Extended Data Fig. 7: Genetic instrument extraction process for the MR analyses investigating the causal links between genetic liability to autism and IBD, UC, and Crohn’s.

Between phenotype pairs, GWAS summary data were restricted to a common set of SNPs and then clumped in PLINK 1.90 using the 1000 Genomes phase 3 European ancestry reference panel, and an r² = 0.01, within a 10,000 Kb window. Among the independent variants, instruments were defined using a genome-wide significance threshold of P ≤ 5×10⁻⁸. The only exception was autism, as only two independent and genome-wide significant variants were identified. We therefore relaxed the P-value threshold to 5 × 10⁻⁷ to improve statistical power, as used previously⁷²).