Trait: apolipoprotein A 1 measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004614
Description Is a quantification of serum lipoprotein A. Apolipoprotein A-I, encoded in humans by the APOA1 gene and is the major protein component of high density lipoprotein (HDL) in plasma. It is is implicated as a risk factor for atherosclerotic diseases such as coronary heart disease and stroke.
Trait categories
Cardiovascular measurement
Inflammatory measurement
Lipid or lipoprotein measurement
Synonyms 2 synonyms
  • Serum amyloid A-1 protein levels
  • lipoprotein A-1 levels

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)
PGS000671
(snpnet.Apolipoprotein_A)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Apolipoprotein A [g/L] apolipoprotein A 1 measurement 19,324
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000671/ScoringFiles/PGS000671.txt.gz - Check Terms/Licenses
PGS001888
(portability-PLR_apoA)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Apolipoprotein A apolipoprotein A 1 measurement 74,596
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001888/ScoringFiles/PGS001888.txt.gz
PGS002101
(portability-ldpred2_apoA)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Apolipoprotein A apolipoprotein A 1 measurement 681,234
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002101/ScoringFiles/PGS002101.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
PPM001399 PGS000671
(snpnet.Apolipoprotein_A)
PSS000637|
African Ancestry|
5,550 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Apolipoprotein A [g/L] : 0.1486
Spearman's ρ: 0.213
Age, sex, PCs(1-40)
PPM001434 PGS000671
(snpnet.Apolipoprotein_A)
PSS000638|
East Asian Ancestry|
974 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Apolipoprotein A [g/L] : 0.32046
Spearman's ρ: 0.329
Age, sex, PCs(1-40)
PPM001469 PGS000671
(snpnet.Apolipoprotein_A)
PSS000639|
European Ancestry|
21,403 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Apolipoprotein A [g/L] : 0.31504
Spearman's ρ: 0.385
Age, sex, PCs(1-40)
PPM001504 PGS000671
(snpnet.Apolipoprotein_A)
PSS000640|
South Asian Ancestry|
6,682 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Apolipoprotein A [g/L] : 0.29281
Spearman's ρ: 0.358
Age, sex, PCs(1-40)
PPM001539 PGS000671
(snpnet.Apolipoprotein_A)
PSS000641|
European Ancestry|
57,932 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Apolipoprotein A [g/L] : 0.30509
Spearman's ρ: 0.398
Age, sex, PCs(1-40)
PPM001580 PGS000671
(snpnet.Apolipoprotein_A)
PSS000795|
European Ancestry|
1,378 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Apolipoprotein A [g/L] Spearman's ρ: 0.241 Age, sex
PPM007280 PGS000671
(snpnet.Apolipoprotein_A)
PSS007086|
African Ancestry|
5,632 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Apolipoprotein A : 0.14722 [0.13131, 0.16312]
Incremental R2 (full-covars): 0.04255
PGS R2 (no covariates): 0.03865 [0.02947, 0.04784]
age, sex, UKB array type, Genotype PCs
PPM007281 PGS000671
(snpnet.Apolipoprotein_A)
PSS007087|
East Asian Ancestry|
1,462 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Apolipoprotein A : 0.28691 [0.25071, 0.3231]
Incremental R2 (full-covars): 0.07041
PGS R2 (no covariates): 0.08155 [0.0567, 0.10641]
age, sex, UKB array type, Genotype PCs
PPM007282 PGS000671
(snpnet.Apolipoprotein_A)
PSS007088|
European Ancestry|
21,609 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Apolipoprotein A : 0.28381 [0.27434, 0.29329]
Incremental R2 (full-covars): 0.11215
PGS R2 (no covariates): 0.12323 [0.11558, 0.13087]
age, sex, UKB array type, Genotype PCs
PPM007283 PGS000671
(snpnet.Apolipoprotein_A)
PSS007089|
South Asian Ancestry|
6,776 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Apolipoprotein A : 0.26533 [0.24858, 0.28209]
Incremental R2 (full-covars): 0.1056
PGS R2 (no covariates): 0.11603 [0.1027, 0.12937]
age, sex, UKB array type, Genotype PCs
PPM007284 PGS000671
(snpnet.Apolipoprotein_A)
PSS007090|
European Ancestry|
58,749 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.
