A case-control evaluation of 143 single nucleotide polymorphisms for breast cancer risk stratification with classical factors and mammographic density

Research output: Contribution to journalArticle

  • External authors:
  • Adam R Brentnall
  • Elke Van Veen
  • Saijad Rafiq
  • Sarah Sampson
  • Jack Cuzick
  • D Gareth Evans


Panels of single nucleotide polymorphisms (SNPs) stratify risk for breast cancer in women from the general population, but studies are needed assess their use in a fully-comprehensive model including classical risk factors, mammographic density and more than 100 SNPs associated with breast cancer. A case-control study was designed (1668 controls, 405 cases) in women aged 47-73 years attending routine screening in Manchester UK, and enrolled in a wider study to assess methods for risk assessment. Risk from classical questionnaire risk factors was assessed using the Tyrer-Cuzick model; mean percentage visual mammographic density was scored by two independent readers. DNA extracted from saliva was genotyped at selected SNPs using the OncoArray. A pre-defined polygenic risk score based on 143 SNPs was calculated (SNP143). The odds ratio (and 95% confidence interval, CI) per inter-quartile range (IQ-OR) of SNP143 was estimated unadjusted and adjusted for Tyrer-Cuzick and breast density. Secondary analysis assessed risk by estrogen-receptor status. The primary polygenic risk score was well calibrated (O/E odds ratio 1.10, 95%CI 0.86-1.34) and accuracy was retained after adjustment for Tyrer-Cuzick risk and mammographic density (IQ-OR unadjusted 2.12, 95%CI%CI 1.75-2.42; adjusted 2.06, 95%CI 1.75-2.42). SNP143 was a risk factor for ER+ and ER- breast cancer (adjusted IQ-OR, ER+ 2.11, 95%CI 1.78-2.51; ER- 1.81, 95%CI 1.16-2.84). In conclusion, polygenic risk scores based on a large number of SNPs improve risk stratification in combination with classical risk factors and mammographic density, and SNP143 was similarly predictive for estrogen-receptor positive and negative disease.

Bibliographical metadata

Original languageEnglish
JournalInt. J. Cancer
Early online date28 Jun 2019
Publication statusPublished - 2019