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Original Article
The impact of a panel of 18 SNPs on breast cancer risk in women attending a UK familial screening clinic: a case–control study
  1. D Gareth Evans1,2,3,
  2. Adam Brentnall4,
  3. Helen Byers2,3,
  4. Elaine Harkness5,
  5. Paula Stavrinos2,3,
  6. Anthony Howell1,6,
  7. FH-risk study Group,
  8. William G Newman2,3,
  9. Jack Cuzick4
    1. 1Genesis Breast Cancer Prevention Centre and Nightingale Breast Screening Centre, University Hospital of South Manchester, Manchester, UK
    2. 2Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
    3. 3Central Manchester Foundation Trust, Manchester, UK
    4. 4Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, UK
    5. 5Centre for Imaging Sciences, Institute for Population Health, University of Manchester, Manchester, UK
    6. 6The Christie NHS Foundation Trust, Manchester, UK
    1. Correspondence to Professor D Gareth Evans, Genomic Medicine, MAHSC, St. Mary's Hospital, Oxford Road, Manchester M13 9WL, UK; gareth.evans{at}


    Background Breast cancer familial risk clinics offer screening and preventive strategies. While BRCA1/BRCA2 genetic testing provides important risk information for some women, panels of more common breast cancer risk genetic variants may have relevance to greater numbers of women with familial risk.

    Methods Three polygenic risk scores (PRS) based on 18 SNPs were investigated in a case–control study of women attending a familial risk clinic. PRS were derived from published general European population allele ORs and frequencies (18-SNPs (SNP18)). In women with BRCA1/BRCA2 mutations, 3 SNPs/13 SNPs, respectively, generated the PRS estimates. In total, 364 incident breast cancer cases (112 with BRCA1/2 mutations) were matched with 1605 controls (691 BRCA1/2) by age last mammogram and BRCA1/2 genetic test result. 87 women with cancer before attendance were also considered. Logistic regression was used to measure PRS performance through ORs per IQR and calibration of the observed to expected (O/E) logarithm relative risk when unadjusted and adjusted for phenotypic risk factors assessed by the Tyrer-Cuzick (TC) model.

    Results SNP18 was predictive for non-carriers of BRCA1/2 mutations (IQR OR 1.55, 95% CI 1.29 to 1.87, O/E 96%). Findings were unaffected by adjustment from TC (IQR OR 1.56, 95% CI 1.29 to 1.89) or when prior cancers were included (IQR OR 1.55, 95% CI 1.30 to 1.87). There was some evidence to support polygenic scores with weights for individuals with BRCA1/2 mutations (BRCA1 IQR OR 1.44, 95% CI 1.17 to 1.76; BRCA2 IQ OR 1.44, 95% CI 0.90 to 2.31).

    Conclusions PRS may be used to refine risk assessment for women at increased familial risk who test negative/have low likelihood of BRCA1/2 mutations. They may alter the recommended prevention strategy for many women attending family history clinics.

    • BRCA1
    • BRCA2
    • familial breast cancer
    • Single Nucleotide Polymorphisms (SNPs)
    • Polygenic Risk Score (PRS)

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    • Collaborators FH-Risk Study Group: Susan Astley, Mary Wilson, David French, Michelle Harvie, Donna Watterson, Paula Stavrinos, Jill Fox, Sarah Sampson, Sarah Ingham, Sarah Sahin, Lynne Fox.

    • Contributors DGE and AB are joint first authors. Conception: DGE, AH and JC. Data acquisition: HB, PS and DGE. Data analysis: AB, JC, DGE and EH. Manuscript writing: all. Approval of final version: all.

    • Funding The study received grant support from the NIHR and the Genesis Breast Cancer Prevention Appeal. This paper presents independent research funded by the National Institute for Health Research (NIHR) under its Programme Grants for Applied Research (Reference Number RP-PG-0707-10031).

    • Competing interests DGE has received a one-off consultancy fee from Astazeneca. DGE is an NIHR senior investigator.

    • Ethics approval NHS North Manchester Research Committee (08/H1006/77) and University of Manchester ethics committees (08229).

    • Provenance and peer review Not commissioned; externally peer reviewed.

    • Data sharing statement Data in this article can be shared on request.