Reported Trait: Apolipoprotein A : 0.27548 [0.26974, 0.28122]
Incremental R2 (full-covars): 0.12135
PGS R2 (no covariates): 0.1349 [0.1301, 0.13969]
age, sex, UKB array type, Genotype PCs
PPM009988 PGS001888
(portability-PLR_apoA)
PSS009384|
European Ancestry|
17,339 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.4103 [0.3978, 0.4226] sex, age, birth date, deprivation index, 16 PCs
PPM009990 PGS001888
(portability-PLR_apoA)
PSS008712|
European Ancestry|
5,765 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.4138 [0.3921, 0.435] sex, age, birth date, deprivation index, 16 PCs
PPM009991 PGS001888
(portability-PLR_apoA)
PSS008486|
Greater Middle Eastern Ancestry|
1,033 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.3636 [0.3089, 0.4158] sex, age, birth date, deprivation index, 16 PCs
PPM009992 PGS001888
(portability-PLR_apoA)
PSS008264|
South Asian Ancestry|
5,470 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.3639 [0.3406, 0.3867] sex, age, birth date, deprivation index, 16 PCs
PPM009993 PGS001888
(portability-PLR_apoA)
PSS008042|
East Asian Ancestry|
1,543 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.35 [0.3051, 0.3933] sex, age, birth date, deprivation index, 16 PCs
PPM009994 PGS001888
(portability-PLR_apoA)
PSS007828|
African Ancestry|
2,151 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.2555 [0.2154, 0.2948] sex, age, birth date, deprivation index, 16 PCs
PPM009995 PGS001888
(portability-PLR_apoA)
PSS008932|
African Ancestry|
3,389 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.2218 [0.1894, 0.2536] sex, age, birth date, deprivation index, 16 PCs
PPM009989 PGS001888
(portability-PLR_apoA)
PSS009158|
European Ancestry|
3,563 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.4163 [0.3887, 0.4432] sex, age, birth date, deprivation index, 16 PCs
PPM011664 PGS002101
(portability-ldpred2_apoA)
PSS009384|
European Ancestry|
17,339 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.4018 [0.3893, 0.4143] sex, age, birth date, deprivation index, 16 PCs
PPM011665 PGS002101
(portability-ldpred2_apoA)
PSS009158|
European Ancestry|
3,563 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.4015 [0.3735, 0.4288] sex, age, birth date, deprivation index, 16 PCs
PPM011666 PGS002101
(portability-ldpred2_apoA)
PSS008712|
European Ancestry|
5,765 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.4118 [0.3901, 0.433] sex, age, birth date, deprivation index, 16 PCs
PPM011667 PGS002101
(portability-ldpred2_apoA)
PSS008486|
Greater Middle Eastern Ancestry|
1,033 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.3567 [0.3017, 0.4093] sex, age, birth date, deprivation index, 16 PCs
PPM011668 PGS002101
(portability-ldpred2_apoA)
PSS008264|
South Asian Ancestry|
5,470 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.3678 [0.3447, 0.3906] sex, age, birth date, deprivation index, 16 PCs
PPM011670 PGS002101
(portability-ldpred2_apoA)
PSS007828|
African Ancestry|
2,151 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.2377 [0.1973, 0.2774] sex, age, birth date, deprivation index, 16 PCs
PPM011671 PGS002101
(portability-ldpred2_apoA)
PSS008932|
African Ancestry|
3,389 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.2133 [0.1808, 0.2453] sex, age, birth date, deprivation index, 16 PCs
PPM011669 PGS002101
(portability-ldpred2_apoA)
PSS008042|
East Asian Ancestry|
1,543 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein A Partial Correlation (partial-r): 0.353 [0.3082, 0.3962] 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
PSS009158 3,563 individuals European Poland (NE Europe) UKB
PSS008264 5,470 individuals South Asian India (South Asia) UKB
PSS008932 3,389 individuals African unspecified Nigeria (West Africa) UKB
PSS008042 1,543 individuals East Asian China (East Asia) UKB
PSS008712 5,765 individuals European Italy (South Europe) UKB
PSS007828 2,151 individuals African American or Afro-Caribbean Carribean UKB
PSS000637 5,550 individuals African unspecified UKB
PSS000638 974 individuals East Asian UKB
PSS000639 21,403 individuals European Non-British White UKB
PSS000640 6,682 individuals South Asian UKB
PSS000641 57,932 individuals European
(British)
UKB
PSS008486 1,033 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009384 17,339 individuals European UK (+ Ireland) UKB
PSS007086 5,632 individuals African unspecified UKB
PSS007087 1,462 individuals East Asian UKB
PSS000795 1,378 individuals European Participants self-identifying as white MESA
PSS007088 21,609 individuals European non-white British ancestry UKB
PSS007089 6,776 individuals South Asian UKB
PSS007090 58,749 individuals European white British ancestry UKB Testing cohort (heldout set)