Datasets:
PGS Sample Set (PSS) large_stringlengths 9 9 | Polygenic Score (PGS) ID large_stringlengths 9 2.77k | Number of Individuals int64 1 5.33M | Number of Cases float64 0 389k ⌀ | Number of Controls float64 0 1.14M ⌀ | Percent of Participants Who are Male float64 0 100 ⌀ | Sample Age large_stringclasses 733 values | Broad Ancestry Category large_stringclasses 73 values | Ancestry (e.g. French, Chinese) large_stringclasses 90 values | Country of Recruitment large_stringclasses 140 values | Additional Ancestry Description large_stringclasses 131 values | Phenotype Definitions and Methods large_stringclasses 798 values | Followup Time large_stringclasses 141 values | GWAS Catalog Study ID (GCST...) large_stringclasses 8 values | Source PubMed ID (PMID) float64 1.25M 39.9M ⌀ | Source DOI large_stringclasses 13 values | Cohort(s) large_stringclasses 460 values | Additional Sample/Cohort Information large_stringclasses 245 values |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PSS000001 | PGS000001 | 67,054 | 33,673 | 33,381 | null | null | European | null | Australia, Belarus, Belgium, Canada, Denmark, Finland, France, Germany, Greece, Ireland, Netherlands, Norway, Poland, Sweden, UK, USA | null | All breast cancer | null | null | null | null | ABCFS|MCCS|HMBCS|LMBC|MTLGEBCS|CGPS|KBCP|OBCS|CECILE|BBCC|BSUCH|ESTHER|GENICA|MARIE|SKKDKFZS|DEMOKRITOS|BIGGS|ABCS|ORIGO|NorBCS|SZBCS|PBCS|pKARMA|SASBAC|SBCS|SEARCH|MCBCS|UKBGS|NBHS|CTS|MEC|RPCI|OSU | iCOGS |
PSS000002 | PGS000003 | 38,722 | 5,738 | 32,984 | null | null | European | null | Australia, Belarus, Belgium, Canada, Denmark, Finland, France, Germany, Greece, Ireland, Netherlands, Norway, Poland, Sweden, UK, USA | null | ER-negative breast cancer | null | null | null | null | ABCFS|MCCS|HMBCS|LMBC|MTLGEBCS|CGPS|KBCP|OBCS|CECILE|BBCC|BSUCH|ESTHER|GENICA|MARIE|SKKDKFZS|DEMOKRITOS|BIGGS|ABCS|ORIGO|NorBCS|SZBCS|PBCS|pKARMA|SASBAC|SBCS|SEARCH|MCBCS|UKBGS|NBHS|CTS|MEC|RPCI|OSU | iCOGS |
PSS000003 | PGS000002 | 53,923 | 21,365 | 32,558 | null | null | European | null | Australia, Belarus, Belgium, Canada, Denmark, Finland, France, Germany, Greece, Ireland, Netherlands, Norway, Poland, Sweden, UK, USA | null | ER-positive breast cancer | null | null | null | null | ABCFS|MCCS|HMBCS|LMBC|MTLGEBCS|CGPS|KBCP|OBCS|CECILE|BBCC|BSUCH|ESTHER|GENICA|MARIE|SKKDKFZS|DEMOKRITOS|BIGGS|ABCS|ORIGO|NorBCS|SZBCS|PBCS|pKARMA|SASBAC|SBCS|SEARCH|MCBCS|UKBGS|NBHS|CTS|MEC|RPCI|OSU | iCOGS |
PSS000004 | PGS000001, PGS000004, PGS000007 | 29,751 | 11,428 | 18,323 | 0 | null | European | null | Denmark, France, Germany, Greece, Italy, Norway, Spain, Sweden, The Netherlands, UK, USA | null | Invasive breast cancer-affected | null | null | null | null | AHS|BGS|EPIC|FHRISK|NHS|NHS2|PLCO|PROCAS|KARMA|SISTER | Prospective Test Set |
PSS000005 | PGS000002, PGS000005, PGS000008 | 11,428 | 7,992 | 3,436 | 0 | null | European | null | Denmark, France, Germany, Greece, Italy, Norway, Spain, Sweden, The Netherlands, UK, USA | null | ER-positive breast cancer cases | null | null | null | null | AHS|BGS|EPIC|FHRISK|NHS|NHS2|PLCO|PROCAS|SISTER|KARMA | Prospective Test Set |
PSS000006 | PGS000003, PGS000006, PGS000009 | 11,428 | 1,259 | 10,169 | 0 | null | European | null | Denmark, France, Germany, Greece, Italy, Norway, Spain, Sweden, The Netherlands, UK, USA | null | ER-negative breast cancer cases | null | null | null | null | AHS|BGS|EPIC|FHRISK|NHS|NHS2|PLCO|PROCAS|SISTER|KARMA | Prospective Test Set |
PSS000007 | PGS000004 | 190,040 | 3,215 | 186,825 | 0 | null | European | null | UK | null | Incident registry-confirmed invasive breast cancers developed | null | null | null | null | UKB | Prospective Test Set (UKB) |
