Germline whole exome sequencing and large-scale replication identifies <i>FANCM</i> as a likely high grade serous ovarian cancer susceptibility gene.


We analyzed whole exome sequencing data in germline DNA from 412 high grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas Project and identified 5,517 genes harboring a predicted deleterious germline coding mutation in at least one HGSOC case. Gene-set enrichment analysis showed enrichment for genes involved in DNA repair (p = 1.8×10<sup>-3</sup>). Twelve DNA repair genes - <i>APEX1, APLF, ATX, EME1, FANCL, FANCM, MAD2L2, PARP2, PARP3, POLN, RAD54L</i> and <i>SMUG1</i> - were prioritized for targeted sequencing in up to 3,107 HGSOC cases, 1,491 cases of other epithelial ovarian cancer (EOC) subtypes and 3,368 unaffected controls of European origin. We estimated mutation prevalence for each gene and tested for associations with disease risk. Mutations were identified in both cases and controls in all genes except <i>MAD2L2</i>, where we found no evidence of mutations in controls. In <i>FANCM</i> we observed a higher mutation frequency in HGSOC cases compared to controls (29/3,107 cases, 0.96 percent; 13/3,368 controls, 0.38 percent; P=0.008) with little evidence for association with other subtypes (6/1,491, 0.40 percent; P=0.82). The relative risk of HGSOC associated with deleterious <i>FANCM</i> mutations was estimated to be 2.5 (95% CI 1.3 - 5.0; P=0.006). In summary, whole exome sequencing of EOC cases with large-scale replication in case-control studies has identified <i>FANCM</i> as a likely novel susceptibility gene for HGSOC, with mutations associated with a moderate increase in risk. These data may have clinical implications for risk prediction and prevention approaches for high-grade serous ovarian cancer in the future and a significant impact on reducing disease mortality.

  • Alsop J
  • Bogdanova N
  • Bowtell DD
  • Brenton JD
  • Cicek MS
  • Crawford R
  • Cunningham JM
  • Dicks E
  • Dörk T
  • Dürst M
  • Fridley BL
  • Gayther SA
  • Gentry-Maharaj A
  • Goode EL
  • Goranova T
  • Group AS
  • Harrington P
  • Hillemanns P
  • Intermaggio MP
  • Jimenez-Linan M
  • Kar S
  • Karlan BY
  • Kent E
  • Lele S
  • Lester J
  • Levine D
  • McGuire V
  • Menon U
  • Moysich KB
  • Odunsi K
  • Oudenhove EV
  • Paul J
  • Pharoah DPP
  • Piskorz A
  • Poblete S
  • Ramus SJ
  • Siddiqui N
  • Sieh W
  • Song H
  • Sucheston-Campbell L
  • Tischkowitz M
  • Tyrer JP
  • Whittemore AS
PubMed ID
Appears In
Oncotarget, 2017, 8 (31)