| Publication Information (EuropePMC) | |
| Title | Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts. |
| PubMed ID | 33579919(Europe PMC) |
| doi | 10.1038/s41467-021-21288-z |
| Publication Date | Feb. 12, 2021 |
| Journal | Nat Commun |
| 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. |
| 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) |
|---|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
|
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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. Nat Commun (2021) |
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 |
| PPM000207 | PGS000087 (CC_Thyroid) |
PSS000126| European Ancestry| 411,118 individuals |
PGP000050 | Graff RE et al. Nat Commun (2021) |
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. Nat Commun (2021) |
Reported Trait: Testicular cancer | OR: 2.29 [2.13, 2.47] | — | — | Genotyping array, age, 10 PCs. | — |
| PPM000204 | PGS000084 (CC_Prostate) |
PSS000123| European Ancestry| 201,516 individuals |
PGP000050 | Graff RE et al. Nat Commun (2021) |
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. Sample overlap: the GERA dataset contributed to the effect estimates for 4 of the 161 variants in the prostate cancer PRS. |
|
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
100.0 % Male samples |
— | 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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
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 | — | [ ,
46.0 % Male samples |
Mean = 58.0 years | European | — | GERA, UKB | — |