PSS000008 | PGS000010 | 27,271 | null | null | 38.7 | null | European | Swedish | Sweeden | null | Coronary heart disease represented a composite of fatal or non-fatal myocardial infarction, coronary artery bypass grafting, or percutaneous coronary intervention | null | null | null | null | MDC | Primary prevention cohorts |
PSS000008 | PGS000010 | 8,749 | 108 | 8,641 | 67.8 | null | European | null | null | null | Coronary heart disease represented a composite of fatal or non-fatal myocardial infarction, coronary artery bypass grafting, or percutaneous coronary intervention | null | null | null | null | JUPITER | Primary prevention cohorts |
PSS000008 | PGS000010 | 6,978 | 149 | 6,829 | 79.7 | null | European | null | null | null | Coronary heart disease represented a composite of fatal or non-fatal myocardial infarction, coronary artery bypass grafting, or percutaneous coronary intervention | null | null | null | null | ASCOT | Primary prevention cohorts |
PSS000009 | PGS000010 | 2,878 | 320 | 2,558 | 86.1 | null | European | null | null | null | Coronary heart disease represented a composite of fatal or non-fatal myocardial infarction, coronary artery bypass grafting, or percutaneous coronary intervention | null | null | null | null | CARE_b | Secondary prevention cohorts |
PSS000009 | PGS000010 | 1,999 | 229 | 1,770 | 77.5 | null | European | null | null | null | Coronary heart disease represented a composite of fatal or non-fatal myocardial infarction, coronary artery bypass grafting, or percutaneous coronary intervention | null | null | null | null | PROVEIT | Secondary prevention cohorts |
PSS000010 | PGS000010, PGS000011 | 23,595 | 2,213 | 21,382 | 38.029243 | null | European | Swedish | Sweeden | null | Incident CHD was defined as coronary revascularization, fatal or nonfatal myocardial infarction, or death due to ischemic heart disease. | null | null | 8,429,286 | null | MDC | Prospective study |
PSS000011 | PGS000010, PGS000012 | 3,406 | 587 | 2,819 | 45 | null | European | null | USA | null | The main outcome of interest was incident CHD event before age 75y. We used the definition of CHD as employed by the Framingham study, namely, one of • MI recognized, with diagnostic ECG (FHS event code #1) • MI recognized, without diagnostic ECG, with enzymes and history (#2) • MI recognized, without diagnostic ECG, with autopsy evidence (new event) (#3) • MI unrecognized, silent (#4) • MI unrecognized, not silent (#5) • Angina pectoris (AP), first episode only (#6) • Coronary insufficiency (CI), definite by both history and ECG (#7) • Questionable MI at exam 1 (#8) • Acute MI by autopsy, previously coded as 1 or 2 (#9) • Death, CHD sudden, with 1 hour (#21) • Death, CHD 1–23 hours, non sudden (#22) • Death, CHD 24-47 hours, non sudden (#23) • Death, CHD, 48 hours or more, non sudden (#24) | null | null | null | null | FHS | FHS Original, FHS Offspring |
PSS000012 | PGS000010, PGS000012 | 12,676 | 757 | 11,919 | 46 | null | European | Finnish | Finland | null | Coronary heart disease (CHD) was defined as falling into any of the following categories: • I21 or I22 (ICD-10) / 410 (ICD-8/9) as the direct or as a contributing cause of death or I20-I25 (ICD-10) /410-414 (ICD-9) as the underlying cause of death • I21 or I22 (ICD-10) / 410 (ICD-8/9) as the main or secondary diagnosis at hospital discharge. • Coronary bypass surgery or coronary angioplasty at hospital discharge or identified from the Finnish registry of invasive cardiac procedures. | null | null | null | null | FINRISK | FR92, FR97, FR02 |
PSS000013 | PGS000016 | 288,978 | 4,576 | 284,402 | null | null | European | null | UK | null | Atrial fibrillation ascertainment was based on self-report of atrial fibrillation, atrial flutter, or cardioversion in an interview with a trained nurse, an ICD-9 code of 427.3 or ICD-10 code of I48.X in hospitalization records, or a history of a percutaneous ablation or cardioversion based on the OPCS-4 coded procedure (K57.1, K62.1, K62.2, K62.3, or K 62.4), as performed previously | null | null | null | null | UKB | UKB Phase 2 |
PSS000014 | PGS000015 | 157,895 | 6,586 | 151,309 | 0 | null | European | null | UK | null | Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 codes (174 or 174.9) or ICD-10 codes (C50.X) in hospitalization records, or a breast cancer diagnosis reported to the national registry before the date of enrollment. | null | null | null | null | UKB | UKB Phase 2 |
PSS000015 | PGS000013 | 288,978 | 8,676 | 280,302 | null | null | European | null | UK | null | CAD ascertainment was based on a composite of myocardial infarction or coronary revascularization. Myocardial infarction was based on self-report or hospital admission diagnosis, as performed centrally. This included individuals with ICD-9 codes of 410.X, 411.0, 412.X, or 429.79, or ICD-10 codes of I21.X, I22.X, I23.X, I24.1, or I25.2 in hospitalization records. Coronary revascularization was assessed based on an OPCS-4 coded procedure for coronary artery bypass grafting (K40.1–40.4, K41.1–41.4, or K45.1–45.5), or coronary angioplasty with or without stenting (K49.1–49.2, K49.8–49.9, K50.2, K75.1–75.4, or K75.8–75.9). | null | null | null | null | UKB | UKB Phase 2 |
PSS000016 | PGS000017 | 288,978 | 5,853 | 283,125 | null | null | European | null | UK | null | Inflammatory bowel disease ascertainment was based on report in an interview with a trained nurse, or an ICD-9 code of 555.X or ICD-10 code of K51.X in hospitalization records. | null | null | null | null | UKB | UKB Phase 2 |
PSS000017 | PGS000014 | 288,978 | 5,853 | 283,125 | null | null | European | null | UK | null | Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records. | null | null | null | null | UKB | UKB Phase 2 |
PSS000018 | PGS000011, PGS000012, PGS000018 | 482,629 | 22,242 | 460,387 | 45.6 | null | European, NR | null | UK | ~95% European ancestry samples, <5% non-European ancestry | CAD was defined as fatal or nonfatal myocardial infarction (MI) cases, percutaneous transluminal coronary angioplasty (PTCA), or coronary artery bypass grafting (CABG). Prevalent versus incident status was relative to the UKB enrollment assessment. In UKB self-reported data, cases were defined as having had a heart attack diagnosed by a doctor (data field #6150); “non-cancer illnesses that self-reported as heart attack” (data field #20002); or self-reported operation including PTCA, CABG, or triple heart bypass (data field #20004). In HES hospital episodes data and death registry data, MI was defined as hospital admission or cause of death due to ICD-9 410 to 412, or ICD-10 I21 to I24 or I25.2; CABG and PTCA were defined as hospital admission OPCS-4 K40 to K46, K49, K50.1,or K75. | null | null | null | null | UKB | null |
PSS000019 | PGS000013, PGS000018 | 5,762 | 173 | 5,589 | 41.291045 | null | European | French Canadian | Canada | null | Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). | null | null | null | null | CARTaGENE | null |
PSS000020 | PGS000013, PGS000018 | 862 | 446 | 416 | null | null | European | French Canadian | Canada | null | Recurrent CAD event during the follow- up period (median follow-up time =3.9 years [range =1.1–7), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). | null | null | null | null | MHI | Phase 1 |
PSS000020 | PGS000013, PGS000018 | 2,333 | 937 | 1,396 | null | null | European | French Canadian | Canada | null | Recurrent CAD event during the follow- up period (median follow-up time =3.9 years [range =1.1–7), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). | null | null | null | null | MHI | Phase 2 |
PSS000021 | PGS000013, PGS000018 | 1,964 | 974 | 976 | 72.695519 | null | European | French Canadian | Canada | null | Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). | null | null | null | null | MHI | Phase 1 |
PSS000022 | PGS000013, PGS000018 | 3,309 | 2,492 | 817 | 72.383197 | null | European | French Canadian | Canada | null | Prevalent Coronary artery disease (CAD), where CAD is defined as previous diagnosis of myocardial infarction or revascularization procedures (percutaneous coronary intervention or coronary artery bypass grafting). | null | null | null | null | MHI | Phase 2 |
PSS000023 | PGS000019 | 725 | 206 | 519 | 42.8 | null | European | null | Canada | null | CAD case endpoints were defined as: angina, myocardial infarction, coronary angioplasty, and coronary bypass surgery. Participants are described as Caucasian with diagnosed Familial hypercholesterolemia(FH; Dutch Lipid Criteria score >= 3 [possible, probable, or definite FH]) and carriers of classical French Canadian mutations in the LDLR gene including del .15 kb of the promoter and exon 1, del .5 kb of exons 2 and 3, W66G (exon 3), E207K (exon 4), Y468X (exon 10), and C646Y (exon 14). | null | null | null | null | CNMA | Nutrition, Metabolism and Atherosclerosis Clinic (CNMA) of Institut de recherches cliniques de Montréal |
PSS000024 | PGS000019 | 725 | 231 | 494 | 42.8 | null | European | null | Canada | null | Cerebrovascular disease (CVD) case endpoints were defined as: transient ischemic attack, stroke, and carotid endarterectomy. Participants are described as Caucasian with diagnosed Familial hypercholesterolemia(FH; Dutch Lipid Criteria score >= 3 [possible, probable, or definite FH]) and carriers of classical French Canadian mutations in the LDLR gene including del .15 kb of the promoter and exon 1, del .5 kb of exons 2 and 3, W66G (exon 3), E207K (exon 4), Y468X (exon 10), and C646Y (exon 14). | null | null | null | null | CNMA | Nutrition, Metabolism and Atherosclerosis Clinic (CNMA) of Institut de recherches cliniques de Montréal |
PSS000025 | PGS000020 | 6,280 | 302 | 5,978 | 55 | null | European | Estonian | Estonia | null | Incident cases of Type 2 Diabetes in 5.63 years follow-up | null | null | null | null | EB | null |
PSS000026 | PGS000021 | 223 | 46 | 177 | 46.300448 | null | European | null | UK | null | Cases were defined on the presence or absence of severe insulin deficiency (requiring insulin treatment at 3 years after diagnosis). We cate- gorized people as severely insulin defi- cient if they received continuous insulin treatment at ,3 years from the time of diagnosis and had a low measured C-peptide level (nonfasting measured ,0.6 nmol/L or equivalent fasting blood glucose level or posthome meal urine C-peptide–to–creatinine ratio) | null | null | null | null | P2ID | A cross-sectional cohort of people in whom diabetes was diagnosed between the ages of 20 and 40 years (n = 223), who had had diabetes for .3 years, and who had self-reported as white European from Devon and Cornwall in South West England. Known monogenic diabetes and secondary diabetes pa- tients were excluded. |
PSS000027 | PGS000022 | 299 | 84 | 63 | 33.78 | null | African American or Afro-Caribbean | null | USA | null | Type 1 diabetes status was assigned according to clinician diagnosis. | null | null | null | null | UFDI | Total sample number contains the number of controls, cases, and includes the number of first/second-degree relatives and samples identified as "at risk" (autoantibody positive) used in other analyses. |
PSS000028 | PGS000022 | 252 | 65 | 43 | 44.84 | null | Hispanic or Latin American | null | USA | Samples labeled Caucasian (Hispanic ethnicity) in the original publication. | Type 1 diabetes status was assigned according to clinician diagnosis. | null | null | null | null | UFDI | Total sample number contains the number of controls, cases, and includes the number of first/second-degree relatives and samples identified as "at risk" (autoantibody positive) used in other analyses. |
PSS000029 | PGS000022 | 1,447 | 478 | 290 | 47.34 | null | European | null | USA | Samples labeled Caucasian (non-Hispanic) in the original publication. | Type 1 diabetes status was assigned according to clinician diagnosis. | null | null | null | null | UFDI | Total sample number contains the number of controls, cases, and includes the number of first/second-degree relatives and samples identified as "at risk" (autoantibody positive) used in other analyses. |
PSS000030 | PGS000021, PGS000023 | 3,949 | 1,021 | 2,928 | null | null | African unspecified | null | null | null | null | null | null | null | null | GoKinD|NYCP|T1DGC|UAB|SEARCH|BDC|CLEAR | null |
PSS000031 | PGS000023 | 145 | 61 | 54 | null | null | African unspecified | null | USA | null | Cases are diagnosed with type 1 diabetes. | null | null | null | null | UOF | null |
PSS000032 | PGS000021, PGS000024 | 374,000 | 387 | 373,613 | null | null | European | null | UK | null | Type 1 Diabetes Case Definition = Clinical diagnosis of diabetes at less than or equal to 20 years of age; On insulin within 1 year from the time of diagnosis; Still on insulin at the time of recruit- ment; Not using oral antihyperglycemic agents; Did not ever self-report as having type 2 diabetes (T2D) | null | null | null | null | UKB | null |
PSS000033 | PGS000025 | 19,687 | 2,782 | null | null | null | European | null | null | null | Most of the studies used standard screening procedures based on history, medical review, screening questions, and cognitive assessments that flagged participants with potential cognitive impairment. These participants underwent complete neurological and neuropsychological evaluation. An initial decision was made regarding the presence or absence of dementia, using the DSM-IV criteria; a diagnosis of possible, probable, or definite AD was made as a second step using NINCDS-ADRDA (National Institute of Neurological Disorders and Stroke Alzheimer’s Disease and Related Disorders Association) criteria. | null | null | 27,340,842 | null | 3C|ACT|ROSMAP|WHICAP|CHS|FHS|AGES|RS | As one SNP (rs9271192) was missing in FHS, WHICAP, and Rotterdam because of poor imputation quality, an 18 SNP-based GRS was computed in these cohorts. As the samples used in this project were partially overlapping with the ones used in the original IGAP study, we ran an additional IGAP meta-analysis after excluding those and did not find significant changes in the estimations of HRs for the SNPs considered |
PSS000034 | PGS000025 | 4,353 | null | null | null | null | European | null | null | null | Most of the studies used standard screening procedures based on history, medical review, screening questions, and cognitive assessments that flagged participants with potential cognitive impairment. These participants underwent complete neurological and neuropsychological evaluation. An initial decision was made regarding the presence or absence of dementia, using the DSM-IV criteria; a diagnosis of possible, probable, or definite AD was made as a second step using NINCDS-ADRDA (National Institute of Neurological Disorders and Stroke Alzheimer’s Disease and Related Disorders Association) criteria. | null | null | 27,340,842 | null | 3C|ACT|ROSMAP|WHICAP|CHS|FHS|AGES|RS | As one SNP (rs9271192) was missing in FHS, WHICAP, and Rotterdam because of poor imputation quality, an 18 SNP-based GRS was computed in these cohorts. As the samples used in this project were partially overlapping with the ones used in the original IGAP study, we ran an additional IGAP meta-analysis after excluding those and did not find significant changes in the estimations of HRs for the SNPs considered |
PSS000035 | PGS000025 | 15,334 | null | null | null | null | European | null | null | null | Most of the studies used standard screening procedures based on history, medical review, screening questions, and cognitive assessments that flagged participants with potential cognitive impairment. These participants underwent complete neurological and neuropsychological evaluation. An initial decision was made regarding the presence or absence of dementia, using the DSM-IV criteria; a diagnosis of possible, probable, or definite AD was made as a second step using NINCDS-ADRDA (National Institute of Neurological Disorders and Stroke Alzheimer’s Disease and Related Disorders Association) criteria. | null | null | 27,340,842 | null | 3C|ACT|ROSMAP|WHICAP|CHS|FHS|AGES|RS | As one SNP (rs9271192) was missing in FHS, WHICAP, and Rotterdam because of poor imputation quality, an 18 SNP-based GRS was computed in these cohorts. As the samples used in this project were partially overlapping with the ones used in the original IGAP study, we ran an additional IGAP meta-analysis after excluding those and did not find significant changes in the estimations of HRs for the SNPs considered |
PSS000036 | PGS000026 | 17,956 | 6,984 | 10,972 | 40.505747 | null | European | null | null | null | Cases are patients with clinically diagnosed AD and compared to cognitively normal older individuals | null | null | null | null | ADGC | ADGC Phase 2 |
PSS000037 | PGS000027 | 288,016 | null | null | 45 | null | European | null | null | null | null | null | null | null | null | UKB | null |
PSS000038 | PGS000028, PGS000029 | 102 | 51 | 51 | 0 | null | East Asian | null | USA | null | Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. | null | null | null | null | CPMCBHC | Nested case-control study from the CPMC Breast Health Cohort. |
PSS000039 | PGS000028 | 774 | 387 | 387 | 0 | null | European | null | USA | null | Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. | null | null | null | null | CPMCBHC | Nested case-control study from the CPMC Breast Health Cohort. |
PSS000040 | PGS000028 | 981 | 495 | 486 | 0 | null | East Asian, European, Hispanic or Latin American | null | USA | null | Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. | null | null | null | null | CPMCBHC | Nested case-control study from the CPMC Breast Health Cohort. |
PSS000041 | PGS000030 | 74,849 | 46,939 | 27,910 | 100 | null | European | null | USA, Europe (multiple countries) | null | For each cohort core data on disease status, age at diagnosis (age at observation or questionnaire for controls), family history of PrCa, and clinical factors for cases (for example, PSA at diagnosis and Gleason score) was extracted | null | null | null | null | MCCS|SEARCH|MEC|HPFS|EPIC|COSM|CPCS|CPS|PLCO|SAAR|FHCRC|Gene-PARE|HZ|IPO-Porto|IMPACT|LAAPC|MCC-Spain|MDACCS|MOFFITT_PC|CONOR|PCMUS|PHS|Poland|PRAGGA|PROCAP|PROFILE|PROGReSS_PrCa|ProMPT|ProtecT|APCB|RAPPER|SFPCS|SNP_Prostate_Ghent|SPAG|PCPT|SWOG-SELECT|TAMPERE|TOR|UKGPCS|ERSPC|QLD|STHM | These samples (OncoArray) were also used in the GWAS meta-analysis |
PSS000042 | PGS000031, PGS000032, PGS000033 | 820 | 118 | 702 | 38.8 | null | African American or Afro-Caribbean | null | USA | null | T2D was defined by a fasting plasma glucose ≥7.0 mmol/L (≥126 mg/dL) or report of taking diabetes medications | null | null | null | null | CARDIA | null |
PSS000043 | PGS000031, PGS000032, PGS000033 | 1,650 | 97 | 1,553 | 46.5 | null | European | null | USA | null | T2D was defined by a fasting plasma glucose ≥7.0 mmol/L (≥126 mg/dL) or report of taking diabetes medications | null | null | null | null | CARDIA | null |
PSS000044 | PGS000031, PGS000032, PGS000033 | 3,471 | 446 | 3,025 | 46.6 | null | European | null | USA | null | T2D was defined by a fasting plasma glucose ≥7.0 mmol/L (≥126 mg/dL) or report of taking diabetes medications | null | null | null | null | FOS | null |
PSS000045 | PGS000034 | 1,699 | null | null | 100 | null | European | null | USA | null | BMI difference between ages 21 and 45 | null | null | null | null | HPFS | null |
PSS000046 | PGS000034 | 1,634 | null | null | 100 | null | European | null | USA | null | BMI difference between ages 45 and 65 | null | null | null | null | HPFS | null |
PSS000047 | PGS000034 | 2,020 | null | null | 100 | null | European | null | USA | null | BMI difference between ages 65 and 80 | null | null | null | null | HPFS | null |
PSS000048 | PGS000034 | 5,956 | null | null | 0 | null | European | null | USA | null | BMI difference between ages 18 and 45 | null | null | null | null | NHS | null |
PSS000049 | PGS000034 | 6,705 | null | null | 0 | null | European | null | USA | null | BMI difference between age 18 and Menopause | null | null | null | null | NHS | null |
PSS000050 | PGS000034 | 5,640 | null | null | 0 | null | European | null | USA | null | BMI difference between ages 45 and 65 | null | null | null | null | NHS | null |
PSS000051 | PGS000034 | 2,942 | null | null | 0 | null | European | null | USA | null | BMI difference between ages 65 and 80 | null | null | null | null | NHS | null |
PSS000052 | PGS000034 | 6,436 | null | null | 0 | null | European | null | USA | null | BMI difference between Menopause and age 65 | null | null | null | null | NHS | null |
PSS000053 | PGS000035 | 4,606 | 580 | 4,026 | 45.896657 | null | European, NR | null | USA | FHS is principally composed of individuals of European ancestry | Participants were classified as having AF if an arrhythmia was present on an ECG obtained at a study visit or encounter with external clinicians, Holter monitoring, or noted in hospital records during a median 9.4 years of follow-up. | null | null | null | null | FHS | Samples were obtained from the following FHS cohorts: Original, Offspring, and Third Generation. Participants were eligible for inclusion if they were AF free at an average age of 55. |
PSS000054 | PGS000036 | 324,870 | 13,480 | 311,390 | null | null | European | null | null | null | Prevalent T2D status was defined using self-reported medical history and medication | null | null | 31,322,649 | null | UKB | null |
PSS000055 | PGS000037 | 880 | 305 | 575 | 51 | null | European | null | New Zealand | null | Current asthma status was assessed at ages 9, 11, 13, 15, 18, 21, 26, 32, and 38 years from standardised interviews of study members (or their mothers if the participant was younger than 13 years) done by pulmonary specialists. Current asthma was defined as a diagnosis of asthma in addition to positive symptoms within the past 12 months, including asthma attack, recurrent wheeze (excluding study members reporting only one or two episodes lasting less than 1 h), or medical treatment for asthma. Age at asthma onset was defined as the earliest age at which wheezing symptoms or diagnosis by a physician were recorded. | median:38.0;range:[0.0,38.0];unit:years | null | null | null | DMHDS | null |
PSS000056 | PGS000037 | 187 | null | null | null | null | European | null | New Zealand | null | Current asthma status was assessed at ages 9, 11, 13, 15, 18, 21, 26, 32, and 38 years from standardised interviews of study members (or their mothers if the participant was younger than 13 years) done by pulmonary specialists. Current asthma was defined as a diagnosis of asthma in addition to positive symptoms within the past 12 months, including asthma attack, recurrent wheeze (excluding study members reporting only one or two episodes lasting less than 1 h), or medical treatment for asthma. Age at asthma onset was defined as the earliest age at which wheezing symptoms or diagnosis by a physician were recorded. | null | null | null | null | DMHDS | Subset of children from DMHDS with asthma onset in childhood (before age 13 years) |
