Publication: Cross-Cancer Evaluation of Polygenic Risk Scores for 17 Cancer Types in Two Large Cohorts

Information

PGS Catalog Publication (PGP) ID: PGP000050
PubMed ID: None
doi: 10.1101/2020.01.18.911578

Publication Date: Jan. 19, 2020

Journal: bioRxiv

Authors: 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.

PGS Associated with PGP000050

PGS Developed By This Study

Polygenic Score (PGS) ID PGS Name Publication ID Reported Trait Mapped Trait(s) (EFO) Number of Variants PGS Download Links
PGS000071 CC_Bladder Graff RE et al. bioRxiv (2020) Bladder cancer bladder carcinoma 15 FTP Link
PGS000072 CC_Breast Graff RE et al. bioRxiv (2020) Breast cancer breast carcinoma 187 FTP Link
PGS000073 CC_Cervix Graff RE et al. bioRxiv (2020) Cervical cancer cervical carcinoma 10 FTP Link
PGS000074 CC_Colorectal Graff RE et al. bioRxiv (2020) Colorectal cancer colorectal cancer 103 FTP Link
PGS000075 CC_Endo Graff RE et al. bioRxiv (2020) Endometrial cancer endometrial carcinoma 9 FTP Link
PGS000076 CC_Kidney Graff RE et al. bioRxiv (2020) Kidney cancer renal cell carcinoma 19 FTP Link
PGS000077 CC_LL Graff RE et al. bioRxiv (2020) Lymphocytic leukemia lymphoid leukemia 75 FTP Link
PGS000078 CC_Lung Graff RE et al. bioRxiv (2020) Lung cancer lung carcinoma 109 FTP Link
PGS000079 CC_Melanoma Graff RE et al. bioRxiv (2020) Melanoma melanoma 24 FTP Link
PGS000080 CC_NHL Graff RE et al. bioRxiv (2020) Non-Hodgkin's lymphoma non-Hodgkins lymphoma 19 FTP Link
PGS000081 CC_Oral Graff RE et al. bioRxiv (2020) Oral cavity and pharyngeal cancers oral cavity cancer
carcinoma of pharynx
14 FTP Link
PGS000082 CC_Ovary Graff RE et al. bioRxiv (2020) Ovarian cancer ovarian carcinoma 36 FTP Link
PGS000083 CC_Pancreas Graff RE et al. bioRxiv (2020) Pancreatic cancer pancreatic carcinoma 22 FTP Link
PGS000084 CC_Prostate Graff RE et al. bioRxiv (2020) Prostate cancer prostate carcinoma 161 FTP Link
PGS000085 CC_Stomach Graff RE et al. bioRxiv (2020) Esophageal and stomach cancers gastric carcinoma
Barrett's esophagus
13 FTP Link
PGS000086 CC_Testis Graff RE et al. bioRxiv (2020) Testicular cancer testicular carcinoma
Testicular Germ Cell Tumor
52 FTP Link
PGS000087 CC_Thyroid Graff RE et al. bioRxiv (2020) Thyroid cancer thyroid carcinoma 12 FTP Link

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 (PPM) ID Evaluated Score PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000191 PGS000071 (CC_Bladder) PSS000110 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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 Graff RE et al. (2020) 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
PPM000206 PGS000086 (CC_Testis) PSS000125 Graff RE et al. (2020) Reported Trait: Testicular cancer OR: 2.29 [2.13 - 2.47] Genotyping array, age, 10 PCs.
PPM000207 PGS000087 (CC_Thyroid) PSS000126 Graff RE et al. (2020) 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

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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 412,602 individuals
[ 2,248 cases, 410,354 controls]
0.46 % Male samples
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 237,549 individuals
[ 17,901 cases, 219,648 controls]
0.00 % 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 226,216 individuals
[ 6,568 cases, 219,648 controls]
0.00 % 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 416,249 individuals
[ 5,895 cases, 410,354 controls]
0.46 % Male samples
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 221,699 individuals
[ 2,051 cases, 219,648 controls]
0.00 % 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 411,695 individuals
[ 1,341 cases, 410,354 controls]
0.46 % Male samples
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 411,207 individuals
[ 853 cases, 410,354 controls]
0.46 % Male samples
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 412,842 individuals
[ 2,488 cases, 410,354 controls]
0.46 % Male samples
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 417,136 individuals
[ 6,782 cases, 410,354 controls]
0.46 % Male samples
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 412,765 individuals
[ 2,411 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB
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 411,577 individuals
[ 1,223 cases, 410,354 controls]
0.46 % Male samples
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 220,909 individuals
[ 1,261 cases, 219,648 controls]
0.00 % 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 411,019 individuals
[ 665 cases, 410,354 controls]
0.46 % Male samples
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 201,516 individuals
[ 10,810 cases, 190,706 controls]
1.00 % 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 411,448 individuals
[ 1,094 cases, 410,354 controls]
0.46 % 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 170,680 individuals
[ 713 cases, 169,967 controls]
1.00 % 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 411,118 individuals
[ 764 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB