Polygenic Score (PGS) ID: PGS000873

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Aug. 26, 2021
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Score Details

Score Construction
PGS Name SNP143
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 143
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000216
Citation (link to publication) Brentnall AR et al. Int J Cancer (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
PGS Evaluation
Not Reported: 90%
East Asian: 10%
10 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004988
Europe PMC: 29059683
 139,274 individuals European NR

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) 		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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 —
PPM018697 PSS011069|
East Asian Ancestry|
495 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.6 [0.58, 0.63] Hazard ratio (HR, high vs low tertile): 2.68 [1.97, 3.66] age at recruitment —

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 —
PSS011069 — — 495 individuals,
0.0 % Male samples
 Median = 53.0 years
IQR = [48.0, 59.0] years		 East Asian
(Chinese)		 — SCHS —