PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data
Figure 4
PUMA identifies associations for Wellcome Trust Case Control Consortium (WTCCC) data that are novel and that overlap hits from previous GWAS.
Genome-wide plot of associations identified by analyzing the WTCCC data for type 1 diabetes using PUMA and single marker tests. Replications from independent (not including WTCCC data) and non-independent (including WTCCC data) GWAS of the same disease are indicated with pink boxes and diamonds, respectively. For comparison, markers identified using a single marker association analysis are presented in black circles, where we note that these same hits are all identified by PUMA methods. Also for comparison, we relaxed the Bonferroni threshold for single marker analysis (open circles) until the same number of associations as found by PUMA methods are reported, where we note that many of these additional hits tend not to overlap PUMA hits or previous GWAS hits. Arrows indicate novel associations that are biologically interpretable (see Table 6).