PGS Preprint: PGP000050

Publication Information (EuropePMC)
Title Cross-Cancer Evaluation of Polygenic Risk Scores for 17 Cancer Types in Two Large Cohorts
doi 10.1101/2020.01.18.911578
Publication Date Jan. 19, 2020
Journal bioRxiv Preprint
Author(s) Graff RE, Cavazos TB, Thai KK, Kachuri L, Rashkin SR, Hoffman JD, Alexeeff SE, Blatchins M, Meyers TJ, Leong L, Tai CG, Emami NC, Corley DA, Kushi LH, Ziv E, Van Den Eeden SK, Jorgenson E, Hoffmann TJ, Habel LA, Witte JS, Sakoda LC.
Released in PGS Catalog: Feb. 12, 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)
PGS000072
(CC_Breast)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Breast cancer breast carcinoma 187
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000072/ScoringFiles/PGS000072.txt.gz
PGS000073
(CC_Cervix)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Cervical cancer cervical carcinoma 10
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000073/ScoringFiles/PGS000073.txt.gz
PGS000074
(CC_Colorectal)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Colorectal cancer colorectal cancer 103
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000074/ScoringFiles/PGS000074.txt.gz
PGS000076
(CC_Kidney)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Kidney cancer renal cell carcinoma 19
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000076/ScoringFiles/PGS000076.txt.gz
PGS000077
(CC_LL)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Lymphocytic leukemia lymphoid leukemia 75
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000077/ScoringFiles/PGS000077.txt.gz
PGS000079
(CC_Melanoma)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Melanoma melanoma 24
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000079/ScoringFiles/PGS000079.txt.gz
PGS000080
(CC_NHL)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Non-Hodgkin's lymphoma non-Hodgkins lymphoma 19
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000080/ScoringFiles/PGS000080.txt.gz
PGS000071
(CC_Bladder)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Bladder cancer bladder carcinoma 15
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000071/ScoringFiles/PGS000071.txt.gz
PGS000086
(CC_Testis)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Testicular cancer testicular carcinoma,
Testicular Germ Cell Tumor
52
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000086/ScoringFiles/PGS000086.txt.gz
PGS000085
(CC_Stomach)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Esophageal and stomach cancers gastric carcinoma,
Barrett's esophagus
13
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000085/ScoringFiles/PGS000085.txt.gz
PGS000075
(CC_Endo)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Endometrial cancer endometrial carcinoma 9
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000075/ScoringFiles/PGS000075.txt.gz
PGS000078
(CC_Lung)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Lung cancer lung carcinoma 109
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000078/ScoringFiles/PGS000078.txt.gz
PGS000081
(CC_Oral)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Oral cavity and pharyngeal cancers carcinoma of pharynx,
oral cavity cancer
14
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000081/ScoringFiles/PGS000081.txt.gz
PGS000083
(CC_Pancreas)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Pancreatic cancer pancreatic carcinoma 22
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000083/ScoringFiles/PGS000083.txt.gz
PGS000087
(CC_Thyroid)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Thyroid cancer thyroid carcinoma 12
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000087/ScoringFiles/PGS000087.txt.gz
PGS000082
(CC_Ovary)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Ovarian cancer ovarian carcinoma 36
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000082/ScoringFiles/PGS000082.txt.gz
PGS000084
(CC_Prostate)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Prostate cancer prostate carcinoma 161
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000084/ScoringFiles/PGS000084.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
PPM000191 PGS000071
(CC_Bladder)
PSS000110|
European Ancestry|
412,602 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Bladder cancer OR: 1.3 [1.25, 1.36] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000192 PGS000072
(CC_Breast)
PSS000111|
European Ancestry|
237,549 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Breast cancer OR: 1.26 [1.24, 1.28] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000193 PGS000073
(CC_Cervix)
PSS000112|
European Ancestry|
226,216 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Cervical cancer OR: 1.22 [1.19, 1.25] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000194 PGS000074
(CC_Colorectal)
PSS000113|
European Ancestry|
416,249 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Colorectal cancer OR: 1.37 [1.33, 1.4] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000195 PGS000075
(CC_Endo)
PSS000114|
European Ancestry|
