PGS Publication: PGP000216

Publication Information (EuropePMC)
Title A case-control evaluation of 143 single nucleotide polymorphisms for breast cancer risk stratification with classical factors and mammographic density.
PubMed ID 31251818(Europe PMC)
doi 10.1002/ijc.32541
Publication Date July 13, 2019
Journal Int J Cancer
Author(s) Brentnall AR, van Veen EM, Harkness EF, Rafiq S, Byers H, Astley SM, Sampson S, Howell A, Newman WG, Cuzick J, Evans DGR.
Released in PGS Catalog: Aug. 26, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000873
(SNP143)
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Breast cancer breast carcinoma 143
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000873/ScoringFiles/PGS000873.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM002456 PGS000873
(SNP143)
 PSS001111|
Ancestry Not Reported|
2,073 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Breast cancer — — Odds Ratio (OR, per interquartile range unit change): 2.12 [1.81, 2.49] Age —
PPM002458 PGS000873
(SNP143)
 PSS001105|
Ancestry Not Reported|
2,021 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Estrogen-receptor positive breast cancer — — Odds Ratio (OR, per interquartile range unit change): 2.17 [1.83, 2.58] Age —
PPM002460 PGS000873
(SNP143)
 PSS001108|
Ancestry Not Reported|
1,707 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Estrogen-receptor negative breast cancer — — Odds Ratio (OR, per interquartile range unit change): 1.86 [1.18, 2.91] Age —
PPM002462 PGS000873
(SNP143)
 PSS001113|
Ancestry Not Reported|
1,991 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Invasive breast cancer — — Odds Ratio (OR, per interquartile range unit change): 2.14 [1.79, 2.55] Age —
PPM002464 PGS000873
(SNP143)
 PSS001112|
Ancestry Not Reported|
1,750 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Breast ductal cancer in situ — — Odds Ratio (OR, per interquartile range unit change): 2.0 [1.46, 2.75] Age —
PPM002466 PGS000873
(SNP143)
 PSS001107|
Ancestry Not Reported|
1,956 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Invasive estrogen-receptor positive breast cancer — — Odds Ratio (OR, per interquartile range unit change): 2.55 [1.86, 2.7] Age —
PPM002468 PGS000873
(SNP143)
 PSS001106|
Ancestry Not Reported|
1,733 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Estrogen-receptor positive breast ductal cancer in situ — — Odds Ratio (OR, per interquartile range unit change): 1.84 [1.3, 2.6] Age —
PPM002470 PGS000873
(SNP143)
 PSS001110|
Ancestry Not Reported|
1,694 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Invasive estrogen-receptor negative breast cancer — — Odds Ratio (OR, per interquartile range unit change): 1.44 [0.84, 2.47] Age —
PPM002471 PGS000873
(SNP143)
 PSS001109|
Ancestry Not Reported|
1,681 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Estrogen-receptor negative breast ductal cancer in situ — — Odds Ratio (OR, per interquartile range unit change): 3.12 [1.41, 6.88] Age —
PPM002457 PGS000873
(SNP143)
 PSS001111|
Ancestry Not Reported|
2,073 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Breast cancer — — Odds Ratio (OR, per interquartile range unit change): 2.06 [1.75, 2.42] Age, ln(Tyrer-Cuzick model 10-year risk), mammographic density —
PPM002459 PGS000873
(SNP143)
 PSS001105|
Ancestry Not Reported|
2,021 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Estrogen-receptor positive breast cancer — — Odds Ratio (OR, per interquartile range unit change): 2.11 [1.78, 2.51] Age, ln(Tyrer-Cuzick model 10-year risk), mammographic density —
PPM002461 PGS000873
(SNP143)
 PSS001108|
Ancestry Not Reported|
1,707 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Estrogen-receptor negative breast cancer — — Odds Ratio (OR, per interquartile range unit change): 1.81 [1.16, 2.84] Age, ln(Tyrer-Cuzick model 10-year risk), mammographic density —
PPM002463 PGS000873
(SNP143)
 PSS001113|
Ancestry Not Reported|
1,991 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Invasive breast cancer — — Odds Ratio (OR, per interquartile range unit change): 2.07 [1.74, 2.48] Age, ln(Tyrer-Cuzick model 10-year risk), mammographic density —
PPM002465 PGS000873
(SNP143)
 PSS001112|
Ancestry Not Reported|
1,750 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Breast ductal cancer in situ — — Odds Ratio (OR, per interquartile range unit change): 1.93 [1.41, 2.65] Age, ln(Tyrer-Cuzick model 10-year risk), mammographic density —
PPM002469 PGS000873
(SNP143)
 PSS001106|
Ancestry Not Reported|
1,733 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Estrogen-receptor positive breast ductal cancer in situ — — Odds Ratio (OR, per interquartile range unit change): 1.77 [1.24, 2.51] Age, ln(Tyrer-Cuzick model 10-year risk), mammographic density —
PPM002472 PGS000873
(SNP143)
 PSS001109|
Ancestry Not Reported|
1,681 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Estrogen-receptor negative breast ductal cancer in situ — — Odds Ratio (OR, per interquartile range unit change): 2.99 [1.35, 6.6] Age, ln(Tyrer-Cuzick model 10-year risk), mammographic density —
PPM002467 PGS000873
(SNP143)
 PSS001107|
Ancestry Not Reported|
1,956 individuals
 PGP000216 |
Brentnall AR et al. Int J Cancer (2019)
 Reported Trait: Invasive estrogen-receptor positive breast cancer — — Odds Ratio (OR, per interquartile range unit change): 2.18 [1.81, 2.63] Age, ln(Tyrer-Cuzick model 10-year risk), mammographic density —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS001105 Breast cancer diagnosis (invasive or ductal carcinoma in situ [DCIS]) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems. All cases had ER+ subtype —
[
  • 353 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 — Not reported — PROCAS —
PSS001106 Breast cancer diagnosis (ductal carcinoma in situ [DCIS]) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems. All cases had ER+ subtype —
[
  • 65 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 — Not reported — PROCAS —
PSS001107 Breast cancer diagnosis (invasive) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems. All cases had ER+ subtype —
[
  • 288 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 — Not reported — PROCAS —
PSS001108 Breast cancer diagnosis (invasive or ductal carcinoma in situ [DCIS]) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems. All cases had ER- subtype. —
[
  • 39 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 — Not reported — PROCAS —
PSS001109 Breast cancer diagnosis (ductal carcinoma in situ [DCIS]) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems. All cases had ER- subtype. —
[
  • 13 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 — Not reported — PROCAS —
PSS001110 Breast cancer diagnosis (invasive) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems. All cases had ER- subtype. —
[
  • 26 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 — Not reported — PROCAS —
PSS001111 Breast cancer diagnosis (invasive or ductal carcinoma in situ [DCIS]) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems —
[
  • 405 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 Median = 60.0 years Not reported — PROCAS —
PSS001112 Breast cancer diagnosis (ductal carcinoma in situ [DCIS]) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems —
[
  • 82 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 — Not reported — PROCAS —
PSS001113 Breast cancer diagnosis (invasive) was at the entry screen (10/2009–06/2015) or subsequently before January 5, 2017, and was ascertained through monthly updates from (National Health Service) Breast Screening Systems —
[
  • 323 cases
  • , 1,668 controls
]
,
0.0 % Male samples
 — Not reported — PROCAS —