Trait: benign prostatic hyperplasia

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000284
Description A non-cancerous nodular enlargement of the prostate gland. It is characterized by the presence of epithelial cell nodules, and stromal nodules containing fibrous and smooth muscle elements. It is the most common urologic disorder in men, causing blockage of urine flow. [NCIT: C2897]
Trait category
Other disease
Synonyms 52 synonyms
  • Adenofibromatous hypertrophy of prostate
  • Adenofibromatous hypertrophy of prostate, NOS
  • Adenoma, Prostatic
  • Adenomas, Prostatic
  • Adenomyomatous hyperplasia of prostate gland
  • BEP - Benign enlargement of prostate
  • BPH
  • BPH - Benign prostatic hypertrophy
  • Benign Hyperplasia of Prostate
  • Benign Hyperplasia of the Prostate
  • Benign Prostate Hyperplasia
  • Benign Prostatic Hyperplasia - BPH
  • Benign adenoma of prostate
  • Benign enlargement of prostate
  • Benign enlargement of prostate, NOS
  • Benign fibroma of prostate
  • Benign myoma of prostate
  • Benign prostatic hyperplasia (disorder)
  • Benign prostatic hyperplasia, NOS
  • Enlarged prostate - benign
  • Fibromuscular hyperplasia of prostate gland
  • Glandular, stromal AND/OR muscular hyperplasia of prostate gland
  • Glandular, stromal and muscular hyperplasia of prostate gland
  • Hyperplasia of prostate
  • Hyperplasia of prostate (disorder)
  • Hyperplasia of prostate, NOS
  • Hyperplasia, Prostatic
  • Hypertrophy (benign) of prostate
  • Hypertrophy, Benign Prostatic
  • Lobular hyperplasia of prostate gland
  • Nodular hyperplasia of prostate gland
  • Prostatauxe
  • Prostatic Adenoma
  • Prostatic Adenomas
  • Prostatic Hyperplasia
  • Prostatic Hyperplasia, Benign
  • Prostatic Hypertrophy, Benign
  • Prostatic area hypertrophy
  • Prostatic hyper -benign
  • Prostatic hypertrophy
  • benign hyperplasia of prostate
  • benign hyperplasia of the prostate
  • benign hypertrophy of prostate NOS
  • benign prostate hyperplasia
  • benign prostatic Hypertrophy
  • benign prostatic hyperplasia
  • benign prostatic hyperplasia (disease)
  • benign prostatic hyperplasia - BPH
  • benign prostatic hypertrophy
  • prostate hypertrophy
  • prostatic hyperplasia, benign
  • prostatic hypertrophy
Mapped terms 18 mapped terms
  • DOID:11132
  • DOID:2883
  • HP:0008711
  • ICD10:N40
  • ICD9:600
  • ICD9:600.0
  • ICD9:600.20
  • MEDGEN:312369
  • MESH:D011470
  • MONDO:0010811
  • MeSH:D011470
  • MedDRA:10004446
  • NCIT:C2897
  • NCIt:C2897
  • OMIM:600082
  • SCTID:266569009
  • SNOMEDCT:266569009
  • UMLS:C1704272

