Trait: Abnormal circulating lipid concentration

Trait Information
Identifier HP_0003119
Description Any deviation from the normal concentration of a lipid in the blood circulation. [HPO: probinson]
Trait category
Other trait
Mapped terms 6 mapped terms
  • MSH:D050171
  • NCIt:C80385
  • SNOMEDCT:370992007
  • SNOMEDCT_US:370992007
  • UMLS:C0242339
  • UMLS:C4025650
Child trait(s) Hypercholesterolemia

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
Note: This table shows all PGS for "Abnormal circulating lipid concentration" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000936
(GBE_HC269)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
High cholesterol Hypercholesterolemia 5,987
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000936/ScoringFiles/PGS000936.txt.gz
PGS001821
(portability-PLR_272)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Disorders of lipoid metabolism Abnormal circulating lipid concentration 22,313
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001821/ScoringFiles/PGS001821.txt.gz
PGS002029
(portability-ldpred2_272)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Disorders of lipoid metabolism Abnormal circulating lipid concentration 764,390
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002029/ScoringFiles/PGS002029.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
PPM007507 PGS000936
(GBE_HC269)
PSS004394|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: High cholesterol AUROC: 0.71982 [0.7005, 0.73913] : 0.11508
Incremental AUROC (full-covars): 0.00533
PGS R2 (no covariates): 0.00875
PGS AUROC (no covariates): 0.55909 [0.53701, 0.58116]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007508 PGS000936
(GBE_HC269)
PSS004395|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: High cholesterol AUROC: 0.72115 [0.67901, 0.76329] : 0.11225
Incremental AUROC (full-covars): 0.01895
PGS R2 (no covariates): 0.01737
PGS AUROC (no covariates): 0.58299 [0.53527, 0.6307]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007509 PGS000936
(GBE_HC269)
PSS004396|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: High cholesterol AUROC: 0.73677 [0.72785, 0.7457] : 0.1386
Incremental AUROC (full-covars): 0.03212
PGS R2 (no covariates): 0.03624
PGS AUROC (no covariates): 0.62158 [0.61091, 0.63225]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007510 PGS000936
(GBE_HC269)
PSS004397|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: High cholesterol AUROC: 0.68493 [0.67098, 0.69888] : 0.10135
Incremental AUROC (full-covars): 0.01608
PGS R2 (no covariates): 0.01913
PGS AUROC (no covariates): 0.57791 [0.56213, 0.5937]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007511 PGS000936
(GBE_HC269)
PSS004398|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: High cholesterol AUROC: 0.72791 [0.72273, 0.73309] : 0.13664
Incremental AUROC (full-covars): 0.03518
PGS R2 (no covariates): 0.03794
PGS AUROC (no covariates): 0.61972 [0.6136, 0.62583]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009468 PGS001821
(portability-PLR_272)
PSS009291|
European Ancestry|
20,000 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.097 [0.0833, 0.1107] sex, age, birth date, deprivation index, 16 PCs
PPM009469 PGS001821
(portability-PLR_272)
PSS009065|
European Ancestry|
4,136 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0977 [0.0674, 0.1279] sex, age, birth date, deprivation index, 16 PCs
PPM009470 PGS001821
(portability-PLR_272)
PSS008619|
European Ancestry|
6,660 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0945 [0.0706, 0.1183] sex, age, birth date, deprivation index, 16 PCs
PPM009471 PGS001821
(portability-PLR_272)
PSS008395|
Greater Middle Eastern Ancestry|
1,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0789 [0.022, 0.1354] sex, age, birth date, deprivation index, 16 PCs
PPM009472 PGS001821
(portability-PLR_272)
PSS008173|
South Asian Ancestry|
6,331 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0889 [0.0644, 0.1134] sex, age, birth date, deprivation index, 16 PCs
PPM009473 PGS001821
(portability-PLR_272)
PSS007960|
East Asian Ancestry|
1,810 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0321 [-0.0143, 0.0783] sex, age, birth date, deprivation index, 16 PCs
PPM009475 PGS001821
(portability-PLR_272)
PSS008844|
African Ancestry|
3,924 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0363 [0.0049, 0.0676] sex, age, birth date, deprivation index, 16 PCs
PPM009474 PGS001821
(portability-PLR_272)
PSS007741|
African Ancestry|
2,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.068 [0.0286, 0.1072] sex, age, birth date, deprivation index, 16 PCs
PPM011106 PGS002029
(portability-ldpred2_272)
PSS009291|
European Ancestry|
20,000 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0996 [0.0858, 0.1133] sex, age, birth date, deprivation index, 16 PCs
PPM011108 PGS002029
(portability-ldpred2_272)
PSS008619|
European Ancestry|
6,660 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0952 [0.0713, 0.119] sex, age, birth date, deprivation index, 16 PCs
PPM011109 PGS002029
(portability-ldpred2_272)
PSS008395|
Greater Middle Eastern Ancestry|
1,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0977 [0.0409, 0.1539] sex, age, birth date, deprivation index, 16 PCs
PPM011110 PGS002029
(portability-ldpred2_272)
PSS008173|
South Asian Ancestry|
6,331 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0926 [0.0681, 0.117] sex, age, birth date, deprivation index, 16 PCs
PPM011111 PGS002029
(portability-ldpred2_272)
PSS007960|
East Asian Ancestry|
1,810 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0539 [0.0075, 0.0999] sex, age, birth date, deprivation index, 16 PCs
PPM011113 PGS002029
(portability-ldpred2_272)
PSS008844|
African Ancestry|
3,924 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.05 [0.0186, 0.0812] sex, age, birth date, deprivation index, 16 PCs
PPM011107 PGS002029
(portability-ldpred2_272)
PSS009065|
European Ancestry|
4,136 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.1035 [0.0732, 0.1337] sex, age, birth date, deprivation index, 16 PCs
PPM011112 PGS002029
(portability-ldpred2_272)
PSS007741|
African Ancestry|
2,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0769 [0.0375, 0.116] sex, age, birth date, deprivation index, 16 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
PSS009065 4,136 individuals European Poland (NE Europe) UKB
PSS009291 20,000 individuals European UK (+ Ireland) UKB
PSS008619 6,660 individuals European Italy (South Europe) UKB
PSS008395 1,200 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008173 6,331 individuals South Asian India (South Asia) UKB
PSS008844 3,924 individuals African unspecified Nigeria (West Africa) UKB
PSS004394
[
  • 718 cases
  • , 5,779 controls
]
African unspecified UKB
PSS004395
[
  • 164 cases
  • , 1,540 controls
]
East Asian UKB
PSS004396
[
  • 2,910 cases
  • , 21,995 controls
]
European non-white British ancestry UKB
PSS004397
[
  • 1,551 cases
  • , 6,280 controls
]
South Asian UKB
PSS004398
[
  • 8,999 cases
  • , 58,426 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS007960 1,810 individuals East Asian China (East Asia) UKB
PSS007741 2,484 individuals African American or Afro-Caribbean Carribean UKB