Polygenic Score (PGS) ID: PGS000327

Predicted Trait
Reported Trait Autism spectrum disorder
Mapped Trait(s) autism spectrum disorder (EFO_0003756)
Released in PGS: Sept. 18, 2020
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Score Details

Score Construction
PGS Name ASD2019
Variants
Original Genome Build GRCh37
Number of Variants 35,087
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 > 0.9
PGS Source
PGS Catalog Publication (PGP) ID PGP000098
Citation (link to publication) Grove J et al. Nat Genet (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST007556
EuropePMC: 30804558
46,350 individuals European
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
Cases were selected from the iPSYCH sample as those diagnosed with ASD in 2013 or earlier by a psychiatrist 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.
[
  • 10,461 cases
  • , 18,131 controls
]
European 8 cohorts
  • ACE
  • ,AGP
  • ,AGRE
  • ,MONBOS
  • ,NIMH
  • ,PGC
  • ,SSC
  • ,iPSYCH
Samples used in the GWAS (PGC and 4/5ths of iPSYCH) were also used to select the optimal C+T parameters

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000879 PSS000435 PGP000098
Grove J et al. (2019)
Reported Trait: Autism spectrum disorder OR: 1.33[1.3, 1.36] : 0.0245 Genetic PCs, genotyping wave *Pooled cross-validation performance on 1/5th of iPSYCH sample. PRS is based on full iPSYCH+PGC GWAS

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000435 Cases were selected from the iPSYCH sample as those diagnosed with ASD in 2013 or earlier by a psychiatrist 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.
[
  • 2,615 cases
  • , 4,532 controls
]
Mean (Age At Diagnosis) = 10.0 years
Range = [10.0, 14.0] years
European iPSYCH Average case/control numbers of each fold used in cross-validation (1/5th of total iPSYCH).