PGS Catalog - PGS004585 / Gestational thrombocytopenia (Polygenic Score)

Polygenic Score (PGS) ID: PGS004585

Predicted Trait
Reported Trait	Gestational thrombocytopenia
Mapped Trait(s)	Thrombocytopenia (HP_0001873)

Released in PGS Catalog: Jan. 26, 2024

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Score Details

Score Construction
PGS Name	PRSice_GT
Development Method
Name	PRSice-2
Parameters	clump r2 threshold: 0.2, clump-kb: 500kb, p-value threshold: 0.14
Variants
Original Genome Build	GRCh38
Number of Variants	475,029
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% 96,432 individuals (100%)
Score Development/Training	East Asian: 100% 3,341 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: GCST90302234	96,432 individuals [ 11,138 cases , 85,294 controls ] , 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
—	3,341 individuals [ 344 cases , 2,997 controls ] , 0.0 % Male samples	East Asian (Chinese)	NIPT PLUS	Pregnancy has at least one platelet count less than 150×109/L in the second or third trimester of pregnancy. Pregnancies complicated by preeclampsia, HELLP syndrome (hemolysis, elevated liver enzymes, and low platelet count), primary immune thrombocytopenia, HIV infection, hepatitis B virus, and hepatitis C virus infection or with one or more platelet count less than 50×109/L during pregnancy were excluded.	—	—	—	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
PPM020700	PSS011368\| East Asian Ancestry\| 936 individuals	PGP000563 \| Yang Z et al. Blood (2023)	Reported Trait: Gestational Thrombocytopenia	—	AUROC: 0.636	R²: 0.04	—	—

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
PSS011368	Pregnancy has at least one platelet count less than 150×109/L in the second or third trimester of pregnancy. Pregnancies complicated by preeclampsia, HELLP syndrome (hemolysis, elevated liver enzymes, and low platelet count), primary immune thrombocytopenia, HIV infection, hepatitis B virus, and hepatitis C virus infection or with one or more platelet count less than 50×109/L during pregnancy were excluded.	—	936 individuals [ 97 cases , 839 controls ] , 0.0 % Male samples	—	East Asian (Chinese)	—	NIPT PLUS	5,733 Chinese pregnant women underwent non-invasive prenatal PLUS testing.