PGS Publication: PGP000470

Publication Information (EuropePMC)
Title Prognostic evaluation of polygenic risk score underlying pan-cancer analysis: evidence from two large-scale cohorts.
PubMed ID 36739632(Europe PMC)
doi 10.1016/j.ebiom.2023.104454
Publication Date Feb. 3, 2023
Journal EBioMedicine
Author(s) Xin J, Jiang X, Li H, Chen S, Zhang Z, Wang M, Gu D, Du M, Christiani DC.
Released in PGS Catalog: June 1, 2023

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:
Display options:
Ancestry legend
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)
PGS003736
(PRS13_BlC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Bladder cancer urinary bladder cancer 13
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003736/ScoringFiles/PGS003736.txt.gz
PGS003743
(PRS118_PrC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Prostate cancer prostate carcinoma 118
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003743/ScoringFiles/PGS003743.txt.gz
PGS003744
(PRS14_RC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Renal cancer renal carcinoma 14
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003744/ScoringFiles/PGS003744.txt.gz
PGS003746
(PRS11_TC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Thyroid cancer thyroid carcinoma 11
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003746/ScoringFiles/PGS003746.txt.gz
PGS003737
(PRS26_BrC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Brain cancer brain neoplasm 26
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003737/ScoringFiles/PGS003737.txt.gz
PGS003738
(PRS136_BC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Breast cancer breast carcinoma 136
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003738/ScoringFiles/PGS003738.txt.gz
PGS003739
(PRS81_CoC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Colorectal cancer colorectal carcinoma 81
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003739/ScoringFiles/PGS003739.txt.gz
PGS003740
(PRS16_CU)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Corpus Uteri uterine corpus cancer 16
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003740/ScoringFiles/PGS003740.txt.gz
PGS003741
(PRS28_OC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Ovarian cancer ovarian carcinoma 28
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003741/ScoringFiles/PGS003741.txt.gz
PGS003742
(PRS19_PC)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Pancreatic cancer pancreatic neoplasm 19
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003742/ScoringFiles/PGS003742.txt.gz
PGS003745
(PRS57_SM)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Skin Melanoma cutaneous melanoma 57
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003745/ScoringFiles/PGS003745.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
PPM018492 PGS003736
(PRS13_BlC)
 PSS010986|
European Ancestry|
327 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Bladder cancer OR: 1.14 [1.01, 1.29] — — — —
PPM018493 PGS003737
(PRS26_BrC)
 PSS010987|
European Ancestry|
890 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Brain cancer OR: 1.5 [1.38, 1.63] — — — —
PPM018494 PGS003738
(PRS136_BC)
 PSS010985|
European Ancestry|
738 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Breast cancer OR: 1.4 [1.27, 1.54] — — — —
PPM018495 PGS003739
(PRS81_CoC)
 PSS010988|
European Ancestry|
470 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Colorectal cancer OR: 1.37 [1.24, 1.51] — — — —
PPM018496 PGS003740
(PRS16_CU)
 PSS010989|
European Ancestry|
372 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Corpus Uteri OR: 1.38 [1.2, 1.58] — — — —
PPM018497 PGS003741
(PRS28_OC)
 PSS010991|
European Ancestry|
501 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Ovarian cancer OR: 1.15 [1.04, 1.28] — — — —
PPM018498 PGS003742
(PRS19_PC)
 PSS010993|
European Ancestry|
153 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Pancreatic cancer OR: 1.33 [1.13, 1.57] — — — —
PPM018499 PGS003743
(PRS118_PrC)
 PSS010992|
European Ancestry|
408 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Prostate cancer OR: 1.58 [1.41, 1.76] — — — —
PPM018500 PGS003744
(PRS14_RC)
 PSS010994|
European Ancestry|
692 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Renal cancer OR: 1.24 [1.14, 1.35] — — — —
PPM018501 PGS003745
(PRS57_SM)
 PSS010995|
European Ancestry|
448 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Skin Melanoma OR: 1.49 [1.34, 1.66] — — — —
PPM018502 PGS003746
(PRS11_TC)
 PSS010996|
European Ancestry|
360 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Thyroid cancer OR: 1.63 [1.44, 1.85] — — — —

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
PSS010985 — — 738 individuals Mean = 59.35 years European — TCGA —
PSS010986 — — 327 individuals Mean = 69.11 years European — TCGA —
PSS010987 — — 890 individuals Mean = 50.88 years European — TCGA —
PSS010988 — — 470 individuals Mean = 67.3 years European — TCGA —
PSS010989 — — 372 individuals Mean = 64.72 years European — TCGA —
PSS010991 — — 501 individuals Mean = 60.09 years European — TCGA —
PSS010992 — — 408 individuals Mean = 61.67 years European — TCGA —
PSS010993 — — 153 individuals Mean = 65.63 years European — TCGA —
PSS010994 — — 692 individuals Mean = 60.99 years European — TCGA —
PSS010995 — — 448 individuals Mean = 58.23 years European — TCGA —
PSS010996 — — 360 individuals Mean = 48.04 years European — TCGA —