelian-randomization - Primary MR analysis that pleiotropy tests validate
• fine-mapping - Identify causal variants at instrument loci
• population-genetics/association-testing - GWAS data for MR instruments