Trait: medical procedure

Experimental Factor Ontology (EFO) Information
Identifier EFO_0002571
Description An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects.
Trait category
Other trait
Synonyms 7 synonyms
  • Intervention
  • Intervention Strategies
  • Intervention or Procedure
  • Interventional
  • Procedure
  • SURGICAL AND MEDICAL PROCEDURES
  • interventionDescription
Mapped terms 4 mapped terms
  • ICD10:Z41
  • NCIt:C25218
  • NCIt:C79751
  • SNOMEDCT:50731006
Child trait(s) 4 child traits

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
Note: This table shows all PGS for "medical procedure" and any child terms of this trait in the EFO hierarchy by default.
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)
PGS000995
(GBE_BIN_FC6006149)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Dentures dentures 6,042
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000995/ScoringFiles/PGS000995.txt.gz
PGS001786
(1kgeur_gbmi_leaveUKBBout_Appendectomy_pst_eff_a1_b0.5_phiauto)
 PGP000262 |
Wang Y et al. Cell Genom (2023)
 Appendectomy appendectomy 899,660
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001786/ScoringFiles/PGS001786.txt.gz
PGS002749
(PRS10_TKR)
 PGP000362 |
Lacaze P et al. Arthritis Rheumatol (2022)
 Total knee replacement osteoarthritis, knee,
total knee arthroplasty		 10
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002749/ScoringFiles/PGS002749.txt.gz
PGS002750
(PRS37_THR)
 PGP000362 |
Lacaze P et al. Arthritis Rheumatol (2022)
 Total hip replacement total hip arthroplasty,
osteoarthritis, hip		 37
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002750/ScoringFiles/PGS002750.txt.gz
PGS004507
(disease.Z95.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Z95 (Presence of cardiac and vascular implants and grafts) medical procedure 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004507/ScoringFiles/PGS004507.txt.gz
PGS004508
(disease.Z96.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Z96 (Presence of other functional implants) medical procedure 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004508/ScoringFiles/PGS004508.txt.gz
PGS004577
(meta.Z95.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Z95 (Presence of cardiac and vascular implants and grafts) medical procedure 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004577/ScoringFiles/PGS004577.txt.gz
PGS004578
(meta.Z96.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Z96 (Presence of other functional implants) medical procedure 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004578/ScoringFiles/PGS004578.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
PPM007738 PGS000995
(GBE_BIN_FC6006149)
 PSS003989|
African Ancestry|
6,343 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.73289 [0.71604, 0.74974] R²: 0.16329
Incremental AUROC (full-covars): -0.00229
PGS R2 (no covariates): 0.00043
PGS AUROC (no covariates): 0.51216 [0.49281, 0.53151]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007739 PGS000995
(GBE_BIN_FC6006149)
 PSS003990|
East Asian Ancestry|
1,639 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.72417 [0.69434, 0.75399] R²: 0.15399
Incremental AUROC (full-covars): 0.00318
PGS R2 (no covariates): 0.01291
PGS AUROC (no covariates): 0.56189 [0.52824, 0.59554]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007740 PGS000995
(GBE_BIN_FC6006149)
 PSS003991|
European Ancestry|
24,793 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.75891 [0.7509, 0.76692] R²: 0.19117
Incremental AUROC (full-covars): 0.00459
PGS R2 (no covariates): 0.01565
PGS AUROC (no covariates): 0.57525 [0.56558, 0.58491]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007741 PGS000995
(GBE_BIN_FC6006149)
 PSS003992|
South Asian Ancestry|
7,528 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.72384 [0.70578, 0.74191] R²: 0.12209
Incremental AUROC (full-covars): -0.00241
PGS R2 (no covariates): 0.00154
PGS AUROC (no covariates): 0.52294 [0.50172, 0.54417]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007742 PGS000995
(GBE_BIN_FC6006149)
 PSS003993|
European Ancestry|
67,277 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Dentures — AUROC: 0.72652 [0.72179, 0.73124] R²: 0.15104
Incremental AUROC (full-covars): 0.00704
PGS R2 (no covariates): 0.01052
PGS AUROC (no covariates): 0.55906 [0.55338, 0.56474]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009290 PGS001786
(1kgeur_gbmi_leaveUKBBout_Appendectomy_pst_eff_a1_b0.5_phiauto)
 PSS007709|
European Ancestry|
357,112 individuals
 PGP000262 |
Wang Y et al. Cell Genom (2023)
 Reported Trait: Appendectomy — AUROC: 0.574 Nagelkerke's R2 (covariates regressed out): 0.00175 sex,age,age2,age*sex,age^2*sex, 20PCs —
PPM014939 PGS002749
(PRS10_TKR)
 PSS009936|
European Ancestry|
1,422 individuals
 PGP000362 |
Lacaze P et al. Arthritis Rheumatol (2022)
 Reported Trait: Knee replacement OR: 1.13 [1.07, 1.2] — — Age, sex, body mass index, education, and index of relative socioeconomic advantage and disadvantage —
PPM014940 PGS002750
(PRS37_THR)
 PSS009935|
European Ancestry|
1,257 individuals
 PGP000362 |
Lacaze P et al. Arthritis Rheumatol (2022)
 Reported Trait: Hip replacement OR: 1.23 [1.16, 1.3] — — Age, sex, body mass index, education, and index of relative socioeconomic advantage and disadvantage —
PPM014941 PGS002750
(PRS37_THR)
 PSS009935|
European Ancestry|
1,257 individuals
 PGP000362 |
Lacaze P et al. Arthritis Rheumatol (2022)
 Reported Trait: Hip replacement in men OR: 1.15 [1.06, 1.26] — — Age, body mass index, education, and index of relative socioeconomic advantage and disadvantage —
PPM014942 PGS002750
(PRS37_THR)
 PSS009935|
European Ancestry|
1,257 individuals
 PGP000362 |
Lacaze P et al. Arthritis Rheumatol (2022)
 Reported Trait: Hip replacement in women OR: 1.3 [1.2, 1.4] — — Age, body mass index, education, and index of relative socioeconomic advantage and disadvantage —
PPM020622 PGS004507
(disease.Z95.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: Z95 (Presence of cardiac and vascular implants and grafts) OR: 1.22068 — — — —
PPM020623 PGS004508
(disease.Z96.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: Z96 (Presence of other functional implants) OR: 1.14042 — — — —
PPM020692 PGS004577
(meta.Z95.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: Z95 (Presence of cardiac and vascular implants and grafts) OR: 1.29829 — — — —
PPM020693 PGS004578
(meta.Z96.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: Z96 (Presence of other functional implants) OR: 1.11875 — — — —

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
PSS011364 — — 56,192 individuals — European — UKB —
PSS009936 — — 1,422 individuals — European — ASPREE —
PSS007709 — —
[
  • 2,173 cases
  • , 354,938 controls
]
 — European — UKB —
PSS009935 — — 1,257 individuals — European — ASPREE —
PSS003989 — —
[
  • 1,042 cases
  • , 5,301 controls
]
 — African unspecified — UKB —
PSS003990 — —
[
  • 340 cases
  • , 1,299 controls
]
 — East Asian — UKB —
PSS003991 — —
[
  • 3,977 cases
  • , 20,816 controls
]
 — European non-white British ancestry UKB —
PSS003992 — —
[
  • 812 cases
  • , 6,716 controls
]
 — South Asian — UKB —
PSS003993 — —
[
  • 11,773 cases
  • , 55,504 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)