Fig. 2: Identifying variants nominated by MTAG and LSMM methods in wave 1 schizophrenia GWAS results and their results in the wave 2 GWAS results. | Communications Biology

Fig. 2: Identifying variants nominated by MTAG and LSMM methods in wave 1 schizophrenia GWAS results and their results in the wave 2 GWAS results.

From: Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value

Fig. 2

Manhattan plots of schizophrenia GWAS waves 1 (SCZ1; a, c) and 2(SCZ2; b, d) with the variants nominated by MTAG (a, b) using bipolar disorder GWAS wave 1 (BPD1) as the pleiotropic trait and the LSMM method using a global FDR (LSMM) (c, d) highlighted in green. P-values were derived from the publicly available downloads of SCZ1 and SCZ2 provided by the Psychiatric Genomics Consortium, respectively. These plots include the full downloadable GWAS summary statistics for both SCZ GWAS waves, without excluding significant GWAS1 regions.

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