This is the first study of its kind to systematically investigate the use of repetitive transcranial magnetic stimulation (rTMS) in non-remitters of a selective serotonin-reuptake inhibitor (SSRI) followed by an serotonin-norepinephrine reuptake inhibitor (SNRI) trial with the capacity to identify gene variants that predict rTMS response. The study is similar in design to the STAR*D study in that it will be the third treatment stage for a study of subjects with major depressive disorder (MDD). rTMS is a novel intervention which was FDA approved for treatment of MDD in October 2008 and was not clinically available at the time of the STAR*D study.