PGS Publication: PGP000328

Publication Information (EuropePMC)
Title Evaluating polygenic risk scores in assessing risk of nine solid and hematologic cancers in European descendants.
PubMed ID 32588423(Europe PMC)
doi 10.1002/ijc.33176
Publication Date July 9, 2020
Journal Int J Cancer
Author(s) Choi J, Jia G, Wen W, Long J, Zheng W.
Released in PGS Catalog: June 9, 2022

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)
PGS002299
(PRS3_gastric)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Gastric cancer gastric cancer 3
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002299/ScoringFiles/PGS002299.txt.gz
PGS002300
(PRS19_endometrial)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Endometrial cancer endometrial cancer 19
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002300/ScoringFiles/PGS002300.txt.gz
PGS002298
(PRS14_esophageal)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Esophageal cancer esophageal carcinoma 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002298/ScoringFiles/PGS002298.txt.gz
PGS002305
(PRS43_CLL)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Chronic lymphoid leukemia lymphoid leukemia 43
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002305/ScoringFiles/PGS002305.txt.gz
PGS002306
(PRS23_MM)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Multiple myeloma multiple myeloma 23
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002306/ScoringFiles/PGS002306.txt.gz
PGS002302
(PRS28_glioma)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Glioma glioma 28
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002302/ScoringFiles/PGS002302.txt.gz
PGS002304
(PRS6_FL)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Follicular lymphoma follicular lymphoma 6
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002304/ScoringFiles/PGS002304.txt.gz
PGS002303
(PRS9_DLBCL)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Diffuse large B-cell lymphoma diffuse large B-cell lymphoma 9
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002303/ScoringFiles/PGS002303.txt.gz
PGS002301
(PRS22_melanoma)
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Melanoma melanoma 22
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002301/ScoringFiles/PGS002301.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
PPM013027 PGS002298
(PRS14_esophageal)
 PSS009661|
European Ancestry|
406 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Esophageal cancer — AUROC: 0.53 [0.51, 0.56] — — —
PPM013028 PGS002299
(PRS3_gastric)
 PSS009662|
European Ancestry|
272 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Gastric cancer — AUROC: 0.56 [0.54, 0.58] — — —
PPM013029 PGS002300
(PRS19_endometrial)
 PSS009660|
European Ancestry|
629 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Endometrial cancer — AUROC: 0.64 [0.61, 0.67] — — —
PPM013030 PGS002301
(PRS22_melanoma)
 PSS009664|
European Ancestry|
1,226 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Melanoma — AUROC: 0.59 [0.55, 0.63] — — —
PPM013031 PGS002302
(PRS28_glioma)
 PSS009663|
European Ancestry|
312 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Glioma — AUROC: 0.61 [0.57, 0.64] — — —
PPM013032 PGS002303
(PRS9_DLBCL)
 PSS009657|
European Ancestry|
308 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Diffuse large B-cell lymphoma — AUROC: 0.56 [0.53, 0.6] — — —
PPM013033 PGS002304
(PRS6_FL)
 PSS009658|
European Ancestry|
197 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Follicular lymphoma — AUROC: 0.61 [0.59, 0.63] — — —
PPM013034 PGS002305
(PRS43_CLL)
 PSS009656|
European Ancestry|
265 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Chronic lymphoid leukemia — AUROC: 0.57 [0.54, 0.6] — — —
PPM013035 PGS002306
(PRS23_MM)
 PSS009659|
European Ancestry|
290 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Multiple myeloma — AUROC: 0.69 [0.64, 0.7] — — —
PPM013037 PGS002300
(PRS19_endometrial)
 PSS009660|
European Ancestry|
629 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Endometrial cancer — — Hazard ratio (HR top 5% vs average): 1.34 [0.96, 1.88] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —
PPM013038 PGS002301
(PRS22_melanoma)
 PSS009664|
European Ancestry|
1,226 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Melanoma — — Hazard ratio (HR top 5% vs average): 2.31 [1.85, 2.88] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —
PPM013039 PGS002302
(PRS28_glioma)
 PSS009663|
European Ancestry|
312 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Glioma — — Hazard ratio (HR top 5% vs average): 2.55 [1.72, 3.77] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —
PPM013040 PGS002303
(PRS9_DLBCL)
 PSS009657|
European Ancestry|
308 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Diffuse large B-cell lymphoma — — Hazard ratio (HR top 5% vs average): 1.6 [1.01, 2.54] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —
PPM013041 PGS002304
(PRS6_FL)
 PSS009658|
European Ancestry|
197 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Follicular lymphoma — — Hazard ratio (HR top 5% vs average): 2.33 [1.38, 3.93] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —
PPM013042 PGS002305
(PRS43_CLL)
 PSS009656|
European Ancestry|
265 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Chronic lymphoid leukemia — — Hazard ratio (HR top 5% vs average): 4.33 [2.92, 6.42] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —
PPM013043 PGS002306
(PRS23_MM)
 PSS009659|
European Ancestry|
290 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Multiple myeloma — — Hazard ratio (HR top 5% vs average): 2.41 [1.56, 3.72] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —
PPM013036 PGS002299
(PRS3_gastric)
 PSS009662|
European Ancestry|
272 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Gastric cancer — — Hazard ratio (HR top 5% vs average): 1.27 [0.75, 2.15] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —

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
PSS009656 chronic lymphoid leukemia (ICD-9 = 204.1 or ICD-10 = C91.1) — 265 individuals — European — UKB —
PSS009657 diffuse large B-cell lymphoma (ICD-10 = C83.3) — 308 individuals — European — UKB —
PSS009658 follicular lymphoma (ICD- 10 = C82 or ICD-O: 9690) — 197 individuals — European — UKB —
PSS009659 multiple myeloma (ICD-9 = 203 or ICD-10 = C90.0) — 290 individuals — European — UKB —
PSS009660 endometrial cancer (ICD-9 = 182 or ICD-10 = C54) — 629 individuals — European — UKB —
PSS009661 esophageal cancer (ICD-9 = 150 or ICD-10 = C15) — 406 individuals — European — UKB —
PSS009662 gastric cancer (ICD- 9 = 151 or ICD-10 = C16) — 272 individuals — European — UKB —
PSS009663 glioma (ICD-9 = 191 or ICD-10 = C71; ICD-O: 9380-9480) — 312 individuals — European — UKB —
PSS009664 melanoma (ICD-9 = 172 or ICD-10 = C43) — 1,226 individuals — European — UKB —