PGS Publication: PGP000186

Publication Information (EuropePMC)
Title Pan-cancer analysis demonstrates that integrating polygenic risk scores with modifiable risk factors improves risk prediction.
PubMed ID 33247094(Europe PMC)
doi 10.1038/s41467-020-19600-4
Publication Date Nov. 27, 2020
Journal Nat Commun
Author(s) Kachuri L, Graff RE, Smith-Byrne K, Meyers TJ, Rashkin SR, Ziv E, Witte JS, Johansson M.
Released in PGS Catalog: May 28, 2021

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:
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Ancestry legend
Multi-ancestry (including European)
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Additional Asian Ancestries
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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)
PGS000789
(CC_Lung_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Lung cancer lung carcinoma 109
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000789/ScoringFiles/PGS000789.txt.gz
PGS000784
(CC_Cervix_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Cervical cancer cervical carcinoma 10
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000784/ScoringFiles/PGS000784.txt.gz
PGS000786
(CC_Endo_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Endometrial cancer endometrial carcinoma 9
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000786/ScoringFiles/PGS000786.txt.gz
PGS000787
(CC_Kidney_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Kidney cancer renal cell carcinoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000787/ScoringFiles/PGS000787.txt.gz
PGS000791
(CC_NHL_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Non-Hodgkin's lymphoma non-Hodgkins lymphoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000791/ScoringFiles/PGS000791.txt.gz
PGS000793
(CC_Ovary_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Ovarian cancer ovarian carcinoma 36
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000793/ScoringFiles/PGS000793.txt.gz
PGS000795
(CC_Prostate_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Prostate cancer prostate carcinoma 161
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000795/ScoringFiles/PGS000795.txt.gz
PGS000796
(CC_Testis_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Testicular cancer testicular carcinoma,
Testicular Germ Cell Tumor		 52
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000796/ScoringFiles/PGS000796.txt.gz
PGS000783
(CC_Breast_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Breast cancer breast carcinoma 162
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000783/ScoringFiles/PGS000783.txt.gz
PGS000790
(CC_Melanoma_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Melanoma melanoma 24
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000790/ScoringFiles/PGS000790.txt.gz
PGS000794
(CC_Pancreas_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Pancreatic cancer pancreatic carcinoma 22
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000794/ScoringFiles/PGS000794.txt.gz
PGS000792
(CC_Oral_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Oral cavity and pharyngeal cancers oral cavity cancer,
pharynx cancer		 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000792/ScoringFiles/PGS000792.txt.gz
PGS000788
(CC_LL_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Lymphocytic leukemia lymphoid leukemia 75
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000788/ScoringFiles/PGS000788.txt.gz
PGS000782
(CC_Bladder_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Bladder cancer urinary bladder carcinoma 15
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000782/ScoringFiles/PGS000782.txt.gz
PGS000785
(CC_Colorectal_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Colorectal cancer colorectal cancer 103
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000785/ScoringFiles/PGS000785.txt.gz
PGS000797
(CC_Thyroid_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Thyroid cancer thyroid carcinoma 12
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000797/ScoringFiles/PGS000797.txt.gz

External PGS Evaluated 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)
PGS000071
(CC_Bladder)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Bladder cancer urinary bladder carcinoma 15
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000071/ScoringFiles/PGS000071.txt.gz
PGS000072
(CC_Breast)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Breast cancer breast carcinoma 187
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000072/ScoringFiles/PGS000072.txt.gz
PGS000073
(CC_Cervix)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Cervical cancer cervical carcinoma 10
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000073/ScoringFiles/PGS000073.txt.gz
PGS000074
(CC_Colorectal)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Colorectal cancer colorectal cancer 103
