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)

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000723
(PRS_Bladder)
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Bladder cancer urinary bladder carcinoma 14
-
 https://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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000724/ScoringFiles/PGS000724.txt.gz
PGS000722
(PRS_Kidney)
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Kidney cancer renal carcinoma 15
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000722/ScoringFiles/PGS000722.txt.gz
PGS000721
(PRS_Lung)
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Lung cancer lung carcinoma 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000721/ScoringFiles/PGS000721.txt.gz
PGS000725
(PRS_Pancreas)
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Pancreatic cancer pancreatic carcinoma 22
-
 https://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
-
 https://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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000720/ScoringFiles/PGS000720.txt.gz

External PGS Evaluated By This Publication

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)
PGS000004
(PRS313_BC)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Breast cancer breast carcinoma 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.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
PPM001644 PGS000719
(PRS_Prostate)
 PSS000860|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident prostate cancer — AUROC: 0.662 [0.655, 0.67] — Genotyping array —
PPM001645 PGS000719
(PRS_Prostate)
 PSS000860|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (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|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (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|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (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|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident colorectal cancer — AUROC: 0.609 [0.598, 0.62] — Genotyping array —
PPM001649 PGS000720
(PRS_Colorectal)
 PSS000855|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (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|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident lung cancer — AUROC: 0.591 [0.576, 0.606] — Genotyping array —
PPM001651 PGS000721
(PRS_Lung)
 PSS000857|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (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|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident kidney cancer — AUROC: 0.567 [0.543, 0.591] — Genotyping array —
PPM001653 PGS000723
(PRS_Bladder)
 PSS000853|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident bladder cancer — AUROC: 0.583 [0.559, 0.607] — Genotyping array —
PPM001654 PGS000724
(PRS_Ovary)
 PSS000858|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident epithelial ovarian cancer — AUROC: 0.568 [0.537, 0.598] — Genotyping array —
PPM001655 PGS000725
(PRS_Pancreas)
 PSS000859|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident Pancreatic cancer — AUROC: 0.639 [0.613, 0.664] — Genotyping array —

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
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 —