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Table 2 Risk estimation examples using the CanRisk tool

From: Polygenic score distribution differences across European ancestry populations: implications for breast cancer risk prediction

Samples used for the standardization

Mean (SD)

Standardized PRSa

Percentage based on CanRisk tool (%)

Lifetime risk based on CanRisk toolb (%)

NICE Risk categoryc

Individual from Greece with raw PRS313 = 0.34 (falling into the 90–95% percentile category in the full BCAC dataset)

 CanRisk toold

 − 0.424 (0.611)

1.253

89.5

14.1

Moderate

 Controls Greece (raw)e

 − 0.305 (0.612)

1.056

85.5

13.3

Population

 Controls Greece adjusted for 6 PCs (raw)e

 − 0.420 (0.696)

1.094

86.3

13.5

Population

 Controls Greece, using Empirical Bayes methode

 − 0.325 (0.554)

1.204

88.6

13.9

Moderate

Individual from Ireland with raw PRS313 = 0.27 (falling into the 85–90% percentile category in the full BCAC dataset)

 CanRisk toold

 − 0.424 (0.611)

1.14

87.3

13.7

Population

 Controls Ireland (raw)e

 − 0.519 (0.624)

1.27

89.8

14.2

Moderate

 Controls Ireland adjusted for 6 PCs (raw)e

 − 0.456 (0.74)

0.985

83.8

13

Population

 Controls Ireland, Empirical Bayes methode

 − 0.503 (0.562)

1.38

91.7

14.7

Moderate

  1. Mean and SD used to standardize PRS313 of a 50-year-old woman with a raw PRS313 equal to 0.34 from Greece and another 50-year-old woman with a raw PRS313 equal to 0.27 from Ireland; the risk estimation and categorization were performed when using the CanRisk tool
  2. aStandardized based on the mean and SD specified in the second column
  3. bAbsolute risk of developing breast cancer by the age of 80
  4. cThese breast cancer risk categories provided from the CanRisk tool are based on the risk assessment and according to the National Institute for Health and Care Excellence guideline (NICE-CG164) on familial breast cancer and correspond to “Near population risk”, “Moderate risk” and “High risk”
  5. dWhen a variant call format (vcf) file is uploaded to the CanRisk tool, a raw PRS313 can be calculated and standardized using the mean (SD): − 0.424 (0.611)
  6. eAdjusted for array type
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Breast Cancer Research

ISSN: 1465-542X

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