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 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

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) : 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) : 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) : 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) : 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) : 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 : 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 : 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 : 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 : 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 : 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

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)
PSS008933 3,626 individuals African unspecified Nigeria (West Africa) UKB
PSS009159 3,935 individuals European Poland (NE Europe) UKB
PSS008487 1,115 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008713 6,296 individuals European Italy (South Europe) UKB
PSS008265 5,953 individuals South Asian India (South Asia) UKB
PSS008043 1,705 individuals East Asian China (East Asia) UKB
PSS007096 6,044 individuals African unspecified UKB
PSS009385 18,910 individuals European UK (+ Ireland) UKB
PSS007097 1,605 individuals East Asian UKB
PSS007829 2,325 individuals African American or Afro-Caribbean Carribean UKB
PSS007098 23,638 individuals European non-white British ancestry UKB
PSS007099 7,362 individuals South Asian 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