Polygenic Score (PGS) ID: PGS002039

Predicted Trait
Reported Trait Other peripheral nerve disorders
Mapped Trait(s) peripheral nervous system disease (EFO_0009387)
Additional Trait Information neurological
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_351
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 799,326
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM011178 PSS009302|
European Ancestry|
19,840 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other peripheral nerve disorders Partial Correlation (partial-r): 0.0728 [0.059, 0.0867] sex, age, birth date, deprivation index, 16 PCs
PPM011179 PSS009076|
European Ancestry|
4,112 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other peripheral nerve disorders Partial Correlation (partial-r): 0.0556 [0.025, 0.0861] sex, age, birth date, deprivation index, 16 PCs
PPM011180 PSS008630|
European Ancestry|
6,611 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other peripheral nerve disorders Partial Correlation (partial-r): 0.0652 [0.0412, 0.0892] sex, age, birth date, deprivation index, 16 PCs
PPM011182 PSS008184|
South Asian Ancestry|
6,277 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other peripheral nerve disorders Partial Correlation (partial-r): 0.0433 [0.0186, 0.068] sex, age, birth date, deprivation index, 16 PCs
PPM011183 PSS007968|
East Asian Ancestry|
1,801 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other peripheral nerve disorders Partial Correlation (partial-r): 0.0229 [-0.0235, 0.0693] sex, age, birth date, deprivation index, 16 PCs
PPM011184 PSS007750|
African Ancestry|
2,471 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other peripheral nerve disorders Partial Correlation (partial-r): 0.0037 [-0.0359, 0.0432] sex, age, birth date, deprivation index, 16 PCs
PPM011185 PSS008854|
African Ancestry|
3,898 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other peripheral nerve disorders Partial Correlation (partial-r): 0.005 [-0.0265, 0.0365] sex, age, birth date, deprivation index, 16 PCs
PPM011181 PSS008404|
Greater Middle Eastern Ancestry|
1,191 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other peripheral nerve disorders Partial Correlation (partial-r): 0.0081 [-0.0492, 0.0654] 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
PSS007750 2,471 individuals African American or Afro-Caribbean Carribean UKB
PSS009076 4,112 individuals European Poland (NE Europe) UKB
PSS008404 1,191 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008630 6,611 individuals European Italy (South Europe) UKB
PSS009302 19,840 individuals European UK (+ Ireland) UKB
PSS008184 6,277 individuals South Asian India (South Asia) UKB
PSS008854 3,898 individuals African unspecified Nigeria (West Africa) UKB
PSS007968 1,801 individuals East Asian China (East Asia) UKB