Predicted Trait | |
Reported Trait | Type 2 diabetes (T2D) |
Mapped Trait(s) | type 2 diabetes mellitus (MONDO_0005148) |
Score Construction | |
PGS Name | ldpred_t2d |
Development Method | |
Name | LDpred |
Parameters | p = 0.003, LD radius = 2000, LD reference panel: European ancestry in 1000 Genomes |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 6,431,973 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000271 |
Citation (link to publication) | Mars N et al. Cell Genom (2022) |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
---|---|---|---|
GWAS Catalog: GCST004773 Europe PMC: 28566273 |
159,208 individuals | European | NR |
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 |
---|---|---|---|---|---|---|---|---|
— | [
|
European (Finnish) |
FinnGen | — | — | — | — | — |
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 |
---|---|---|---|---|---|---|---|---|
PPM012733 | PSS009522| European Ancestry| 258,402 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.58 [1.56, 1.6] | — | — | age, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
PPM012737 | PSS009518| European Ancestry| 110,597 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.55 [1.51, 1.59] | — | — | age, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
PPM012741 | PSS009514| East Asian Ancestry| 178,726 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.37 [1.36, 1.39] | — | — | age, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
PPM012745 | PSS009526| European Ancestry| 69,422 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.64 [1.6, 1.69] | — | — | birth year, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
PPM012749 | PSS009534| European Ancestry| 25,696 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.46 [1.41, 1.51] | — | — | age, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
PPM012753 | PSS009530| African Ancestry| 1,535 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.24 [1.09, 1.42] | — | — | age, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
PPM012757 | PSS009542| European Ancestry| 343,676 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.78 [1.75, 1.81] | — | — | age, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
PPM012762 | PSS009538| African Ancestry| 7,618 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.46 [1.32, 1.62] | — | — | age, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
PPM012767 | PSS009546| South Asian Ancestry| 7,628 individuals |
PGP000271 | Mars N et al. Cell Genom (2022) |
Reported Trait: Type 2 diabetes | OR: 1.66 [1.55, 1.79] | — | — | age, sex, 10 PCs (+/- dataset-specific technical covariates) | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS009534 | — | — | [
|
— | European | — | MGBB | — |
PSS009538 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS009542 | — | — | [
|
— | European | British | UKB | — |
PSS009514 | — | — | [
|
— | East Asian (Japanese) |
— | BBJ | — |
PSS009546 | — | — | [
|
— | South Asian | — | UKB | — |
PSS009518 | — | — | [
|
— | European (Estonian) |
— | EB | — |
PSS009522 | — | — | [
|
— | European (Finnish) |
— | FinnGen | — |
PSS009526 | — | — | [
|
— | European | Norwegian | HUNT | — |
PSS009530 | — | — | [
|
— | African American or Afro-Caribbean | — | MGBB | — |