PGS Publication: PGP000075

Publication Information (EuropePMC)
Title Systematic evaluation of cancer-specific genetic risk score for 11 types of cancer in The Cancer Genome Atlas and Electronic Medical Records and Genomics cohorts.
PubMed ID 30968590(Europe PMC)
doi 10.1002/cam4.2143
Publication Date April 9, 2019
Journal Cancer Med
Author(s) Shi Z, Yu H, Wu Y, Lin X, Bao Q, Jia H, Perschon C, Duggan D, Helfand BT, Zheng SL, Xu J.
Released in PGS Catalog: April 29, 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:
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)
PGS000158
(cGRS_Ovarian)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Ovarian cancer ovarian carcinoma 11
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000158/ScoringFiles/PGS000158.txt.gz
PGS000152
(cGRS_Bladder)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Bladder cancer urinary bladder carcinoma 10
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000152/ScoringFiles/PGS000152.txt.gz
PGS000156
(cGRS_Lung)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Lung cancer lung carcinoma 6
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000156/ScoringFiles/PGS000156.txt.gz
PGS000162
(cGRS_Thyroid)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Thyroid cancer thyroid carcinoma 6
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000162/ScoringFiles/PGS000162.txt.gz
PGS000154
(cGRS_Colorectal)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Colorectal cancer colorectal cancer 30
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000154/ScoringFiles/PGS000154.txt.gz
PGS000157
(cGRS_Melanoma)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Melanoma melanoma 17
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000157/ScoringFiles/PGS000157.txt.gz
PGS000161
(cGRS_Renal)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Renal cancer renal carcinoma 10
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000161/ScoringFiles/PGS000161.txt.gz
PGS000153
(cGRS_Breast)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Breast cancer breast carcinoma 66
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000153/ScoringFiles/PGS000153.txt.gz
PGS000155
(cGRS_Glioma)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Glioma glioma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000155/ScoringFiles/PGS000155.txt.gz
PGS000159
(cGRS_Pancreatic)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Pancreatic cancer pancreatic carcinoma 9
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000159/ScoringFiles/PGS000159.txt.gz
PGS000160
(cGRS_Prostate)
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Prostate cancer prostate carcinoma 79
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000160/ScoringFiles/PGS000160.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
PPM000475 PGS000155
(cGRS_Glioma)
 PSS000275|
European Ancestry|
14,419 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Glioma — — Mean realative risk: 1.22 [1.18, 1.26]
Wilcoxon test (case vs. control) p-value: 1.39e-37		 — —
PPM000474 PGS000154
(cGRS_Colorectal)
 PSS000274|
European Ancestry|
13,814 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Colorectal cancer — — Mean realative risk: 1.08 [1.04, 1.12]
Wilcoxon test (case vs. control) p-value: 8.29e-06		 — —
PPM000487 PGS000156
(cGRS_Lung)
 PSS000276|
European Ancestry|
14,335 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Lung cancer — — Odds Ratio (OR; high vs. average risk groups): 0.88 [0.57, 1.36] — —
PPM000472 PGS000152
(cGRS_Bladder)
 PSS000272|
European Ancestry|
13,770 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Bladder cancer — — Mean realative risk: 1.04 [1.0, 1.08]
Wilcoxon test (case vs. control) p-value: 0.00377		 — —
PPM000493 PGS000162
(cGRS_Thyroid)
 PSS000282|
European Ancestry|
13,814 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Thyroid cancer — — Odds Ratio (OR; high vs. average risk groups): 1.7 [1.29, 2.25] — —
PPM000492 PGS000161
(cGRS_Renal)
 PSS000281|
European Ancestry|
13,880 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Renal cancer — — Odds Ratio (OR; high vs. average risk groups): 1.58 [1.14, 2.18] — —
PPM000491 PGS000160
(cGRS_Prostate)
 PSS000280|
European Ancestry|
6,828 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Prostate cancer — — Odds Ratio (OR; high vs. average risk groups): 1.73 [1.38, 2.17] — —
PPM000490 PGS000159
(cGRS_Pancreatic)
 PSS000279|
European Ancestry|
13,590 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Pancreatic cancer — — Odds Ratio (OR; high vs. average risk groups): 1.67 [1.1, 2.53] — —
PPM000489 PGS000158
(cGRS_Ovarian)
 PSS000278|
European Ancestry|
7,551 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Ovarian cancer — — Odds Ratio (OR; high vs. average risk groups): 1.63 [1.3, 2.06] — —
PPM000488 PGS000157
(cGRS_Melanoma)
 PSS000277|
European Ancestry|
13,877 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Melanoma — — Odds Ratio (OR; high vs. average risk groups): 1.72 [1.37, 2.16] — —
PPM000486 PGS000155
(cGRS_Glioma)
 PSS000275|
European Ancestry|
