This study identified two genome-wide significant genetic loci (P < 5 × 10–8) for lean PCOS (n = 2,919 cases and 166,655 controls) on chromosome 9 in DENND1A (led by rs12000707; P = 1.55 × 10–12) and on chromosome 22 in XBP1 (led by rs2228260; P = 3.68 × 108) (Supplementary Fig. 2 and Supplementary Fig. 3). This evidence concerns the gene DENND1A and polycystic ovary syndrome.