PGS Catalog - PGS004583 / Platelet count during the second trimester (Polygenic Score)

Polygenic Score (PGS) ID: PGS004583

Predicted Trait
Reported Trait	Platelet count during the second trimester
Mapped Trait(s)	platelet count (EFO_0004309)

Released in PGS Catalog: Jan. 26, 2024

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Score Details

Score Construction
PGS Name	PRSice_T2
Development Method
Name	PRSice-2
Parameters	clump r2 threshold: 0.2, clump-kb: 500kb, p-value threshold: 0.0221001
Variants
Original Genome Build	GRCh38
Number of Variants	104,759
Effect Weight Type	beta

PGS Source
PGS Catalog Publication (PGP) ID	PGP000563
Citation (link to publication)	Yang Z et al. Blood (2023)

Ancestry Distribution
Source of Variant Associations (GWAS)	East Asian: 100% 72,816 individuals (100%)
Score Development/Training	East Asian: 100% 3,167 individuals (100%)
PGS Evaluation	East Asian: 100% 1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
GWAS Catalog: GCST90302225	72,816 individuals, 0.0 % Male samples	East Asian (Chinese)	SZ-MONN-NIPT

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
—	3,167 individuals, 0.0 % Male samples	East Asian (Chinese)	NIPT PLUS	Pregnancy with at least one platelet count measurements in each trimester during pregnancy. If multiple platelet count measurements were available, the earilest platelet count measurements within each trimester was chosen.	—	—	—	5,733 Chinese pregnant women underwent non-invasive prenatal PLUS testing.

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
PPM020698	PSS011370\| East Asian Ancestry\| 878 individuals	PGP000563 \| Yang Z et al. Blood (2023)	Reported Trait: Gestational Thrombocytopenia	—	AUROC: 0.637	R²: 0.035	—	—

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
PSS011370	Pregnancy with at least one platelet count measurements in each trimester during pregnancy. If multiple platelet count measurements were available, the earilest platelet count measurements within each trimester was chosen.	—	878 individuals, 0.0 % Male samples	—	East Asian (Chinese)	—	NIPT PLUS	5,733 Chinese pregnant women underwent non-invasive prenatal PLUS testing.