Trait: age at diagnosis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004918
Description The age, measured from some defined time point e.g. birth at which a subject (e.g. a human patient) is diagnosed with some disease e.g. breast cancer.
Trait category
Other measurement
Mapped term SNOMEDCT:423493009

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000935
(GBE_INI2966)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
High blood pressure, age at diagnosis age at diagnosis,
Increased blood pressure
370
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000935/ScoringFiles/PGS000935.txt.gz
PGS001371
(GBE_INI2976)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Age diabetes diagnosed diabetes mellitus,
age at diagnosis
26
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001371/ScoringFiles/PGS001371.txt.gz

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)
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
PPM007034 PGS001371
(GBE_INI2976)
PSS006890|
European Ancestry|
3,195 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.28031 [0.27455, 0.28606]
Incremental R2 (full-covars): 0.02294
PGS R2 (no covariates): 0.03923 [0.03636, 0.0421]
age, sex, UKB array type, Genotype PCs
PPM007033 PGS001371
(GBE_INI2976)
PSS006889|
South Asian Ancestry|
1,335 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.20384 [0.18792, 0.21975]
Incremental R2 (full-covars): -0.00895
PGS R2 (no covariates): 0.00042 [-0.00049, 0.00133]
age, sex, UKB array type, Genotype PCs
PPM007032 PGS001371
(GBE_INI2976)
PSS006888|
European Ancestry|
1,059 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.37828 [0.36879, 0.38778]
Incremental R2 (full-covars): 0.02371
PGS R2 (no covariates): 0.04728 [0.04214, 0.05243]
age, sex, UKB array type, Genotype PCs
PPM007031 PGS001371
(GBE_INI2976)
PSS006887|
East Asian Ancestry|
86 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.31131 [0.27489, 0.34772]
Incremental R2 (full-covars): 0.00576
PGS R2 (no covariates): 0.00203 [-0.00223, 0.00629]
age, sex, UKB array type, Genotype PCs
PPM007030 PGS001371
(GBE_INI2976)
PSS006886|
African Ancestry|
673 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.28398 [0.26544, 0.30253]
Incremental R2 (full-covars): -0.00362
PGS R2 (no covariates): 0.00112 [-0.0005, 0.00275]
age, sex, UKB array type, Genotype PCs
PPM007506 PGS000935
(GBE_INI2966)
PSS006885|
European Ancestry|
17,194 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age high BP diagnosed : 0.30232 [0.29652, 0.30811]
Incremental R2 (full-covars): 0.00145
PGS R2 (no covariates): 0.00247 [0.00172, 0.00322]
age, sex, UKB array type, Genotype PCs
PPM007505 PGS000935
(GBE_INI2966)
PSS006884|
South Asian Ancestry|
2,038 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age high BP diagnosed : 0.3864 [0.36951, 0.40329]
Incremental R2 (full-covars): 0.00339
PGS R2 (no covariates): 0.00948 [0.00521, 0.01375]
age, sex, UKB array type, Genotype PCs
PPM007504 PGS000935
(GBE_INI2966)
PSS006883|
European Ancestry|
5,696 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age high BP diagnosed : 0.35176 [0.34221, 0.3613]
Incremental R2 (full-covars): -7e-05
PGS R2 (no covariates): 0.00205 [0.00093, 0.00318]
age, sex, UKB array type, Genotype PCs
PPM007503 PGS000935
(GBE_INI2966)
PSS006882|
East Asian Ancestry|
324 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age high BP diagnosed : 0.45043 [0.41548, 0.48538]
Incremental R2 (full-covars): 0.00012
PGS R2 (no covariates): 0.00802 [-0.0004, 0.01644]
age, sex, UKB array type, Genotype PCs
PPM007502 PGS000935
(GBE_INI2966)
PSS006881|
African Ancestry|
2,132 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age high BP diagnosed : 0.30909 [0.29042, 0.32776]
Incremental R2 (full-covars): -0.00137
PGS R2 (no covariates): 0.00048 [-0.00058, 0.00155]
age, sex, UKB array type, Genotype 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
PSS006881 2,132 individuals African unspecified UKB
PSS006882 324 individuals East Asian UKB
PSS006883 5,696 individuals European non-white British ancestry UKB
PSS006884 2,038 individuals South Asian UKB
PSS006885 17,194 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS006886 673 individuals African unspecified UKB
PSS006887 86 individuals East Asian UKB
PSS006888 1,059 individuals European non-white British ancestry UKB
PSS006889 1,335 individuals South Asian UKB
PSS006890 3,195 individuals European white British ancestry UKB Testing cohort (heldout set)