Trait: apolipoprotein A 1 measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004614
Description Is a quantification of apolipoprotein A 1 in a sample. It is encoded in humans by the APOA1 gene and is the major protein component of high density lipoprotein (HDL) in plasma. Apolipoprotein A 1 relates to lower observational risk of coronary artery disease.
Trait categories
Cardiovascular measurement
Inflammatory measurement
Lipid or lipoprotein measurement
Synonyms 5 synonyms
  • apo-AI levels
  • apoA-I levels
  • apolipoprotein A-1 levels
  • apolipoprotein A-I levels
  • apolipoprotein A1 levels
Mapped term https://www.uniprot.org/uniprotkb/P02647/entry

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
GWAS
Dev
Eval
 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
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] — — R²: 0.32046
Spearman's ρ: 0.329		 Age, sex, PCs(1-40) —
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] — — R²: 0.1486
Spearman's ρ: 0.213		 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] — — R²: 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] — — R²: 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] — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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 — — R²: 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)