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
Download Score FTP directory
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)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST000455
Europe PMC: 19648919
4,170 individualsEuropean6 cohorts
  • B58C
  • ,RMH
  • ,SEARCH
  • ,UKCRC
  • ,UKFOCR
  • ,UKOPS
GWAS Catalog: GCST000802
Europe PMC: 20852632
4,122 individualsEuropean6 cohorts
  • B58C
  • ,CoRGI
  • ,RMH-OCS
  • ,SEARCH-OCS
  • ,UKFOCR
  • ,UKOPS
GWAS Catalog: GCST001258
Europe PMC: 21964575
42,247 individualsEuropean7 cohorts
  • ICR
  • ,LUHR
  • ,NBS
  • ,Nijmegen
  • ,ODZH
  • ,TAMPERE
  • ,deCODE
GWAS Catalog: GCST001917
Europe PMC: 23544013
2,727 individualsEuropeanNR
GWAS Catalog: GCST002748
Europe PMC: 25581431
13,491 individualsEuropeanNR
GWAS Catalog: GCST004462
Europe PMC: 28346442
85,426 individualsEuropean95 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
Showing 1 to 6 of 6 rows

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.

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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
PPM000202PSS000121|
European Ancestry|
220,909 individuals
PGP000050 |
Graff RE et al. Nat Commun (2021)
Reported Trait: Ovarian cancerOR: 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
PPM002048PSS001021|
European Ancestry|
211,958 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		Reported Trait: Incident ovarian cancerHR: 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 bi... rth 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 statusShow moreC-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017174PSS010149|
European Ancestry|
315 individuals
PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		Reported Trait: Ovarian cancerHR: 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 covariatesShow more—
Showing 1 to 3 of 3 rows

Evaluated Samples

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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
PSS000121Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 code... s in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 27040Show more—
[
  • 1,261 cases
  • , 219,648 controls
]
,
0.0 % Male samples
—European—GERA, UKB—
PSS001021Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant pri... mary cancer were defined as cases.Show more—
[
  • 445 cases
  • , 211,513 controls
]
,
0.0 % Male samples
—European—UKB—
PSS010149——
[
  • 20 cases
  • , 295 controls
]
,
0.0 % Male samples
—European—UKB—
Showing 1 to 3 of 3 rows
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