Polygenic Score (PGS) ID: PGS004890

Predicted Trait
Reported Trait Triple negative breast cancer versus luminal breast cancer
Mapped Trait(s) triple-negative breast cancer (EFO_0005537)
Additional Trait Information Luminal breast cancer includes luminal A, luminal B and luminal B-Her2-negative breast cancer
Released in PGS Catalog: June 12, 2024
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Score Details

Score Construction
PGS Name CC-GWAS_PRS
Development Method
Name Genome-wide significant SNPs and additional ones with suggestive associations
Parameters After removal of variants with MAF < 0.01, an imputation quality score r2 of < 0.8, small INDELs, and the C/G or A/T SNPs due to strand ambiguity in the original case-control GWAS，we perfomed CC-GWAS analysis for the comparisons between TNBC, and luminal A-like, luminal B-like, and luminal B/HER2 negative-like breast cancer. Among the SNPs with P<5×10-7 (POLS < 5×10-7) from CC-GWAS, we removed SNPs with P < 5×10-8 in the case-control GWAS of either subtype (as they should be identified as significant variants from original case-control GWAS for subtypes). However, we retained SNPs if their P case-control < 0.01 for subtype I and P case-control < 5×10-8 for subtype II (but not vice versa) to ensure that we would not miss a CC-GWAS signal contributed by both subtypes especially by subtype I. Then, the remaining SNPs were clumped using r2<0.1, and the 1000 Genomes Phase 3 EUR data as the LD reference.
Variants
Original Genome Build GRCh37
Number of Variants 25
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000620
Citation (link to publication) Sun X et al. Cancer Res (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
106,571 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • African
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 16,499 cases
  • , 90,072 controls
]
 European BCAC

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
PPM021270 PSS011672|
Multi-ancestry (including European)|
9,868 individuals
 PGP000620 |
Sun X et al. Cancer Res (2024)
 Reported Trait: Triple negative breast cancer compared to luminal-like breast cancer — — Odds ratio (OR, high vs low tertile): 2.62 [1.44, 4.75] Age at initial pathologic diagnosis of breast cancer, pathologic stage —

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
PSS011672 The molecular intrinsic subtypes of breast cancer were determined following the strategy of Giovanni's work using the PAM50 classifier in the TCGA-BRCA. Basal-like and luminal-like breast cancer were determined by PAM50. —
[
  • 108 cases
  • , 565 controls
]
 — European — TCGA —
PSS011672 Triple-negative breast cancer (TNBC) was defined as ER negative, PR negative and HER2 negative. The luminal breast cancer was defined as ER and/or PR positive. —
[
  • 2,321 cases
  • , 6,874 controls
]
 — African American or Afro-Caribbean — AABCG —