(1), under the worst case scenario of an extreme signal in one phenotype, the false positive rate per SNP is still rather small, i.e. 2.2 × 10−4. Even more, as seen in Andreassen et al., the false positive rate is likely to be substantially lower. Moreover, a worst-case-scenario 2.2 × 10−4 false positive rate is adequate for the pathway analyses73. We used FDR24 to evaluate the approximate significance of the genetic overlap (described by relation (1)) between schizophrenia and smoking phenotypes. To select promising markers for pathway and network analyses we applied a threshold of q-value ≤ 0.16, corresponding to a factor of 2 in Akaike Information Criterion penalty in a likelihood ratio χ2 test with 1 degree of freedom.