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000074/ScoringFiles/PGS000074.txt.gz
PGS000075
(CC_Endo)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Endometrial cancer endometrial carcinoma 9
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000075/ScoringFiles/PGS000075.txt.gz
PGS000076
(CC_Kidney)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Kidney cancer renal cell carcinoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000076/ScoringFiles/PGS000076.txt.gz
PGS000077
(CC_LL)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Lymphocytic leukemia lymphoid leukemia 75
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000077/ScoringFiles/PGS000077.txt.gz
PGS000078
(CC_Lung)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Lung cancer lung carcinoma 109
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000078/ScoringFiles/PGS000078.txt.gz
PGS000079
(CC_Melanoma)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Melanoma melanoma 24
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000079/ScoringFiles/PGS000079.txt.gz
PGS000080
(CC_NHL)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Non-Hodgkin's lymphoma non-Hodgkins lymphoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000080/ScoringFiles/PGS000080.txt.gz
PGS000081
(CC_Oral)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Oral cavity and pharyngeal cancers oral cavity cancer,
pharynx cancer		 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000081/ScoringFiles/PGS000081.txt.gz
PGS000082
(CC_Ovary)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Ovarian cancer ovarian carcinoma 36
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000082/ScoringFiles/PGS000082.txt.gz
PGS000083
(CC_Pancreas)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Pancreatic cancer pancreatic carcinoma 22
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000083/ScoringFiles/PGS000083.txt.gz
PGS000084
(CC_Prostate)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Prostate cancer prostate carcinoma 161
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000084/ScoringFiles/PGS000084.txt.gz
PGS000086
(CC_Testis)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Testicular cancer testicular carcinoma,
Testicular Germ Cell Tumor		 52
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000086/ScoringFiles/PGS000086.txt.gz
PGS000087
(CC_Thyroid)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Thyroid cancer thyroid carcinoma 12
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000087/ScoringFiles/PGS000087.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
PPM002039 PGS000073
(CC_Cervix)
 PSS001012|
European Ancestry|
211,795 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident cervical cancer HR: 1.22 [1.09, 1.37] AUROC: 0.745
C-index: 0.75 (0.017)		 — Age at assessment, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), cigarette pack-years C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002040 PGS000074
(CC_Colorectal)
 PSS001013|
European Ancestry|
393,723 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident colorectal cancer HR: 1.32 [1.27, 1.37] AUROC: 0.704
C-index: 0.704 (0.006)		 — Age at assessment, sex, family history of bowel cancer, genotyping array, PCs(1-15), wasit to hip ratio, cigarette pack years, frequency of processed meat intake (<1 per week vs. ≥1 per week), moderate and/or strenuous physical activity (days per week), alcohol intake C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002041 PGS000075
(CC_Endo)
 PSS001014|
European Ancestry|
212,156 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident endometrial cancer HR: 1.19 [1.1, 1.29] AUROC: 0.755
C-index: 0.749 (0.011)		 — Age at assessment, family history of cancer, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), age at menarche, body mass index, Menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002042 PGS000076
(CC_Kidney)
 PSS001015|
European Ancestry|
391,610 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident kidney cancer HR: 1.16 [1.08, 1.26] AUROC: 0.722
C-index: 0.724 (0.011)		 — Age at assessment, sex, genotyping array, PCs(1-15), body mass index, smoking status (never vs. former vs. current), cigarette pack-years, ever diagnosed with hypertension C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002043 PGS000077
(CC_LL)
 PSS001016|
European Ancestry|
391,338 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident Lymphocytic Leukemia HR: 1.45 [1.31, 1.61] AUROC: 0.719
C-index: 0.735 (0.016)		 — Age at assessment, sex, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002044 PGS000078
(CC_Lung)
 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident lung cancer HR: 1.16 [1.11, 1.22] AUROC: 0.846
