Table 2. Mendelian randomization of discrete biomarkers when using identical or highly correlated genetic variants.

Branched chain amino acid (BCAA)	SNP in PPM1K	Linkage disequilibrium with rs1440581	Effect/other allele	EAF	Standardized Beta (SE) of Metabolite Level per Allele	P-value for BCAA	OR (95% CI) for T2DM per Allele	P-value for T2DM	MR estimate of T2DM per 1-SD higher BCAA	P-value for MR estimate
Leucine	rs1440581	1.0	C/T	53%	0.08 (0.013)	3.9×10−25	1.04 (1.02–1.07)	0.00034	1.85 (1.41–2.42)	7.3×10−6
Isoleucine	rs7678928	0.8	T/C	46%	0.09 (0.013)	5.6×10−19	1.03 (1.01–1.05)	0.0055	1.40 (1.10–1.78)	5.5×10−3
Valine	rs1440581	1.0	C/T	53%	0.10 (0.013)	4.4×10−24	1.04 (1.02–1.07)	0.00034	1.54 (1.28–1.84)	4.2×10−6

Legend: Branched-chain amino acids (BCAAs) are arranged according to the effect size of the single nucleotide polymorphism (SNP) on each trait (sorted from smallest to largest). Given that the association of each SNP with type 2 diabetes mellitus (T2DM) is identical (or near-identical when using rs7678928, in linkage disequilibrium with rs1440581 at r² = 0.79), the MR estimate is scaled to this effect. Therefore, on Mendelian randomization (MR) analysis, leucine has the greatest magnitude of association with risk of T2DM, and valine has the lowest magnitude of association. This analysis reflects how the MR estimates are generated by dividing the SNP–T2DM estimate by SNP–BCAA. When the SNP–BCAA estimate is the smallest (as for leucine), the MR point estimate is the greatest. Critically, none of the MR estimates for the three BCAAs is valid because they all assume that each BCAA individually is causal. EAF, effect allele frequency. Adapted from Lotta, L. A. et al. Genetic predisposition to an impaired metabolism of the branched-chain amino acids and risk of type 2 diabetes: a Mendelian randomisation analysis. PLoS Med. 13, e1002179 (2016).