PGS Publication: PGP000094

Publication Information (EuropePMC)
Title A Polygenic Risk Score for Breast Cancer in US Latinas and Latin American Women.
PubMed ID 31553449(Europe PMC)
doi 10.1093/jnci/djz174
Publication Date June 1, 2020
Journal J Natl Cancer Inst
Author(s) Shieh Y, Fejerman L, Lott PC, Marker K, Sawyer SD, Hu D, Huntsman S, Torres J, Echeverry M, Bohórquez ME, Martínez-Chéquer JC, Polanco-Echeverry G, Estrada-Flórez AP, COLUMBUS Consortium, Haiman CA, John EM, Kushi LH, Torres-Mejía G, Vidaurre T, Weitzel JN, Zambrano SC, Carvajal-Carmona LG, Ziv E, Neuhausen SL.
Released in PGS: Aug. 19, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000317 PRS180 PGP000094
Shieh Y et al. J Natl Cancer Inst (2020)
Breast cancer breast carcinoma 180 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000317/ScoringFiles/PGS000317.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000846 PGS000317 (PRS180) PSS000406 PGP000094
Shieh Y et al. (2020)
Reported Trait: Breast cancer OR: 1.58[1.52, 1.64] AUROC: 0.63[0.62, 0.64] study, genetic ancestry (ADMIXTURE)
PPM000847 PGS000317 (PRS180) PSS000406 PGP000094
Shieh Y et al. (2020)
Reported Trait: Breast cancer OR: 1.7[1.63, 1.78]
PPM000848 PGS000317 (PRS180) PSS000408 PGP000094
Shieh Y et al. (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)
PPM000849 PGS000317 (PRS180) PSS000407 PGP000094
Shieh Y et al. (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)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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