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
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)
PGS001338
(GBE_HC1322)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Hyperplasia of prostate (time-to-event) benign prostatic hyperplasia 1,223
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001338/ScoringFiles/PGS001338.txt.gz
PGS001865
(portability-PLR_600)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Hyperplasia of prostate benign prostatic hyperplasia 1,712
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001865/ScoringFiles/PGS001865.txt.gz
PGS002076
(portability-ldpred2_600)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Hyperplasia of prostate benign prostatic hyperplasia 627,341
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002076/ScoringFiles/PGS002076.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
PPM009176 PGS001338
(GBE_HC1322)
 PSS004258|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE hyperplasia of prostate — AUROC: 0.91126 [0.89869, 0.92382] R²: 0.34787
Incremental AUROC (full-covars): 0.00071
PGS R2 (no covariates): 0.00242
PGS AUROC (no covariates): 0.53731 [0.49821, 0.57641]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009177 PGS001338
(GBE_HC1322)
 PSS004259|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE hyperplasia of prostate — AUROC: 0.94551 [0.92698, 0.96403] R²: 0.41698
Incremental AUROC (full-covars): 0.00046
PGS R2 (no covariates): 0.00828
PGS AUROC (no covariates): 0.58436 [0.49628, 0.67245]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009178 PGS001338
(GBE_HC1322)
 PSS004260|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE hyperplasia of prostate — AUROC: 0.89905 [0.89319, 0.90491] R²: 0.34121
Incremental AUROC (full-covars): 0.00211
PGS R2 (no covariates): 0.00524
PGS AUROC (no covariates): 0.55441 [0.53657, 0.57225]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009179 PGS001338
(GBE_HC1322)
 PSS004261|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE hyperplasia of prostate — AUROC: 0.87601 [0.86407, 0.88795] R²: 0.30354
Incremental AUROC (full-covars): 0.00252
PGS R2 (no covariates): 0.00385
PGS AUROC (no covariates): 0.54159 [0.51313, 0.57004]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009180 PGS001338
(GBE_HC1322)
 PSS004262|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE hyperplasia of prostate — AUROC: 0.88092 [0.87739, 0.88444] R²: 0.32433
Incremental AUROC (full-covars): 0.00471
PGS R2 (no covariates): 0.0067
PGS AUROC (no covariates): 0.55724 [0.54752, 0.56697]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009809 PGS001865
(portability-PLR_600)
 PSS009340|
European Ancestry|
8,710 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0846 [0.0636, 0.1054] sex, age, birth date, deprivation index, 16 PCs —
PPM009810 PGS001865
(portability-PLR_600)
 PSS009114|
European Ancestry|
1,493 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.1233 [0.0727, 0.1733] sex, age, birth date, deprivation index, 16 PCs —
PPM009811 PGS001865
(portability-PLR_600)
 PSS008668|
European Ancestry|
2,859 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0911 [0.0545, 0.1275] sex, age, birth date, deprivation index, 16 PCs —
PPM009812 PGS001865
(portability-PLR_600)
 PSS008442|
Greater Middle Eastern Ancestry|
696 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0715 [-0.0039, 0.146] sex, age, birth date, deprivation index, 16 PCs —
PPM009814 PGS001865
(portability-PLR_600)
 PSS008003|
East Asian Ancestry|
586 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0651 [-0.0173, 0.1467] sex, age, birth date, deprivation index, 16 PCs —
PPM009815 PGS001865
(portability-PLR_600)
 PSS007787|
African Ancestry|
827 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.1134 [0.0448, 0.1809] sex, age, birth date, deprivation index, 16 PCs —
PPM009816 PGS001865
(portability-PLR_600)
 PSS008891|
African Ancestry|
1,703 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0524 [0.0046, 0.0999] sex, age, birth date, deprivation index, 16 PCs —
PPM009813 PGS001865
(portability-PLR_600)
 PSS008222|
South Asian Ancestry|
3,344 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0339 sex, age, birth date, deprivation index, 16 PCs —
PPM011469 PGS002076
(portability-ldpred2_600)
 PSS009340|
European Ancestry|
8,710 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0856 [0.0647, 0.1065] sex, age, birth date, deprivation index, 16 PCs —
PPM011470 PGS002076
(portability-ldpred2_600)
 PSS009114|
European Ancestry|
1,493 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.1369 [0.0864, 0.1866] sex, age, birth date, deprivation index, 16 PCs —
PPM011471 PGS002076
(portability-ldpred2_600)
 PSS008668|
European Ancestry|
2,859 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.1059 [0.0694, 0.1421] sex, age, birth date, deprivation index, 16 PCs —
PPM011472 PGS002076
(portability-ldpred2_600)
 PSS008442|
Greater Middle Eastern Ancestry|
696 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0928 [0.0175, 0.1669] sex, age, birth date, deprivation index, 16 PCs —
PPM011473 PGS002076
(portability-ldpred2_600)
 PSS008222|
South Asian Ancestry|
3,344 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0415 [0.0075, 0.0754] sex, age, birth date, deprivation index, 16 PCs —
PPM011474 PGS002076
(portability-ldpred2_600)
 PSS008003|
East Asian Ancestry|
586 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.071 [-0.0114, 0.1525] sex, age, birth date, deprivation index, 16 PCs —
PPM011475 PGS002076
(portability-ldpred2_600)
 PSS007787|
African Ancestry|
827 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.1389 [0.0706, 0.2059] sex, age, birth date, deprivation index, 16 PCs —
PPM011476 PGS002076
(portability-ldpred2_600)
 PSS008891|
African Ancestry|
1,703 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0775 [0.0299, 0.1248] sex, age, birth date, deprivation index, 16 PCs —

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
PSS004258 — —
[
  • 224 cases
  • , 6,273 controls
]
 — African unspecified — UKB —
PSS004259 — —
[
  • 43 cases
  • , 1,661 controls
]
 — East Asian — UKB —
PSS004260 — —
[
  • 1,093 cases
  • , 23,812 controls
]
 — European non-white British ancestry UKB —
PSS004261 — —
[
  • 408 cases
  • , 7,423 controls
]
 — South Asian — UKB —
PSS004262 — —
[
  • 3,588 cases
  • , 63,837 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS008668 — — 2,859 individuals — European Italy (South Europe) UKB —
PSS007787 — — 827 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008891 — — 1,703 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009114 — — 1,493 individuals — European Poland (NE Europe) UKB —
PSS008442 — — 696 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009340 — — 8,710 individuals — European UK (+ Ireland) UKB —
PSS008222 — — 3,344 individuals — South Asian India (South Asia) UKB —
PSS008003 — — 586 individuals — East Asian China (East Asia) UKB —