Polygenic Score (PGS) ID: PGS002266

Predicted Trait
Reported Trait Nonsyndromic cleft lip with or without cleft palate
Mapped Trait(s)
Released in PGS Catalog: March 16, 2022
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Score Details

Score Construction
PGS Name PRS_29
Development Method
Name Genome-wide significant variants
Parameters p<5E-08, bonferroni corrected p<0.05
Variants
Original Genome Build GRCh37
Number of Variants 29
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000295
Citation (link to publication) Yu Y et al. Hum Mol Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 59.8%
Additional Asian Ancestries: 20.7%
Multi-ancestry (excluding European): 10.3%
  • Hispanic or Latin American
  • African
Not Reported: 5.1%
Hispanic or Latin American: 3.5%
African: 0.6%
30,822 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001628
Europe PMC: 22863734
 3,715 individuals European Bonn
Europe PMC: 26968009
[
  • 399 cases
  • , 1,318 controls
]
 European
(Central European)		 Bonn
GWAS Catalog: GCST004050
Europe PMC: 28054174
 3,969 individuals European NR
GWAS Catalog: GCST004050
Europe PMC: 28054174
 3,161 individuals Hispanic or Latin American, African unspecified NR
GWAS Catalog: GCST004050
Europe PMC: 28054174
 3,763 individuals Asian unspecified NR
GWAS Catalog: GCST004050
Europe PMC: 28054174
 63 individuals Not reported NR
Europe PMC: 27033726
[
  • 170 cases
  • , 835 controls
]
 European NR
Europe PMC: 27033726
[
  • 449 cases
  • , 626 controls
]
 Hispanic or Latin American
(Central/South American)		 NR
Europe PMC: 27033726
[
  • 83 cases
  • , 161 controls
]
 Asian unspecified NR
Europe PMC: 27033726
[
  • 121 cases
  • , 74 controls
]
 African unspecified NR
GWAS Catalog: GCST000547
Europe PMC: 20023658
 1,717 individuals European NR
Europe PMC: 31172578
[
  • 901 cases
  • , 1,700 controls
]
 European NR
Europe PMC: 31817908
[
  • 285 cases
  • , 1,212 controls
]
 Not reported NR
GWAS Catalog: GCST004088
Europe PMC: 28087736
 3,715 individuals European NR
GWAS Catalog: GCST004088
Europe PMC: 28087736
 2,385 individuals Asian unspecified NR

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
PPM012907 PSS009607|
European Ancestry|
72,542 individuals
 PGP000295 |
Yu Y et al. Hum Mol Genet (2022)
 Reported Trait: Nonsyndromic cleft lip with or without cleft palate — AUROC: 0.66 — — —

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
PSS009607 cases diagnosed with cleft lip and palate or cleft lip, unspecified cleft type —
[
  • 46 cases
  • , 72,496 controls
]
 — European
(Non-Hispanic European)		 — BioVU —