14,419 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Glioma — — Odds Ratio (OR; high vs. average risk groups): 1.8 [1.55, 2.1] — —
PPM000485 PGS000154
(cGRS_Colorectal)
 PSS000274|
European Ancestry|
13,814 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Colorectal cancer — — Odds Ratio (OR; high vs. average risk groups): 1.18 [0.87, 1.61] — —
PPM000484 PGS000153
(cGRS_Breast)
 PSS000273|
European Ancestry|
7,847 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Breast cancer — — Odds Ratio (OR; high vs. average risk groups): 1.47 [1.23, 1.76] — —
PPM000483 PGS000152
(cGRS_Bladder)
 PSS000272|
European Ancestry|
13,770 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Bladder cancer — — Odds Ratio (OR; high vs. average risk groups): 1.58 [1.1, 2.25] — —
PPM000482 PGS000162
(cGRS_Thyroid)
 PSS000282|
European Ancestry|
13,814 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Thyroid cancer — — Mean realative risk: 1.09 [1.04, 1.15]
Wilcoxon test (case vs. control) p-value: 4e-05		 — —
PPM000481 PGS000161
(cGRS_Renal)
 PSS000281|
European Ancestry|
13,880 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Renal cancer — — Mean realative risk: 1.09 [1.06, 1.12]
Wilcoxon test (case vs. control) p-value: 8.66e-10		 — —
PPM000480 PGS000160
(cGRS_Prostate)
 PSS000280|
European Ancestry|
6,828 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Prostate cancer — — Mean realative risk: 1.3 [1.21, 1.38]
Wilcoxon test (case vs. control) p-value: 2.07e-18		 — —
PPM000479 PGS000159
(cGRS_Pancreatic)
 PSS000279|
European Ancestry|
13,590 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Pancreatic cancer — — Mean realative risk: 1.13 [1.07, 1.18]
Wilcoxon test (case vs. control) p-value: 0.00015		 — —
PPM000478 PGS000158
(cGRS_Ovarian)
 PSS000278|
European Ancestry|
7,551 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Ovarian cancer — — Mean realative risk: 1.12 [1.08, 1.16]
Wilcoxon test (case vs. control) p-value: 0.00015		 — —
PPM000477 PGS000157
(cGRS_Melanoma)
 PSS000277|
European Ancestry|
13,877 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Melanoma — — Mean realative risk: 1.2 [1.14, 1.26]
Wilcoxon test (case vs. control) p-value: 5.99e-11		 — —
PPM000476 PGS000156
(cGRS_Lung)
 PSS000276|
European Ancestry|
14,335 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Lung cancer — — Mean realative risk: 1.01 [0.99, 1.02]
Wilcoxon test (case vs. control) p-value: 0.0116		 — —
PPM000473 PGS000153
(cGRS_Breast)
 PSS000273|
European Ancestry|
7,847 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Breast cancer — — Mean realative risk: 1.15 [1.11, 1.2]
Wilcoxon test (case vs. control) p-value: 1.48e-14		 — —

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
PSS000272 Primary tumor samples from TCGA —
[
  • 343 cases
  • , 0 controls
]
 Mean = 69.0 years
Sd = 10.0 years		 European — TCGA —
PSS000272 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —
PSS000273 Primary tumor samples from TCGA —
[
  • 827 cases
  • , 0 controls
]
,
0.0 % Male samples
 Mean = 60.0 years
Sd = 13.0 years		 European — TCGA —
PSS000273 — —
[
  • 0 cases
  • , 7,020 controls
]
,
0.0 % Male samples
 — European — eMERGE —
PSS000274 Primary tumor samples from TCGA —
[
  • 387 cases
  • , 0 controls
]
 Mean = 68.0 years
Sd = 13.0 years		 European — TCGA —
PSS000274 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —
PSS000275 Primary tumor samples from TCGA —
[
  • 992 cases
  • , 0 controls
]
 Mean = 52.0 years
Sd = 16.0 years		 European — TCGA —
PSS000275 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —
PSS000276 Primary tumor samples from TCGA —
[
  • 908 cases
  • , 0 controls
]
 Mean = 67.0 years
Sd = 9.0 years		 European — TCGA —
PSS000276 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —
PSS000277 Primary tumor samples from TCGA —
[
  • 450 cases
  • , 0 controls
]
 Mean = 59.0 years
Sd = 16.0 years		 European — TCGA —
PSS000277 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —
PSS000278 Primary tumor samples from TCGA —
[
  • 531 cases
  • , 0 controls
]
,
0.0 % Male samples
 Mean = 60.0 years
Sd = 12.0 years		 European — TCGA —
PSS000278 — —
[
  • 0 cases
  • , 7,020 controls
]
,
0.0 % Male samples
 — European — eMERGE —
PSS000279 Primary tumor samples from TCGA —
[
  • 163 cases
  • , 0 controls
]
 Mean = 66.0 years
Sd = 11.0 years		 European — TCGA —
PSS000279 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —
PSS000280 Primary tumor samples from TCGA —
[
  • 421 cases
  • , 0 controls
]
,
100.0 % Male samples
 Mean = 62.0 years
Sd = 7.0 years		 European — TCGA —
PSS000280 — —
[
  • 0 cases
  • , 6,407 controls
]
,
100.0 % Male samples
 — European — eMERGE —
PSS000281 Primary tumor samples from TCGA —
[
  • 453 cases
  • , 0 controls
]
 Mean = 62.0 years
Sd = 12.0 years		 European — TCGA —
PSS000281 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —
PSS000282 Primary tumor samples from TCGA —
[
  • 387 cases
  • , 0 controls
]
 Mean = 49.0 years
Sd = 16.0 years		 European — TCGA —
PSS000282 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —