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 Catalog: Aug. 19, 2020

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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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
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)
PGS000317
(PRS180)
 PGP000094 |
Shieh Y et al. J Natl Cancer Inst (2020)
 Breast cancer breast carcinoma 180
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000317/ScoringFiles/PGS000317.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
PPM000849 PGS000317
(PRS180)
 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 PGS000317
(PRS180)
 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 PGS000317
(PRS180)
 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 PGS000317
(PRS180)
 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] — — — —

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