PGS Publication: PGP000135

Publication Information (EuropePMC)
Title Evaluating the Utility of Polygenic Risk Scores in Identifying High-Risk Individuals for Eight Common Cancers.
PubMed ID 32596635(Europe PMC)
doi 10.1093/jncics/pkaa021
Publication Date March 12, 2020
Journal JNCI Cancer Spectr
Author(s) Jia G, Lu Y, Wen W, Long J, Liu Y, Tao R, Li B, Denny JC, Shu XO, Zheng W.
Released in PGS Catalog: Feb. 3, 2021

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)
PGS000723 PRS_Bladder PGP000135 Jia G et al. JNCI Cancer Spectr (2020) Bladder cancer bladder carcinoma 14 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000723/ScoringFiles/PGS000723.txt.gz
PGS000724 PRS_Ovary PGP000135 Jia G et al. JNCI Cancer Spectr (2020) Epithelial ovarian cancer ovarian carcinoma 31 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000724/ScoringFiles/PGS000724.txt.gz
PGS000725 PRS_Pancreas PGP000135 Jia G et al. JNCI Cancer Spectr (2020) Pancreatic cancer pancreatic carcinoma 22 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000725/ScoringFiles/PGS000725.txt.gz
PGS000719 PRS_Prostate PGP000135 Jia G et al. JNCI Cancer Spectr (2020) Prostate cancer prostate carcinoma 134 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000719/ScoringFiles/PGS000719.txt.gz
PGS000720 PRS_Colorectal PGP000135 Jia G et al. JNCI Cancer Spectr (2020) Colorectal cancer colorectal cancer 95 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000720/ScoringFiles/PGS000720.txt.gz
PGS000721 PRS_Lung PGP000135 Jia G et al. JNCI Cancer Spectr (2020) Lung cancer lung carcinoma 19 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000721/ScoringFiles/PGS000721.txt.gz
PGS000722 PRS_Kidney PGP000135 Jia G et al. JNCI Cancer Spectr (2020) Kidney cancer renal carcinoma 15 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000722/ScoringFiles/PGS000722.txt.gz

External PGS Evaluated 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)
PGS000004 PRS313_BC PGP000002 Mavaddat N et al. Am J Hum Genet (2018) Breast Cancer breast carcinoma 313 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.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
PPM001644 PGS000719
(PRS_Prostate)
PSS000860 PGP000135 Jia G et al. (2020) Reported Trait: Incident prostate cancer AUROC: 0.662 [0.655, 0.67] Genotyping array
PPM001645 PGS000719
(PRS_Prostate)
PSS000860 PGP000135 Jia G et al. (2020) Reported Trait: Incident prostate cancer AUROC: 0.669 [0.661, 0.676] family history of cancer (in first-degree relatives), genotyping array
PPM001646 PGS000004
(PRS313_BC)
PSS000854 PGP000135 Jia G et al. (2020) Ext. Reported Trait: Incident breast cancer AUROC: 0.628 [0.62, 0.637] Genotyping array Missing 25 variants (8%) based on availability of variants in the cohort
PPM001647 PGS000004
(PRS313_BC)
PSS000854 PGP000135 Jia G et al. (2020) Ext. Reported Trait: Incident breast cancer AUROC: 0.633 [0.624, 0.641] family history of cancer (in first-degree relatives), genotyping array Missing 25 variants (8%) based on availability of variants in the cohort
PPM001648 PGS000720
(PRS_Colorectal)
PSS000855 PGP000135 Jia G et al. (2020) Reported Trait: Incident colorectal cancer AUROC: 0.609 [0.598, 0.62] Genotyping array
PPM001649 PGS000720
(PRS_Colorectal)
PSS000855 PGP000135 Jia G et al. (2020) Reported Trait: Incident colorectal cancer AUROC: 0.613 [0.602, 0.624] family history of cancer (in first-degree relatives), genotyping array
PPM001650 PGS000721
(PRS_Lung)
PSS000857 PGP000135 Jia G et al. (2020) Reported Trait: Incident lung cancer AUROC: 0.591 [0.576, 0.606] Genotyping array
PPM001651 PGS000721
(PRS_Lung)
PSS000857 PGP000135 Jia G et al. (2020) Reported Trait: Incident lung cancer AUROC: 0.615 [0.6, 0.629] family history of cancer (in first-degree relatives), genotyping array
PPM001652 PGS000722
(PRS_Kidney)
PSS000856 PGP000135 Jia G et al. (2020) Reported Trait: Incident kidney cancer AUROC: 0.567 [0.543, 0.591] Genotyping array
PPM001653 PGS000723
(PRS_Bladder)
PSS000853 PGP000135 Jia G et al. (2020) Reported Trait: Incident bladder cancer AUROC: 0.583 [0.559, 0.607] Genotyping array
PPM001654 PGS000724
(PRS_Ovary)
PSS000858 PGP000135 Jia G et al. (2020) Reported Trait: Incident epithelial ovarian cancer AUROC: 0.568 [0.537, 0.598] Genotyping array
PPM001655 PGS000725
(PRS_Pancreas)
PSS000859 PGP000135 Jia G et al. (2020) Reported Trait: Incident Pancreatic cancer AUROC: 0.639 [0.613, 0.664] Genotyping array

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
PSS000853 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Bladder cancer =(ICD-9 = 188 or ICD-10 = C67). Median = 5.8 years
[
  • 513 cases
  • , 400,299 controls
]
,
46.5 % Male samples
European UKB
PSS000854 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Breast cancer=(ICD-9 = 174 or ICD-10 = C50). Median = 5.8 years
[
  • 4,340 cases
  • , 396,472 controls
]
,
46.5 % Male samples
European UKB
PSS000855 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Colorectal Cancer=(ICD-9 = 153, 154.1 or ICD-10 = C18, C20) Median = 5.8 years
[
  • 2,458 cases
  • , 398,354 controls
]
,
46.5 % Male samples
European UKB
PSS000856 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Kidney Cancer=(ICD-9 = 189.0 or ICD-10 = C64) Median = 5.8 years
[
  • 545 cases
  • , 400,267 controls
]
,
46.5 % Male samples
European UKB
PSS000857 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Lung cancer=(ICD-9 = 162.2–162.9 or ICD-10 = C34). Median = 5.8 years
[
  • 1,508 cases
  • , 399,304 controls
]
,
46.5 % Male samples
European UKB
PSS000858 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Ovarian cancer=(ICD-9 = 183.0 or ICD-10 = C56; ICD-O: 8441, 8460, 8462, 8380, 8381, 8470, 8471, 8472, 8473, 8480, 8310, 8140, 8260, 8440, 8450, 9000, 8000, and 8010) Median = 5.8 years
[
  • 358 cases
  • , 400,454 controls
]
,
46.5 % Male samples
European UKB
PSS000859 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Pancreatic Cancer=(ICD-9 = 157 or ICD-10 = C25) Median = 5.8 years
[
  • 432 cases
  • , 400,380 controls
]
,
46.5 % Male samples
European UKB
PSS000860 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Prostate=(ICD-9 = 185 or ICD-10 = C61) Median = 5.8 years
[
  • 4,430 cases
  • , 396,382 controls
]
,
46.5 % Male samples
European UKB