221,699 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Endometrial cancer OR: 1.19 [1.14, 1.24] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000196 PGS000076
(CC_Kidney)
PSS000115|
European Ancestry|
411,695 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Kidney cancer OR: 1.21 [1.14, 1.27] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000197 PGS000077
(CC_LL)
PSS000116|
European Ancestry|
411,207 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Lymphocytic leukemia OR: 1.42 [1.33, 1.51] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000198 PGS000078
(CC_Lung)
PSS000117|
European Ancestry|
412,842 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Lung cancer OR: 1.12 [1.08, 1.17] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000199 PGS000079
(CC_Melanoma)
PSS000118|
European Ancestry|
417,136 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Melanoma OR: 1.44 [1.41, 1.48] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000200 PGS000080
(CC_NHL)
PSS000119|
European Ancestry|
412,765 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Non-Hodgkin's lymphoma OR: 1.25 [1.2, 1.3] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000201 PGS000081
(CC_Oral)
PSS000120|
European Ancestry|
411,577 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Oral cavity and pharyngeal cancers OR: 1.08 [1.02, 1.14] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000202 PGS000082
(CC_Ovary)
PSS000121|
European Ancestry|
220,909 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Ovarian cancer OR: 1.14 [1.08, 1.2] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000203 PGS000083
(CC_Pancreas)
PSS000122|
European Ancestry|
411,019 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Pancreatic cancer OR: 1.44 [1.33, 1.55] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000204 PGS000084
(CC_Prostate)
PSS000123|
European Ancestry|
201,516 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Prostate cancer OR: 1.44 [1.41, 1.47] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000205 PGS000085
(CC_Stomach)
PSS000124|
European Ancestry|
411,448 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Esophageal and stomach cancers OR: 1.07 [1.0, 1.13] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000207 PGS000087
(CC_Thyroid)
PSS000126|
European Ancestry|
411,118 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Thyroid cancer OR: 1.55 [1.44, 1.67] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000206 PGS000086
(CC_Testis)
PSS000125|
European Ancestry|
170,680 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Testicular cancer OR: 2.29 [2.13, 2.47] Genotyping array, age, 10 PCs.

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
PSS000120 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 20010, 20020, 20030, 20040, 20050, 20060, 20070, 20080, 20090, and 20100
[
  • 1,223 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000121 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 27040
[
  • 1,261 cases
  • , 219,648 controls
]
,
0.0 % Male samples
European GERA, UKB
PSS000122 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 21100
[
  • 665 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000123 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28010
[
  • 10,810 cases
  • , 190,706 controls
]
,
100.0 % Male samples
European GERA, UKB
PSS000124 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 21010 and 21020
[
  • 1,094 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000125 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28020
[
  • 713 cases
  • , 169,967 controls
]
,
100.0 % Male samples
European UKB
PSS000126 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 32010
[
  • 764 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000110 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 29010
[
  • 2,248 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000111 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 26000
[
  • 17,901 cases
  • , 219,648 controls
]
,
0.0 % Male samples
European GERA, UKB
PSS000112 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 27010
[
  • 6,568 cases
  • , 219,648 controls
]
,
0.0 % Male samples
European GERA, UKB
PSS000113 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 21041 - 21049, 21051, 21052, and 21060
[
  • 5,895 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000114 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 27020
[
  • 2,051 cases
  • , 219,648 controls
]
,
0.0 % Male samples
European GERA, UKB
PSS000115 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 29020
[
  • 1,341 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000116 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 35011 - 35013
[
  • 853 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000117 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 22030
[
  • 2,488 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000118 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 25010
[
  • 6,782 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS000119 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 33041, and 33042
[
  • 2,411 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB