Trait Information | |
Identifier | MONDO_0019338 |
Description | Sarcoidosis is a multisystemic disorder of unknown cause characterized by the formation of immune granulomas in involved organs. [Orphanet: 797] | Trait category |
Other disease
|
Synonyms |
12 synonyms
|
Mapped terms |
13 mapped terms
|
Child trait(s) | skin sarcoidosis |
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000922 (GBE_HC170) |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Sarcoidosis | sarcoidosis | 12 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000922/ScoringFiles/PGS000922.txt.gz |
PGS000923 (GBE_HC639) |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Sarcoidosis (time-to-event) | sarcoidosis | 22 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000923/ScoringFiles/PGS000923.txt.gz |
PGS001872 (portability-PLR_697) |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Sarcoidosis | skin sarcoidosis | 79 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001872/ScoringFiles/PGS001872.txt.gz |
PGS002084 (portability-ldpred2_697) |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Sarcoidosis | skin sarcoidosis | 403,417 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002084/ScoringFiles/PGS002084.txt.gz |
PGS Performance Metric ID (PPM) |
Evaluated Score |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM007440 | PGS000922 (GBE_HC170) |
PSS004322| African Ancestry| 6,497 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Sarcoidosis | — | AUROC: 0.70759 [0.63998, 0.7752] | PGS R2 (no covariates): 0.02057 R²: 0.05219 Incremental AUROC (full-covars): 0.03111 PGS AUROC (no covariates): 0.64298 [0.57429, 0.71167] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007441 | PGS000922 (GBE_HC170) |
PSS004323| European Ancestry| 24,905 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Sarcoidosis | — | AUROC: 0.67662 [0.6145, 0.73874] | R²: 0.03062 Incremental AUROC (full-covars): 0.02209 PGS R2 (no covariates): 0.00799 PGS AUROC (no covariates): 0.60582 [0.54774, 0.66391] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007442 | PGS000922 (GBE_HC170) |
PSS004324| South Asian Ancestry| 7,831 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Sarcoidosis | — | AUROC: 0.66108 [0.58927, 0.7329] | R²: 0.03112 Incremental AUROC (full-covars): 0.00713 PGS R2 (no covariates): 0.00089 PGS AUROC (no covariates): 0.52621 [0.44905, 0.60338] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007443 | PGS000922 (GBE_HC170) |
PSS004325| European Ancestry| 67,425 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Sarcoidosis | — | AUROC: 0.6486 [0.60932, 0.68789] | R²: 0.01916 Incremental AUROC (full-covars): 0.09187 PGS R2 (no covariates): 0.01741 PGS AUROC (no covariates): 0.64282 [0.60353, 0.68211] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007444 | PGS000923 (GBE_HC639) |
PSS004551| African Ancestry| 6,497 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE sarcoidosis | — | AUROC: 0.70171 [0.64012, 0.7633] | R²: 0.05018 Incremental AUROC (full-covars): 0.03514 PGS R2 (no covariates): 0.02657 PGS AUROC (no covariates): 0.66456 [0.60597, 0.72315] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007445 | PGS000923 (GBE_HC639) |
PSS004552| European Ancestry| 24,905 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE sarcoidosis | — | AUROC: 0.67371 [0.61511, 0.7323] | R²: 0.02923 Incremental AUROC (full-covars): 0.00926 PGS R2 (no covariates): 0.00429 PGS AUROC (no covariates): 0.58898 [0.53125, 0.64671] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007446 | PGS000923 (GBE_HC639) |
PSS004553| South Asian Ancestry| 7,831 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE sarcoidosis | — | AUROC: 0.67148 [0.61146, 0.73151] | R²: 0.0372 Incremental AUROC (full-covars): 0.00677 PGS R2 (no covariates): 0.00103 PGS AUROC (no covariates): 0.52237 [0.45814, 0.58661] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007447 | PGS000923 (GBE_HC639) |
PSS004554| European Ancestry| 67,425 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE sarcoidosis | — | AUROC: 0.65455 [0.6217, 0.6874] | R²: 0.02088 Incremental AUROC (full-covars): 0.09004 PGS R2 (no covariates): 0.018 PGS AUROC (no covariates): 0.64561 [0.61168, 0.67954] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009865 | PGS001872 (portability-PLR_697) |
PSS009348| European Ancestry| 19,670 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0199 [0.0059, 0.0338] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM009866 | PGS001872 (portability-PLR_697) |
PSS009122| European Ancestry| 4,059 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0123 [-0.0186, 0.0431] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM009867 | PGS001872 (portability-PLR_697) |
PSS008676| European Ancestry| 6,565 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0166 [-0.0076, 0.0408] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM009868 | PGS001872 (portability-PLR_697) |
PSS008450| Greater Middle Eastern Ancestry| 1,186 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0554 [-0.002, 0.1124] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM009869 | PGS001872 (portability-PLR_697) |
PSS008230| South Asian Ancestry| 6,194 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.018 [-0.0069, 0.0429] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM009871 | PGS001872 (portability-PLR_697) |
PSS008899| African Ancestry| 3,882 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0332 [0.0017, 0.0647] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM009870 | PGS001872 (portability-PLR_697) |
PSS007795| African Ancestry| 2,441 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0157 [-0.0242, 0.0555] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM011533 | PGS002084 (portability-ldpred2_697) |
PSS009348| European Ancestry| 19,670 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0184 [0.0044, 0.0324] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM011534 | PGS002084 (portability-ldpred2_697) |
PSS009122| European Ancestry| 4,059 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0038 [-0.0271, 0.0346] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM011535 | PGS002084 (portability-ldpred2_697) |
PSS008676| European Ancestry| 6,565 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0103 [-0.0139, 0.0345] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM011536 | PGS002084 (portability-ldpred2_697) |
PSS008450| Greater Middle Eastern Ancestry| 1,186 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0603 [0.0029, 0.1173] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM011537 | PGS002084 (portability-ldpred2_697) |
PSS008230| South Asian Ancestry| 6,194 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0182 [-0.0067, 0.0432] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM011538 | PGS002084 (portability-ldpred2_697) |
PSS007795| African Ancestry| 2,441 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0131 [-0.0268, 0.0529] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM011539 | PGS002084 (portability-ldpred2_697) |
PSS008899| African Ancestry| 3,882 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Sarcoidosis | — | — | Partial Correlation (partial-r): 0.0187 [-0.0128, 0.0502] | sex, age, birth date, deprivation index, 16 PCs | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS009348 | — | — | 19,670 individuals | — | European | UK (+ Ireland) | UKB | — |
PSS008676 | — | — | 6,565 individuals | — | European | Italy (South Europe) | UKB | — |
PSS008450 | — | — | 1,186 individuals | — | Greater Middle Eastern (Middle Eastern, North African or Persian) | Iran (Middle East) | UKB | — |
PSS008230 | — | — | 6,194 individuals | — | South Asian | India (South Asia) | UKB | — |
PSS004322 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS004323 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS004324 | — | — | [
|
— | South Asian | — | UKB | — |
PSS004325 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS004551 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS004552 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS004553 | — | — | [
|
— | South Asian | — | UKB | — |
PSS004554 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS007795 | — | — | 2,441 individuals | — | African American or Afro-Caribbean | Carribean | UKB | — |
PSS009122 | — | — | 4,059 individuals | — | European | Poland (NE Europe) | UKB | — |
PSS008899 | — | — | 3,882 individuals | — | African unspecified | Nigeria (West Africa) | UKB | — |