PGS Catalog - PGS003402 / Type 2 diabetes (T2D) (Polygenic Score)

Polygenic Score (PGS) ID: PGS003402

Predicted Trait
Reported Trait	Type 2 diabetes (T2D)
Mapped Trait(s)	type 2 diabetes mellitus (MONDO_0005148)

Released in PGS Catalog: Jan. 19, 2023

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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	PRS_T2D
Development Method
Name	LDpred2
Parameters	p ≤0.0014, h2=0.08
Variants
Original Genome Build	NR
Number of Variants	6,838
Effect Weight Type	log(OR)

PGS Source
PGS Catalog Publication (PGP) ID	PGP000419
Citation (link to publication)	Lamri A et al. Elife (2022)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 62.5% South Asian: 18.1% East Asian: 17% Hispanic or Latin American: 2.3% 110,452 individuals (100%)
Score Development/Training	South Asian: 100% 1,590 individuals (100%)
PGS Evaluation	South Asian: 100% 1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
GWAS Catalog: GCST002352 Europe PMC: 24509480	69,033 individuals	European	NR
GWAS Catalog: GCST002352 Europe PMC: 24509480	18,817 individuals	East Asian	NR
GWAS Catalog: GCST002352 Europe PMC: 24509480	20,019 individuals	South Asian	NR
GWAS Catalog: GCST002352 Europe PMC: 24509480	2,583 individuals	Hispanic or Latin American	NR

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
—	1,590 individuals [ 220 cases , 1,370 controls ] , 0.0 % Male samples	South Asian	BiB, START	—	—	—	—	30% validation set from each cohort

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
PPM017036	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: Fasting glucose x BMI interaction	β: 89.0	—	—	age, BMI, education level, birth region (South Asia vs. other), parity, parental history of diabetes, and genetic PC axes 1-5	—
PPM017037	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: Fasting glucose x Born in South Asia interaction	β: 84.0	—	—	age, BMI, education level, birth region (South Asia vs. other), parity, parental history of diabetes, and genetic PC axes 1-5	—
PPM017038	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: Fasting glucose x Low diet quality interaction (only in START cohort)	β: 0.141 [0.053, 0.228]	—	—	age, BMI, education level, birth region (South Asia vs. other), parity, parental history of diabetes, and genetic PC axes 1-5	—
PPM017039	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: AUC glucose x BMI interaction	β: 77.0	—	—	age, BMI, education level, birth region (South Asia vs. other), parity, parental history of diabetes, and genetic PC axes 1-5	—
PPM017040	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: GDM (IADPSG criteria) x BMI interaction	OR: 0.0	—	—	age, BMI, education level, birth region (South Asia vs. other), parity, parental history of diabetes, and genetic PC axes 1-5	—
PPM017032	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: Fasting glucose	β: 0.085 [0.067, 0.103]	—	—	first five principal components (PCs)	—
PPM017033	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: 2h postload glucose	β: 0.207 [0.157, 0.257]	—	—	first five principal components (PCs)	—
PPM017034	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: AUC glucose	β: 0.155 [0.125, 0.184]	—	—	first five principal components (PCs)	—
PPM017035	PSS010101\| South Asian Ancestry\| 3,712 individuals	PGP000419 \| Lamri A et al. Elife (2022)	Reported Trait: GDM (IADPSG criteria)	OR: 1.45 [1.32, 1.6]	—	—	first five principal components (PCs)	—

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
PSS010101	—	—	3,712 individuals [ 514 cases , 3,198 controls ] , 0.0 % Male samples	—	South Asian	—	BiB, START	70% validation set from each cohort