| 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 |
| 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 |
| 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. Nature (2023) |
Apolipoprotein B | apolipoprotein B measurement | 979,739 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003492/ScoringFiles/PGS003492.txt.gz |
|
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. Nature (2023) |
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. Nature (2023) |
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. Nature (2023) |
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. Nature (2023) |
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. Nature (2023) |
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. Nature (2023) |
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. Nature (2023) |
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. Nature (2023) |
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. Nature (2023) |
Reported Trait: Apolipoprotein B | — | — | partial-R2: 0.06 | sex, age, deprivation index, PC1-16 | — |
|
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 | — |