C-index: 0.849 (0.006)		 — Age at assessment, sex, genotyping array, PCs(1-15), family history of lung cancer, PM2.5 in 2010, cigarettes per day, years of smoking, smoking status (never vs. former vs. current), smoking status*cigarettes per day, smoking stutus*years of smoking C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002045 PGS000079
(CC_Melanoma)
 PSS001018|
European Ancestry|
392,803 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident melanoma HR: 1.43 [1.36, 1.49] AUROC: 0.652
C-index: 0.663 (0.008)		 — Age at assessment, sex, genotyping array, PCs(1-15), frequency of UV protection use (always vs. most times vs. never out in the sun vs. never), time outdoors in summer (hours per day), ease of tanning (very easily, vs. moderate vs mild vs. mostly burn) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002046 PGS000080
(CC_NHL)
 PSS001019|
European Ancestry|
391,968 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident non-hodgkin's lymphoma HR: 1.16 [1.09, 1.24] AUROC: 0.677
C-index: 0.676 (0.01)		 — Age at assessment, sex, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002047 PGS000081
(CC_Oral)
 PSS001020|
European Ancestry|
391,479 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.11 [1.01, 1.21] AUROC: 0.702
C-index: 0.686 (0.015)		 — Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002048 PGS000082
(CC_Ovary)
 PSS001021|
European Ancestry|
211,958 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident ovarian cancer HR: 1.13 [1.04, 1.24] AUROC: 0.656
C-index: 0.655 (0.015)		 — Age at assessment, family history of breast cancer, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), body mass index, Menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), BMI*menopausal status C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002049 PGS000083
(CC_Pancreas)
 PSS001022|
European Ancestry|
391,491 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident pancreatic cancer HR: 1.49 [1.36, 1.62] AUROC: 0.745
C-index: 0.742 (0.012)		 — Age at assessment, sex, genotyping array, PCs(1-15), family history of cancer (prostate, breast, lung, bowel), body mass index, cigarette pack-years, smoking status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002050 PGS000084
(CC_Prostate)
 PSS001023|
European Ancestry|
184,225 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident prostate cancer HR: 1.39 [1.35, 1.43] AUROC: 0.74
C-index: 0.738 (0.004)		 — Age at assessment, family history of prostate cancer, genotyping array, PCs(1-15), family history of prostate cancer C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002051 PGS000086
(CC_Testis)
 PSS001024|
European Ancestry|
179,537 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident testicular cancer HR: 2.18 [1.66, 2.87] AUROC: 0.783
C-index: 0.749 (0.034)		 — Age at assessment, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002052 PGS000087
(CC_Thyroid)
 PSS001025|
European Ancestry|
391,189 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident thyroid cancer HR: 1.57 [1.36, 1.82] AUROC: 0.679
C-index: 0.666 (0.023)		 — Age at assessment, sex,, genotyping array, PCs(1-15), body mass index (BMI <25 vs. 25≤BMI<30, BMI≥30) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002053 PGS000782
(CC_Bladder_IV)
 PSS001010|
European Ancestry|
391,888 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident blader cancer HR: 1.3 [1.22, 1.39] AUROC: 0.804
C-index: 0.814 (0.008)		 R²: 0.628 Age at assessment, sex, genotyping array, PCs(1-15), cigarette pack-years, smoking status(never vs. former vs. current), body mass index C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002054 PGS000783
(CC_Breast_IV)
 PSS001011|
European Ancestry|
216,273 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident breast cancer HR: 1.52 [1.47, 1.56] AUROC: 0.637
C-index: 0.635 (0.004)		 R²: 0.146 Age at assessment, family history of breast cancer, genotyping array, PCs(1-15), parity( ≥1 live birth vs. none), age at menarche, body mass index, menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use, alcool intake, (Body mass index)*(menopausal status) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002055 PGS000784
(CC_Cervix_IV)
 PSS001012|
European Ancestry|
211,795 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident cervical cancer HR: 1.21 [1.07, 1.35] AUROC: 0.745
C-index: 0.749 (0.017)		 R²: 0.437 Age at assessment, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), cigarette pack-years C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002056 PGS000785
(CC_Colorectal_IV)
 PSS001013|
European Ancestry|
393,723 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident colorectal cancer HR: 1.48 [1.43, 1.54] AUROC: 0.716
