Trait: apolipoprotein B measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004615
Description The measurement of ApoB in blood. Apolipoprotein B is a major protein constituent of chylomicrons (apo B-48), LDL (apo B-100) and VLDL (apo B-100). Apo B-100 functions as a recognition signal for the cellular binding and internalization of LDL particles by the apoB/E receptor, and is upregulated in response to enterovirus 71.
Trait category
Lipid or lipoprotein measurement
Mapped term NCIt:C74734

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)
PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Apolipoprotein B [g/L] (statin adjusted) apolipoprotein B measurement 18,666
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000672/ScoringFiles/PGS000672.txt.gz - Check Terms/Licenses
PGS001889
(portability-PLR_apoB)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Apolipoprotein B apolipoprotein B measurement 16,952
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001889/ScoringFiles/PGS001889.txt.gz
PGS002102
(portability-ldpred2_apoB)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Apolipoprotein B apolipoprotein B measurement 315,483
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002102/ScoringFiles/PGS002102.txt.gz
PGS003492
(cont-decay-apoB)
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Apolipoprotein B apolipoprotein B measurement 979,739
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003492/ScoringFiles/PGS003492.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
PPM001400 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS000642|
African Ancestry|
5,962 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.15686
Spearman's ρ: 0.318		 Age, sex, PCs(1-40) —
PPM001470 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS000644|
European Ancestry|
23,448 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.29807
Spearman's ρ: 0.467		 Age, sex, PCs(1-40) —
PPM001540 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS000646|
European Ancestry|
63,491 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.30182
Spearman's ρ: 0.483		 Age, sex, PCs(1-40) —
PPM001435 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS000643|
East Asian Ancestry|
1,074 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.17749
Spearman's ρ: 0.346		 Age, sex, PCs(1-40) —
PPM001505 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS000645|
South Asian Ancestry|
7,275 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.15714
Spearman's ρ: 0.335		 Age, sex, PCs(1-40) —
PPM007285 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS007096|
African Ancestry|
6,044 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.09116 [0.07782, 0.1045]
Incremental R2 (full-covars): 0.08614
PGS R2 (no covariates): 0.08777 [0.07463, 0.10091]		 age, sex, UKB array type, Genotype PCs —
PPM007286 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS007097|
East Asian Ancestry|
1,605 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.11275 [0.08452, 0.14098]
Incremental R2 (full-covars): 0.09788
PGS R2 (no covariates): 0.09846 [0.07165, 0.12527]		 age, sex, UKB array type, Genotype PCs —
PPM007287 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS007098|
European Ancestry|
23,638 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.15705 [0.14875, 0.16535]
Incremental R2 (full-covars): 0.14836
PGS R2 (no covariates): 0.14904 [0.14088, 0.1572]		 age, sex, UKB array type, Genotype PCs —
PPM007288 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS007099|
South Asian Ancestry|
7,362 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.08178 [0.07015, 0.09341]
Incremental R2 (full-covars): 0.05616
PGS R2 (no covariates): 0.06062 [0.05038, 0.07086]		 age, sex, UKB array type, Genotype PCs —
PPM007289 PGS000672
(snpnet.Apolipoprotein_B_adjstatins)
 PSS007100|
European Ancestry|
64,166 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.15112 [0.14614, 0.1561]
Incremental R2 (full-covars): 0.14801
PGS R2 (no covariates): 0.14785 [0.1429, 0.15279]		 age, sex, UKB array type, Genotype PCs —
PPM009997 PGS001889
(portability-PLR_apoB)
 PSS009159|
European Ancestry|
3,935 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3999 [0.3732, 0.4258] sex, age, birth date, deprivation index, 16 PCs —
PPM009998 PGS001889
(portability-PLR_apoB)
 PSS008713|
European Ancestry|
6,296 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3644 [0.3428, 0.3857] sex, age, birth date, deprivation index, 16 PCs —
PPM009999 PGS001889
(portability-PLR_apoB)
 PSS008487|
Greater Middle Eastern Ancestry|
1,115 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3471 [0.2939, 0.3981] sex, age, birth date, deprivation index, 16 PCs —
PPM010000 PGS001889
(portability-PLR_apoB)
 PSS008265|
South Asian Ancestry|
5,953 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.2716 [0.2479, 0.295] sex, age, birth date, deprivation index, 16 PCs —
PPM010001 PGS001889
(portability-PLR_apoB)
 PSS008043|
East Asian Ancestry|
1,705 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3064 [0.2625, 0.349] sex, age, birth date, deprivation index, 16 PCs —
PPM010002 PGS001889
(portability-PLR_apoB)
 PSS007829|
African Ancestry|
2,325 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3326 [0.2958, 0.3684] sex, age, birth date, deprivation index, 16 PCs —
PPM010003 PGS001889
