Table 2.

Prediction of response to TNFi using penalised regional genotypic scores for different types of intermediate traits

Intermediate trait type	No of regional scores	No of filtered scores	Prediction of ∆SJC (%)	Prediction of ∆ESR (%)
Rheumatoid arthritis	37	37	5.3 (0.26)	−1.6 (0)
Immune cell traits	508	470	−0.7 (0)	2.9 (0.17)
eQTLs	94	87	3.4 (0.16)	2.9 (0.17)
eQTLs and mQTLs	268	228	2.5 (0.11)	1.6 (0.09)

Prediction performance is quantified by the difference in test log-likelihood (in nats) between a model with clinical covariates and genotypic scores and a model with clinical covariates only and by the per cent of phenotypic variance explained (in parenthesis). Results from 10-fold cross-validation.

eQTL, expression quantitative trait loci; mQTL, methylation quantitative trait loci.ESR, erythrocyte sedimentation rate; SJC, swollen joint count; TNFi, tumour necrosis factor inhibitors;