Polygenic Score (PGS) ID: PGS001879

Predicted Trait
Reported Trait Ganglion and cyst of synovium, tendon, and bursa
Mapped Trait(s) ganglion or cyst of synovium/tendon/bursa (MONDO_0004874)
Additional Trait Information musculoskeletal
Released in PGS Catalog: Jan. 10, 2022
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 portability-PLR_727.4
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 210
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM009917 PSS009356|
European Ancestry|
18,953 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ganglion and cyst of synovium, tendon, and bursa — — Partial Correlation (partial-r): 0.0188 [0.0046, 0.033] sex, age, birth date, deprivation index, 16 PCs —
PPM009918 PSS009130|
European Ancestry|
3,909 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ganglion and cyst of synovium, tendon, and bursa — — Partial Correlation (partial-r): -0.0022 [-0.0337, 0.0292] sex, age, birth date, deprivation index, 16 PCs —
PPM009919 PSS008684|
European Ancestry|
6,366 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ganglion and cyst of synovium, tendon, and bursa — — Partial Correlation (partial-r): -0.0003 [-0.0249, 0.0243] sex, age, birth date, deprivation index, 16 PCs —
PPM009920 PSS008458|
Greater Middle Eastern Ancestry|
1,137 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ganglion and cyst of synovium, tendon, and bursa — — Partial Correlation (partial-r): -0.0036 [-0.0623, 0.0551] sex, age, birth date, deprivation index, 16 PCs —
PPM009921 PSS008238|
South Asian Ancestry|
5,964 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ganglion and cyst of synovium, tendon, and bursa — — Partial Correlation (partial-r): 0.0056 [-0.0198, 0.031] sex, age, birth date, deprivation index, 16 PCs —
PPM009922 PSS008017|
East Asian Ancestry|
1,759 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ganglion and cyst of synovium, tendon, and bursa — — Partial Correlation (partial-r): -0.0128 [-0.0598, 0.0342] sex, age, birth date, deprivation index, 16 PCs —
PPM009923 PSS007802|
African Ancestry|
2,358 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ganglion and cyst of synovium, tendon, and bursa — — Partial Correlation (partial-r): -0.0261 [-0.0666, 0.0144] sex, age, birth date, deprivation index, 16 PCs —
PPM009924 PSS008906|
African Ancestry|
3,779 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ganglion and cyst of synovium, tendon, and bursa — — Partial Correlation (partial-r): 0.0184 [-0.0135, 0.0504] 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
PSS008458 — — 1,137 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009130 — — 3,909 individuals — European Poland (NE Europe) UKB —
PSS009356 — — 18,953 individuals — European UK (+ Ireland) UKB —
PSS008684 — — 6,366 individuals — European Italy (South Europe) UKB —
PSS008238 — — 5,964 individuals — South Asian India (South Asia) UKB —
PSS008906 — — 3,779 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008017 — — 1,759 individuals — East Asian China (East Asia) UKB —
PSS007802 — — 2,358 individuals — African American or Afro-Caribbean Carribean UKB —