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: April 29, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants 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
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
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
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
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
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
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
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
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

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000475 PGS000155 (cGRS_Glioma) PSS000275 PGP000075
Shi Z et al. (2019)
Reported Trait: Glioma Mean realative risk: 1.22[1.18, 1.26]
Wilcoxon test (case vs. control) p-value: 1.39e-37
PPM000472 PGS000152 (cGRS_Bladder) PSS000272 PGP000075
Shi Z et al. (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 PGP000075
Shi Z et al. (2019)
Reported Trait: Thyroid cancer Odds Ratio (OR; high vs. average risk groups): 1.7[1.29, 2.25]
PPM000492 PGS000161 (cGRS_Renal) PSS000281 PGP000075
Shi Z et al. (2019)
Reported Trait: Renal cancer Odds Ratio (OR; high vs. average risk groups): 1.58[1.14, 2.18]
PPM000491 PGS000160 (cGRS_Prostate) PSS000280 PGP000075
Shi Z et al. (2019)
Reported Trait: Prostate cancer Odds Ratio (OR; high vs. average risk groups): 1.73[1.38, 2.17]
PPM000490 PGS000159 (cGRS_Pancreatic) PSS000279 PGP000075
Shi Z et al. (2019)
Reported Trait: Pancreatic cancer Odds Ratio (OR; high vs. average risk groups): 1.67[1.1, 2.53]
PPM000489 PGS000158 (cGRS_Ovarian) PSS000278 PGP000075
Shi Z et al. (2019)
Reported Trait: Ovarian cancer Odds Ratio (OR; high vs. average risk groups): 1.63[1.3, 2.06]
PPM000488 PGS000157 (cGRS_Melanoma) PSS000277 PGP000075
Shi Z et al. (2019)
Reported Trait: Melanoma Odds Ratio (OR; high vs. average risk groups): 1.72[1.37, 2.16]
PPM000487 PGS000156 (cGRS_Lung) PSS000276 PGP000075
Shi Z et al. (2019)
Reported Trait: Lung cancer Odds Ratio (OR; high vs. average risk groups): 0.88[0.57, 1.36]
PPM000486 PGS000155 (cGRS_Glioma) PSS000275 PGP000075
Shi Z et al. (2019)
Reported Trait: Glioma Odds Ratio (OR; high vs. average risk groups): 1.8[1.55, 2.1]
PPM000485 PGS000154 (cGRS_Colorectal) PSS000274 PGP000075
Shi Z et al. (2019)
Reported Trait: Colorectal cancer Odds Ratio (OR; high vs. average risk groups): 1.18[0.87, 1.61]
PPM000484 PGS000153 (cGRS_Breast) PSS000273 PGP000075
Shi Z et al. (2019)
Reported Trait: Breast cancer Odds Ratio (OR; high vs. average risk groups): 1.47[1.23, 1.76]
PPM000483 PGS000152 (cGRS_Bladder) PSS000272 PGP000075
Shi Z et al. (2019)
Reported Trait: Bladder cancer Odds Ratio (OR; high vs. average risk groups): 1.58[1.1, 2.25]
PPM000482 PGS000162 (cGRS_Thyroid) PSS000282 PGP000075
Shi Z et al. (2019)
Reported Trait: Thyroid cancer Mean realative risk: 1.09[1.04, 1.15]
Wilcoxon test (case vs. control) p-value: 3.64e-05
PPM000481 PGS000161 (cGRS_Renal) PSS000281 PGP000075
Shi Z et al. (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 PGP000075
Shi Z et al. (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 PGP000075
Shi Z et al. (2019)
Reported Trait: Pancreatic cancer Mean realative risk: 1.13[1.07, 1.18]
Wilcoxon test (case vs. control) p-value: 0.000145
PPM000478 PGS000158 (cGRS_Ovarian) PSS000278 PGP000075
Shi Z et al. (2019)
Reported Trait: Ovarian cancer Mean realative risk: 1.12[1.08, 1.16]
Wilcoxon test (case vs. control) p-value: 0.000145
PPM000477 PGS000157 (cGRS_Melanoma) PSS000277 PGP000075
Shi Z et al. (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 PGP000075
Shi Z et al. (2019)
Reported Trait: Lung cancer Mean realative risk: 1.01[0.99, 1.02]
Wilcoxon test (case vs. control) p-value: 0.0116
PPM000474 PGS000154 (cGRS_Colorectal) PSS000274 PGP000075
Shi Z et al. (2019)
Reported Trait: Colorectal cancer Mean realative risk: 1.08[1.04, 1.12]
Wilcoxon test (case vs. control) p-value: 8.29e-06
PPM000473 PGS000153 (cGRS_Breast) PSS000273 PGP000075
Shi Z et al. (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 ID)
Detailed Phenotype Description 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
]
,
1.0 % Male samples
Mean = 62.0 years
Sd = 7.0 years
European TCGA
PSS000280
[
  • 0 cases
  • , 6,407 controls
]
,
1.0 % 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