(portability-PLR_apoB)
 PSS008933|
African Ancestry|
3,626 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.2588 [0.2281, 0.289] sex, age, birth date, deprivation index, 16 PCs —
PPM009996 PGS001889
(portability-PLR_apoB)
 PSS009385|
European Ancestry|
18,910 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3928 [0.3807, 0.4048] sex, age, birth date, deprivation index, 16 PCs —
PPM011672 PGS002102
(portability-ldpred2_apoB)
 PSS009385|
European Ancestry|
18,910 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.391 [0.3789, 0.4031] sex, age, birth date, deprivation index, 16 PCs —
PPM011673 PGS002102
(portability-ldpred2_apoB)
 PSS009159|
European Ancestry|
3,935 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3949 [0.3682, 0.4211] sex, age, birth date, deprivation index, 16 PCs —
PPM011674 PGS002102
(portability-ldpred2_apoB)
 PSS008713|
European Ancestry|
6,296 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3557 [0.3339, 0.3771] sex, age, birth date, deprivation index, 16 PCs —
PPM011675 PGS002102
(portability-ldpred2_apoB)
 PSS008487|
Greater Middle Eastern Ancestry|
1,115 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3441 [0.2908, 0.3953] sex, age, birth date, deprivation index, 16 PCs —
PPM011676 PGS002102
(portability-ldpred2_apoB)
 PSS008265|
South Asian Ancestry|
5,953 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.2734 [0.2497, 0.2968] sex, age, birth date, deprivation index, 16 PCs —
PPM011677 PGS002102
(portability-ldpred2_apoB)
 PSS008043|
East Asian Ancestry|
1,705 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3092 [0.2654, 0.3518] sex, age, birth date, deprivation index, 16 PCs —
PPM011678 PGS002102
(portability-ldpred2_apoB)
 PSS007829|
African Ancestry|
2,325 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.3289 [0.292, 0.3648] sex, age, birth date, deprivation index, 16 PCs —
PPM011679 PGS002102
(portability-ldpred2_apoB)
 PSS008933|
African Ancestry|
3,626 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein B — — Partial Correlation (partial-r): 0.2593 [0.2286, 0.2895] sex, age, birth date, deprivation index, 16 PCs —
PPM017420 PGS003492
(cont-decay-apoB)
 PSS010881|
European Ancestry|
19,039 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017504 PGS003492
(cont-decay-apoB)
 PSS010797|
European Ancestry|
3,924 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017588 PGS003492
(cont-decay-apoB)
 PSS010629|
European Ancestry|
6,144 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017672 PGS003492
(cont-decay-apoB)
 PSS010545|
Greater Middle Eastern Ancestry|
1,086 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017756 PGS003492
(cont-decay-apoB)
 PSS010209|
European Ancestry|
2,234 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017840 PGS003492
(cont-decay-apoB)
 PSS010461|
South Asian Ancestry|
5,900 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017924 PGS003492
(cont-decay-apoB)
 PSS010377|
East Asian Ancestry|
1,694 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM018008 PGS003492
(cont-decay-apoB)
 PSS010293|
African Ancestry|
2,313 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM018092 PGS003492
(cont-decay-apoB)
 PSS010713|
African Ancestry|
3,597 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein B — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —

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
PSS007100 — — 64,166 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS009159 — — 3,935 individuals — European Poland (NE Europe) UKB —
PSS008265 — — 5,953 individuals — South Asian India (South Asia) UKB —
PSS010797 — — 3,924 individuals,
38.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —
PSS010545 — — 1,086 individuals,
60.0 % Male samples
 Mean = 51.9 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010293 — — 2,313 individuals,
37.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS008933 — — 3,626 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008043 — — 1,705 individuals — East Asian China (East Asia) UKB —
PSS010713 — — 3,597 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010461 — — 5,900 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010209 — — 2,234 individuals,
45.0 % Male samples
 Mean = 58.1 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS008713 — — 6,296 individuals — European Italy (South Europe) UKB —
PSS007829 — — 2,325 individuals — African American or Afro-Caribbean Carribean UKB —
PSS000642 — — 5,962 individuals — African unspecified — UKB —
PSS000643 — — 1,074 individuals — East Asian — UKB —
PSS000644 — — 23,448 individuals — European Non-British White UKB —
PSS000645 — — 7,275 individuals — South Asian — UKB —
PSS000646 — — 63,491 individuals — European
(British)		 — UKB —
PSS008487 — — 1,115 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS010881 — — 19,039 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS009385 — — 18,910 individuals — European UK (+ Ireland) UKB —
PSS010629 — — 6,144 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010377 — — 1,694 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS007096 — — 6,044 individuals — African unspecified — UKB —
PSS007097 — — 1,605 individuals — East Asian — UKB —
PSS007098 — — 23,638 individuals — European non-white British ancestry UKB —
PSS007099 — — 7,362 individuals — South Asian — UKB —