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 PGS Scoring File (FTP Link)
PGS000153
(cGRS_Breast)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Breast cancer breast carcinoma 66
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000153/ScoringFiles/PGS000153.txt.gz
PGS000154
(cGRS_Colorectal)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Colorectal cancer colorectal cancer 30
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000154/ScoringFiles/PGS000154.txt.gz
PGS000155
(cGRS_Glioma)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Glioma glioma 19
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000155/ScoringFiles/PGS000155.txt.gz
PGS000161
(cGRS_Renal)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Renal cancer renal carcinoma 10
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000161/ScoringFiles/PGS000161.txt.gz
PGS000162
(cGRS_Thyroid)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Thyroid cancer thyroid carcinoma 6
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000162/ScoringFiles/PGS000162.txt.gz
PGS000152
(cGRS_Bladder)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Bladder cancer bladder carcinoma 10
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000152/ScoringFiles/PGS000152.txt.gz
PGS000160
(cGRS_Prostate)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Prostate cancer prostate carcinoma 79
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000160/ScoringFiles/PGS000160.txt.gz
PGS000156
(cGRS_Lung)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Lung cancer lung carcinoma 6
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000156/ScoringFiles/PGS000156.txt.gz
PGS000158
(cGRS_Ovarian)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Ovarian cancer ovarian carcinoma 11
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000158/ScoringFiles/PGS000158.txt.gz
PGS000157
(cGRS_Melanoma)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Melanoma melanoma 17
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000157/ScoringFiles/PGS000157.txt.gz
PGS000159
(cGRS_Pancreatic)
PGP000075 |
Shi Z et al. Cancer Med (2019)
Pancreatic cancer pancreatic carcinoma 9
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000159/ScoringFiles/PGS000159.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