Polygenic Score (PGS) ID: PGS000082

Predicted Trait
Reported Trait Ovarian cancer
Mapped Trait(s) ovarian carcinoma (EFO_0001075)
Released in PGS Catalog: Feb. 12, 2020
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name CC_Ovary
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 36
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
152,183 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001917
Europe PMC: 23544013
 2,727 individuals European NR
GWAS Catalog: GCST000802
Europe PMC: 20852632
 4,122 individuals European 6 cohorts
  • B58C
  • ,CoRGI
  • ,RMH-OCS
  • ,SEARCH-OCS
  • ,UKFOCR
  • ,UKOPS
GWAS Catalog: GCST002748
Europe PMC: 25581431
 13,491 individuals European NR
GWAS Catalog: GCST004462
Europe PMC: 28346442
 85,426 individuals European 95 cohorts
  • AOCS
  • ,BCFR-AU
  • ,BCFR-NY
  • ,BCFR-PA
  • ,BCFR-UTAH
  • ,BFBOCC
  • ,BMBSA
  • ,BOCC
  • ,BOCS
  • ,BRICOH
  • ,BioVU
  • ,CNIO
  • ,COH
  • ,CONSIT_TEAM
  • ,CopBCS
  • ,DEMOKRITOS
  • ,DFCI
  • ,DKFZ
  • ,DOVE
  • ,DPMS
  • ,EMBRACE
  • ,EPIC
  • ,FCCC
  • ,FOTS
  • ,FROC&GEOCS
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,GOCS
  • ,Georgetown
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HJOCS
  • ,HMOCS
  • ,HOCS
  • ,HOPE
  • ,HUNBOCS
  • ,HUOCS
  • ,HUVH
  • ,HeOCS
  • ,ICO
  • ,IHCC
  • ,INHERIT
  • ,IOVHBOCS
  • ,IPOBCS
  • ,KUMC
  • ,LAC-CCOC
  • ,LUHR
  • ,MALOVA
  • ,MAYO
  • ,MCGILL
  • ,MDACCS
  • ,MEC
  • ,MOCS
  • ,MOF
  • ,MSKCC
  • ,MUV
  • ,NC-BCFR
  • ,NCI
  • ,NCOCS
  • ,NECC
  • ,NHS
  • ,NJOCS
  • ,NNPIO
  • ,NOCS
  • ,NRG_ONCOLOGY
  • ,NSUHS
  • ,OCGN
  • ,OFBCR
  • ,OSUCCG
  • ,OUH
  • ,OVAL-BC
  • ,PLCO
  • ,POCS
  • ,SEARCH
  • ,SHMC
  • ,SWE
  • ,SWE-BRCA
  • ,Sisters
  • ,TBOCS
  • ,UBNS
  • ,UC
  • ,UCIOCS
  • ,UCSF
  • ,UDP
  • ,UKFOCR
  • ,UKGRFOCR
  • ,UPENN
  • ,UPITT
  • ,VFCTG
  • ,WCPSOCCI
  • ,WCRI
  • ,WOCS
  • ,kConFab
GWAS Catalog: GCST001258
Europe PMC: 21964575
 42,247 individuals European 7 cohorts
  • ICR
  • ,LUHR
  • ,NBS
  • ,Nijmegen
  • ,ODZH
  • ,TAMPERE
  • ,deCODE
GWAS Catalog: GCST000455
Europe PMC: 19648919
 4,170 individuals European 6 cohorts
  • B58C
  • ,RMH
  • ,SEARCH
  • ,UKCRC
  • ,UKFOCR
  • ,UKOPS

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) 		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
PPM000202 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
PPM002048 PSS001021|
European Ancestry|
211,958 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident ovarian cancer HR: 1.13 [1.04, 1.24] AUROC: 0.656
C-index: 0.655 (0.015)		 — Age at assessment, family history of breast cancer, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), body mass index, Menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), BMI*menopausal status C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017174 PSS010149|
European Ancestry|
315 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Ovarian cancer HR: 1.09 [0.97, 1.21] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates —

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
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 —
[
  • 1,261 cases
  • , 219,648 controls
]
,
0.0 % Male samples
 — European — GERA, UKB —
PSS001021 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 445 cases
  • , 211,513 controls
]
,
0.0 % Male samples
 — European — UKB —
PSS010149 — —
[
  • 20 cases
  • , 295 controls
]
,
0.0 % Male samples
 — European — UKB —