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Rare and low frequency variants are not well covered in most germline genotyping arrays and are understudied in relation to epithelial ovarian cancer (EOC) risk. To address this gap, we used genotyping arrays targeting rarer protein-coding variation in 8,165 EOC cases and 11,619 controls from the international Ovarian Cancer Association Consortium (OCAC). Pooled association analyses were conducted at the variant and gene level for 98,543 variants directly genotyped through two exome genotyping projects. Only common variants that represent or are in strong linkage disequilibrium (LD) with previously-identified signals at established loci reached traditional thresholds for exome-wide significance ( P &lt;  5.0 × 10  −   7 ). One of the most significant signals (P all histologies  =   1.01 × 10  −   13 ;P serous  =   3.54 × 10  −   14 ) occurred at 3q25.31 for rs62273959, a missense variant mapping to the  LEKR1  gene that is in LD ( r  2  =   0.90) with a previously identified ‘best hit’ (rs7651446) mapping to an intron of  TIPARP.  Suggestive associations (5.0 × 10  −   5  &gt;    P ≥5.0 ×10  −   7 ) were detected for rare and low-frequency variants at 16 novel loci. Four rare missense variants were identified ( ACTBL2  rs73757391 (5q11.2),  BTD  rs200337373 (3p25.1),  KRT13  rs150321809 (17q21.2) and  MC2R  rs104894658 (18p11.21)), but only  MC2R  rs104894668 had a large effect size (OR = 9.66). Genes most strongly associated with EOC risk included  ACTBL2  (P AML  =   3.23 × 10  −   5 ; P SKAT-o  =   9.23 × 10  −   4 ) and  KRT13  (P AML  =   1.67 × 10  −   4 ; P SKAT-o  =   1.07 × 10  −   5 ), reaffirming variant-level analysis. In summary, this large study identified several rare and low-frequency variants and genes that may contribute to EOC susceptibility, albeit with possible small effects. Future studies that integrate epidemiology, sequencing, and functional assays are needed to further unravel the unexplained heritability and biology of this disease.

Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk