We further explored the pathways shared by schizophrenia and ND by selecting all markers with q-values less than 0.16 from the joint analyses between schizophrenia and smoking traits. After mapping the markers to genes, the genes showing potential association with schizophrenia and COT/FTND/TFC were pooled to search for pathways enriched in both conditions. In these analyses, we selected only the genes identified by at least 2 of the 3 smoking traits, yielding a total of 146 genes. After filtering out the human leukocyte antigen genes (HLA-B, HLA-C, HLA-DOA, HLA-DQA1, HLA-DQB1, HLA-DRB1, and HLA-G) due to their strong linkage disequilibrium26, we used the remaining 139 genes in pathway analyses.
