Polygenic Score (PGS) ID: PGS000327

Predicted Trait
Reported Trait Autism spectrum disorder
Mapped Trait(s) autism spectrum disorder (EFO_0003756)
Released in PGS Catalog: Sept. 18, 2020
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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 ASD2019
Development Method
Name Clumping and Thresholding (C+T)
Parameters Clumping (PLINK -clump-p1 1, -clump-p2 1, -clump-r2 0.1 and -clump-kb 500); p-value threshold = 0.1;...  excluded the MHC-region (chr6:25–35MB); MAF > 0.05; INFO > 0.9Show more
Variants
Original Genome Build GRCh37
Number of Variants 35,087
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000098
Citation (link to publication) Grove J et al. Nat Genet (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
46,350 individuals (100%)
Score Development/Training
European: 100%
28,592 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST007556
Europe PMC: 30804558
46,350 individualsEuropean8 cohorts
  • ACE
  • ,AGP
  • ,AGRE
  • ,MONBOS
  • ,NIMH
  • ,PGC
  • ,SSC
  • ,iPSYCH
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Score Development/Training
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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
GWAS Catalog: GCST007556
Europe PMC: 30804558
[
  • 10,461 cases
  • , 18,131 controls
]
European8 cohorts
  • ACE
  • ,AGP
  • ,AGRE
  • ,MONBOS
  • ,NIMH
  • ,PGC
  • ,SSC
  • ,iPSYCH
Cases were selected from the iPSYCH sample as those diagnosed with ASD in 2013 or earlier by a psych... iatrist according to ICD10, including diagnoses of childhood autism (ICD10 code F84.0), atypical autism (F84.1), Asperger’s syndrome (F84.5), other pervasive developmental disorders (F84.8), and pervasive developmental disorder, unspecified (F84.9). As controls we selected from the random iPSYCH control cohort children that did not have an ASD diagnosis by 2013.Show more———Samples used in the GWAS (PGC and 4/5ths of iPSYCH) were also used to select the optimal C+T parameters
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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.

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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
PPM000879PSS000435|
European Ancestry|
7,148 individuals
PGP000098 |
Grove J et al. Nat Genet (2019)
Reported Trait: Autism spectrum disorderOR: 1.33 [1.3, 1.36]—R²: 0.0245Genetic PCs, genotyping wave*Pooled cross-validation performance on 1/5th of iPSYCH sample. PRS is based on full iPSYCH+PGC GWAS
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Evaluated Samples

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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
PSS000435Cases were selected from the iPSYCH sample as those diagnosed with ASD in 2013 or earlier by a psych... iatrist according to ICD10, including diagnoses of childhood autism (ICD10 code F84.0), atypical autism (F84.1), Asperger’s syndrome (F84.5), other pervasive developmental disorders (F84.8), and pervasive developmental disorder, unspecified (F84.9). As controls we selected from the random iPSYCH control cohort children that did not have an ASD diagnosis by 2013.Show more—
[
  • 2,615 cases
  • , 4,532 controls
]
Mean (Age At Diagnosis) = 10.0 years
Range = [10.0, 14.0] years		European—iPSYCHAverage case/control numbers of each fold used in cross-validation (1/5th of total iPSYCH).
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