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: Feb. 12, 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)
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
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
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
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
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
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
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
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
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
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
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
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
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

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
PPM000191 PGS000071 (CC_Bladder) PSS000110 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 PGP000050
Graff RE et al. (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 ID)
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