Permuth, JB;
Pirie, A;
Ann Chen, Y;
Lin, HY;
Reid, BM;
Chen, Z;
Monteiro, A;
... Ovarian Cancer Association Consortium, .; + view all
(2016)
Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk.
Human Molecular Genetics
, 25
(16)
pp. 3600-3612.
10.1093/hmg/ddw196.
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Permuth et al_Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk_Hum Mol Genet_2016.pdf Download (649kB) | Preview |
Abstract
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 < 5.0 × 10 (-) (7)). One of the most significant signals (Pall histologies = 1.01 × 10 (-) (13);Pserous = 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 )>( )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 (PAML = 3.23 × 10 (-) (5); PSKAT-o = 9.23 × 10 (-) (4)) and KRT13 (PAML = 1.67 × 10 (-) (4); PSKAT-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.
| Type: | Article |
|---|---|
| Title: | Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/hmg/ddw196 |
| Publisher version: | http://dx.doi.org/10.1093/hmg/ddw196 |
| Language: | English |
| Additional information: | This is a pre-copyedited, author-produced PDF of an article accepted for publication in Human Molecular Genetics following peer review. The version of record: Jennifer B. Permuth, et al., Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk, Human Molecular Genetics, is available online at: http://dx.doi.org/10.1093/hmg/ddw196. |
| Keywords: | Genes; introns; linkage disequilibrium; ovarian cancer; epithelial ovarian cancer; genotype determination; exome |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Inst of Clinical Trials and Methodology UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Inst of Clinical Trials and Methodology > MRC Clinical Trials Unit at UCL |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1504576 |
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