C-index: 0.716 (0.006)		 R²: 0.345 Age at assessment, sex, family history of bowel cancer, genotyping array, PCs(1-15), wasit to hip ratio, cigarette pack years, frequency of processed meat intake (<1 per week vs. ≥1 per week), moderate and/or strenuous physical activity (days per week), alcohol intake C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002037 PGS000071
(CC_Bladder)
 PSS001010|
European Ancestry|
391,888 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident blader cancer HR: 1.28 [1.2, 1.37] AUROC: 0.803
C-index: 0.813 (0.008)		 — Age at assessment, sex, genotyping array, PCs(1-15), cigarette pack-years, smoking status(never vs. former vs. current), body mass index C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002038 PGS000072
(CC_Breast)
 PSS001011|
European Ancestry|
216,273 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident breast cancer HR: 1.52 [1.47, 1.56] AUROC: 0.637
C-index: 632.0 (0.005)		 — Age at assessment, family history of breast cancer, genotyping array, PCs(1-15), parity( ≥1 live birth vs. none), age at menarche, body mass index, menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use, alcool intake, body mass index*menopausal status Only 162 of the original 187 SNPs used based on those that reached p<5e-8 in the BCAC meta-analysis. C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002057 PGS000786
(CC_Endo_IV)
 PSS001014|
European Ancestry|
212,156 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident endometrial cancer HR: 1.18 [1.09, 1.27] AUROC: 0.754
C-index: 0.749 (0.011)		 R²: 0.486 Age at assessment, family history of cancer, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), age at menarche, body mass index, Menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002058 PGS000787
(CC_Kidney_IV)
 PSS001015|
European Ancestry|
391,610 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident kidney cancer HR: 1.15 [1.07, 1.24] AUROC: 0.722
C-index: 0.723 (0.011)		 R²: 0.366 Age at assessment, sex, genotyping array, PCs(1-15), body mass index, smoking status (never vs. former vs. current), cigarette pack-years, ever diagnosed with hypertension C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002059 PGS000788
(CC_LL_IV)
 PSS001016|
European Ancestry|
391,338 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident Lymphocytic Leukemia HR: 1.7 [1.53, 1.88] AUROC: 0.738
C-index: 0.756 (0.015)		 R²: 0.415 Age at assessment, sex, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002060 PGS000789
(CC_Lung_IV)
 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident lung cancer HR: 1.17 [1.12, 1.23] AUROC: 0.846
C-index: 0.849 (0.006)		 R²: 0.799 Age at assessment, sex, genotyping array, PCs(1-15), family history of lung cancer, PM2.5 in 2010, cigarettes per day, years of smoking, smoking status (never vs. former vs. current), smoking status*cigarettes per day, smoking stutus*years of smoking C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002061 PGS000790
(CC_Melanoma_IV)
 PSS001018|
European Ancestry|
392,803 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident melanoma HR: 1.44 [1.37, 1.5] AUROC: 0.654
C-index: 0.664 (0.008)		 R²: 0.18 Age at assessment, sex, genotyping array, PCs(1-15), frequency of UV protection use (always vs. most times vs. never out in the sun vs. never), time outdoors in summer (hours per day), ease of tanning (very easily, vs. moderate vs mild vs. mostly burn) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002062 PGS000791
(CC_NHL_IV)
 PSS001019|
European Ancestry|
391,968 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident non-hodgkin's lymphoma HR: 1.15 [1.08, 1.22] AUROC: 0.677
C-index: 0.674 (0.01)		 R²: 0.227 Age at assessment, sex, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002063 PGS000792
(CC_Oral_IV)
 PSS001020|
European Ancestry|
391,479 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.12 [1.02, 1.23] AUROC: 0.702
C-index: 0.687 (0.015)		 R²: 0.356 Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002064 PGS000793
(CC_Ovary_IV)
 PSS001021|
European Ancestry|
211,958 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident ovarian cancer HR: 1.2 [1.1, 1.32] AUROC: 0.66
C-index: 0.654 (0.015)		 R²: 0.193 Age at assessment, family history of breast cancer, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), body mass index, Menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), BMI*menopausal status C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002065 PGS000794
(CC_Pancreas_IV)
 PSS001022|
European Ancestry|
391,491 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident pancreatic cancer HR: 1.49 [1.37, 1.63] AUROC: 0.745
C-index: 0.743 (0.012)		 R²: 0.439 Age at assessment, sex, genotyping array, PCs(1-15), family history of cancer (prostate, breast, lung, bowel), body mass index, cigarette pack-years, smoking status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002066 PGS000795
(CC_Prostate_IV)
 PSS001023|
European Ancestry|
