| Predicted Trait | |
| Reported Trait | HDL cholesterol |
| Mapped Trait(s) | high density lipoprotein cholesterol measurement (EFO_0004612) |
| Score Construction | |
| PGS Name | HDL-C_PGS |
| Development Method | |
| Name | Previously associated SNPs |
| Parameters | NR |
| Variants | |
| Original Genome Build | NR |
| Number of Variants | 223 |
| Effect Weight Type | beta |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000647 |
| Citation (link to publication) | Trinder M et al. Arterioscler Thromb Vasc Biol (2019) |
| Ancestry Distribution | |
| Source of Variant Associations (GWAS) | European: 72.4% African: 19.3% Hispanic or Latin American: 8.3% 297,626 individuals (100%) |
| PGS Evaluation | European: 100% 2 Sample Sets |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST006611 Europe PMC: 30275531 |
215,551 individuals | European | MVP |
GWAS Catalog: GCST006611 Europe PMC: 30275531 |
57,332 individuals | African American or Afro-Caribbean | MVP |
GWAS Catalog: GCST006611 Europe PMC: 30275531 |
24,743 individuals | Hispanic or Latin American | MVP |
|
PGS Performance Metric ID (PPM) |
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 |
|---|---|---|---|---|---|---|---|---|
| PPM021379 | PSS011714| European Ancestry| 357,202 individuals |
PGP000647 | Trinder M et al. Arterioscler Thromb Vasc Biol (2019) |
Reported Trait: High-density lipoprotein cholesterol levels | — | — | R²: 0.24 | Age, sex, genotyping array/batch, 4 PCs | — |
| PPM021382 | PSS011716| European Ancestry| 407,558 individuals |
PGP000647 | Trinder M et al. Arterioscler Thromb Vasc Biol (2019) |
Reported Trait: Any infectious hospitilization | HR: 0.94 [0.91, 0.98] | — | — | Age, sex, genotyping array/batch, 4 PCs | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS011714 | — | — | 357,202 individuals, 46.0 % Male samples |
Mean = 57.0 years | European (British) |
— | UKB | — |
| PSS011716 | Infectious disease-related hospitalizations by International Classification of Diseases (ICD) version 10 diagnosis codes included: sepsis (ICD-10 codes: A021 Salmonella septicemia, A227 Antrhrax septicemia, A40 Streptococcal septicemia, A41 Other septicemia, B377 Candidal septicemia, O85 Puerperal sepsis, R651 Systemic Inflammatory Response Syndrome of infectious origin with organ failure, R527 septic shock), pneumonia (ICD-10 codes: B012 Varicella pneumonia, J14 Pneumonia due to Haemophilus influenzae, J12 Viral pneumonia, not elsewhere classified, J16 Pneumonia due to other infectious organisms, not elsewhere classified, J15 Bacterial pneumonia, not elsewhere classified, J17 Pneumonia in diseases classified elsewhere, J18 Pneumonia, organism unspecified), gastroenteritis (ICD-10 codes: A00-A09 Intestinal infectious diseases), skin infection (ICD-10 codes: L00-L08 Infections of the skin and subcutaneous tissue), urinary tract infection (ICD-10 codes: N390 Urinary tract infection, site not specified, O23 Infections of genito-urinary tract in pregnancy), composite any infection (ICD-10 codes: All codes from chapter 1:Certain infectious and parasitic diseases), bacterial infections (ICD-10 codes: A00 Cholera, A01 Typhoid and paratyphoid fevers, A02 Other Salmonella infections, A03 Shigellosis, A04 Other bacterial intestinal infections, A05 Other bacterial foodborne intoxications, A15-A19 Tuberculosis, A20-A28 Certain zoonotic bacterial diseases, A30-A49 Other bacterial diseases, A51 Early syphilis, A52 Late syphilis, A53 Other and unspecified syphilis, A54 Gonococcal infection, A56 Other sexually transmitted chlamydial diseases, A65-A69 Other spirochaetal diseases, A70-A74 Other diseases caused by chlamydiae, A75-A79 Rickettsioses, B90 Sequelae of tuberculosis, B95 Streptococcus and staphylococcus as the cause of diseases classified to other chapters, B96 Other bacterial agents as the cause of diseases classified to other chapters, B98 Other specified infectious agents as the cause of diseases classified to other chapters), viral infections (ICD-10 codes: A08 Viral and other specified intestinal infections, A60 Anogenital herpes viral [herpes simplex] infections, A80-A89 Viral infections of the central nervous system, A92-A99 Arthropod-borne viral fevers and viral haemorrhagic fevers, B00-B09 Viral infections characterized by skin and mucous membrane lesions, B15-B19 Viral hepatitis, B20-B24 Human immunodeficiency virus [HIV] disease, B25-B34 Other viral diseases, B941 Sequelae of viral encephalitis7, B942 Sequelae of viral hepatitis, B97 Viral agents as the cause of diseases classified to other chapters), fungal infections (ICD-10 codes: B35-B49 Mycoses) | — | [ ,
46.0 % Male samples |
Mean = 57.0 years | European (British) |
— | UKB | — |