Polygenic Score (PGS) ID: PGS000317

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Aug. 19, 2020
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Score Details

Score Construction
PGS Name PRS180
Development Method
Name Likelihood ratios for genomewide-significant SNPs
Parameters p < 5e-8; risk-allele frequencies derived from the Latin American (AMR) population in 1000 Genomes; LR method described in PMID:27565998
Variants
Original Genome Build NR
Number of Variants 180
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000094
Citation (link to publication) Shieh Y et al. J Natl Cancer Inst (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 91.2%
Hispanic or Latin American: 8.8%
152,785 individuals (100%)
PGS Evaluation
Hispanic or Latin American: 100%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002662
Europe PMC: 25327703
 4,710 individuals Hispanic or Latin American NR
GWAS Catalog: GCST006985
Europe PMC: 30642363
 8,801 individuals Hispanic or Latin American NR
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
PPM000849 PSS000407|
Hispanic or Latin American Ancestry|
2,001 individuals
 PGP000094 |
Shieh Y et al. J Natl Cancer Inst (2020)
 Reported Trait: Breast cancer (Latin american women) OR: 1.54 [1.45, 1.63] AUROC: 0.62 [0.61, 0.64] — study, genetic ancestry (ADMIXTURE) —
PPM000848 PSS000408|
Hispanic or Latin American Ancestry|
7,317 individuals
 PGP000094 |
Shieh Y et al. J Natl Cancer Inst (2020)
 Reported Trait: Breast cancer (US Latinas) OR: 1.62 [1.52, 1.71] AUROC: 0.63 [0.62, 0.65] — study, genetic ancestry (ADMIXTURE) —
PPM000846 PSS000406|
Hispanic or Latin American Ancestry|
12,280 individuals
 PGP000094 |
Shieh Y et al. J Natl Cancer Inst (2020)
 Reported Trait: Breast cancer OR: 1.58 [1.52, 1.64] AUROC: 0.63 [0.62, 0.64] — study, genetic ancestry (ADMIXTURE) —
PPM000847 PSS000406|
Hispanic or Latin American Ancestry|
12,280 individuals
 PGP000094 |
Shieh Y et al. J Natl Cancer Inst (2020)
 Reported Trait: Breast cancer OR: 1.7 [1.63, 1.78] — — — —
PPM005167 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.2 [1.0, 1.46] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005176 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.54 [0.47, 0.62] R²: 0.05 — —

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
PSS000406 Women with invasive breast cancer were considered cases and those without breast cancer were considered controls. —
[
  • 4,658 cases
  • , 7,622 controls
]
,
0.0 % Male samples
 Mean (Age At Diagnosis, Cases) = 57.0 years
Sd (Age At Diagnosis, Cases) = 13.0 years		 Hispanic or Latin American — 7 cohorts
  • CAMA
  • ,COLUMBUS
  • ,MEC
  • ,NC-BCFR
  • ,PEGEN-BC
  • ,RPEGH
  • ,SFBCS
 See supplement for cohort-specific participant recruitment/ascertainment
PSS000407 Women with invasive breast cancer were considered cases and those without breast cancer were considered controls. —
[
  • 2,962 cases
  • , 2,001 controls
]
,
0.0 % Male samples
 — Hispanic or Latin American — CAMA, COLUMBUS, PEGEN-BC See supplement for cohort-specific participant recruitment/ascertainment
PSS000408 Women with invasive breast cancer were considered cases and those without breast cancer were considered controls. —
[
  • 1,696 cases
  • , 5,621 controls
]
,
0.0 % Male samples
 — Hispanic or Latin American — MEC, NC-BCFR, RPEGH, SFBCS See supplement for cohort-specific participant recruitment/ascertainment
PSS003600 Cases were individuals with breast cancer. Breast cancer cases were defined by at least one occurrence of the following ICD10CM female breast cancer diagnostic codes: C50.01, C50.011, C50.012, C50.019, C50.1, C50.11, C50.111, C50.112, C50.119, C50.2, C50.21, C50.211, C50.212, C50.219, C50.3, C50.31, C50.311, C50.312, C50.319, C50.4, C50.41, C50.411, C50.412, C50.419, C50.5, C50.51, C50.511, C50.512, C50.519, C50.6, C50.61, C50.611, C50.612, C50.619, C50.81, C50.811, C50.812, C50.819, C50.91, C50.911, C50.912, C50.919, D05, D05.1, D05.10, D05.11, D05.12, D05.8, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92, Z85.3,Z86.000 and ICD9CM female breast cancer diagnostic codes: 174, 174, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233, V10.3. Alternatively breast cancer cases were defined by at least two occurrences (from distinct calendar days) of breast cancer history from the following ICD10CM codes: Z85.3, Z86.000 and ICD9CM code: V10.3, if she had no breast cancer diagnostic codes. —
[
  • 147 cases
  • , 2,049 controls
]
,
0.0 % Male samples
 Mean = 59.9 years
Sd = 19.4 years		 Hispanic or Latin American — eMERGE —