184,225 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident prostate cancer HR: 1.77 [1.72, 1.82] AUROC: 0.769
C-index: 0.768 (0.004)		 R²: 0.51 Age at assessment, family history of prostate cancer, genotyping array, PCs(1-15), family history of prostate cancer C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002067 PGS000796
(CC_Testis_IV)
 PSS001024|
European Ancestry|
179,537 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident testicular cancer HR: 2.26 [1.71, 2.99] AUROC: 0.787
C-index: 0.766 (0.033)		 R²: 0.605 Age at assessment, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002068 PGS000797
(CC_Thyroid_IV)
 PSS001025|
European Ancestry|
391,189 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident thyroid cancer HR: 1.75 [1.53, 2.01] AUROC: 0.701
C-index: 0.692 (0.022)		 R²: 0.31 Age at assessment, sex,, genotyping array, PCs(1-15), body mass index (BMI <25 vs. 25≤BMI<30, BMI≥30) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002069 PGS000795
(CC_Prostate_IV)
 PSS001023|
European Ancestry|
184,225 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident prostate cancer — AUROC: 0.766
C-index: 0.763 (0.004)		 R²: 0.496 Age, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002070 PGS000783
(CC_Breast_IV)
 PSS001011|
European Ancestry|
216,273 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident breast cancer — AUROC: 0.626
C-index: 0.62 (0.005)		 R²: 0.122 Age, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002071 PGS000785
(CC_Colorectal_IV)
 PSS001013|
European Ancestry|
393,723 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident colorectal cancer — AUROC: 0.708
C-index: 0.708 (0.006)		 R²: 0.319 Age, sex, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002072 PGS000789
(CC_Lung_IV)
 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident lung cancer — AUROC: 0.71
C-index: 0.711 (0.007)		 R²: 0.322 Age, sex, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002073 PGS000789
(CC_Lung_IV)
 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident lung cancer in never smokers — AUROC: 0.723
C-index: 0.723 (0.02)		 R²: 0.354 Age, sex, genotyping array, PCs(1-15), family history of lung cancer, PM2.5 level in 2010 C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002074 PGS000789
(CC_Lung_IV)
 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident lung cancer in smokers — AUROC: 0.808
C-index: 0.809 (0.007)		 R²: 0.657 Age, sex, genotyping array, PCs(1-15), family history of lung cancer, PM2.5 level in 2010, cigarettes per day, years of smoking, smoking status (former vs. current), years since quitting, (smoking status)*(cigarettes per day), (smoking status*years of smoking) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS001010 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 890 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001011 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 4,760 cases
  • , 211,513 controls
]
,
0.0 % Male samples
 — European — UKB —
PSS001012 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 282 cases
  • , 211,513 controls
]
,
0.0 % Male samples
 — European — UKB —
PSS001013 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 2,725 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001014 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 643 cases
  • , 211,513 controls
]
,
0.0 % Male samples
 — European — UKB —
PSS001015 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 612 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001016 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 340 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001017 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. 207 of the cases were in non-smokers and 1334 were in smokers. —
[
  • 1,541 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001018 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 1,805 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001019 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 970 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001020 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 481 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001021 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 445 cases
  • , 211,513 controls
]
,
0.0 % Male samples
 — European — UKB —
PSS001022 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 493 cases
  • , 390,998 controls
]
 — European — UKB —
PSS001023 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 4,740 cases
  • , 179,485 controls
]
,
100.0 % Male samples
 — European — UKB —
PSS001024 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 52 cases
  • , 179,485 controls
]
,
100.0 % Male samples
 — European — UKB —
PSS001025 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 191 cases
  • , 390,998 controls
]
 — European — UKB —