PSS000057 | PGS000038 | 306,473 | 2,077 | 304,396 | 44.589246 | mean:56.7;sd:7.9;unit:years | European | null | UK | Unrelated White British subset of UKB participants | Incident stroke in was defined based on the UK Biobank (UKB) algorithm, based on medical history and linkage to data on hospital admissions and mortality. The authors also subtyped ischaemic stroke, intracerebral haemorrhage, or subarachnoid haemorrhage. UKB Participants with genetic data were excluded from the analysis based on the following criteria: failing genetic quality control (missingness > 5%, sex mismatch, excessive heterozygosity), having a history of stroke or myocardial infarction (MI), self-report of stroke or MI, missing lifestyle information. | median:7.1;unit:years | null | null | null | UKB | null |
PSS000058 | PGS000038, PGS000039 | 395,393 | 3,075 | 392,318 | 45.7 | mean:54.3;unit:years | European | null | UK | null | Prevalent and incident Ischaemic stroke; defined in http://biobank.ndph.ox.ac.uk/showcase/docs/alg_outcome_stroke.pdf | mean:6.3;sd:1.9;unit:years | null | null | null | UKB | Validation set |
PSS000059 | PGS000040 | 2,476 | 647 | 1,829 | null | null | European | Finnish | Finland | null | null | null | GCST000612 | null | null | Health2000|FINRISK | null |
PSS000060 | PGS000040 | 10,304 | 5,907 | 4,397 | null | null | European | British | UK | null | null | null | GCST005523 | null | null | null | Immunochip |
PSS000061 | PGS000040 | 1,040 | 497 | 543 | null | null | European | Italian | Italy | null | null | null | GCST000612 | null | null | null | null |
PSS000062 | PGS000040 | 1,649 | 803 | 846 | null | null | European | Dutch | Netherlands | null | null | null | GCST000612 | null | null | null | null |
PSS000063 | PGS000040 | 2,200 | 778 | 1,422 | null | null | European | British | UK | null | null | null | GCST000048 | null | null | null | null |
PSS000064 | PGS000040 | 1,696 | 1,259 | 437 | null | null | European | null | USA | null | null | null | GCST002520 | null | null | NIDDK | null |
PSS000065 | PGS000040, PGS000041, PGS000042 | 1,237 | 1,094 | 143 | null | null | European | null | USA | null | The HLA-DQ2.5-positive subset of NIDDK-CIDR | null | GCST002520 | null | null | NIDDK | HLA alleles were imputed using SNP2HLA |
PSS000066 | PGS000043 | 55,965 | 2,100 | 53,865 | null | null | European | null | USA | null | VTE was defined in the MVP cohort using the following diagnosis codes for: - Deep Venous Thrombosis ICD-10 codes: {I80.1, I80.2, I82.22, I82.4, I82.5} and ICD-9 codes: {451.11, 451.19, 453.2, 453.4} - Pulmonary Embolism ICD-10 codes: {I26.0, I26.9} and ICD-9 code {415.1} | null | null | null | null | MVP | MVP Cohort = 3.0 |
PSS000067 | PGS000043 | 10,975 | 690 | 10,285 | 0 | mean:65.0;unit:years | European | null | USA | null | null | null | null | null | null | WHI|WHI-GARNET|WHI-MS|WHI-LLS|WHI-HT | null |
PSS000068 | PGS000044 | 8,796 | 2,148 | 6,648 | 100 | range:[50.0,69.0];unit:years | European | null | UK | null | Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml. | null | null | 12,709,289 | null | ProtecT | null |
PSS000068 | PGS000044 | 5,059 | 4,099 | 960 | 100 | range:[50.0,69.0];unit:years | European | null | UK | null | Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml. | null | null | null | null | SEARCH | null |
PSS000068 | PGS000044 | 3,157 | 3,157 | 0 | 100 | range:[50.0,60.0];unit:years | European | null | UK | null | Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml. | null | null | 1,249,686 | null | UKGPCS | null |
PSS000069 | PGS000044 | 4,967 | 1,089 | 3,878 | 100 | range:[55.0,71.0];unit:years | European | Finnish | Finland | null | Prostate cancer was classified as localised disease with tumour-node-metastasis (TNM) stage T1-2 N0 M0; and advanced disease (regional-distant) with stage T3 and above or any T N1 M1; as non-aggressive tumour, Gleason score <7, and aggressive tumour, Gleason score ⩾7. | median:13.0;unit:years | null | null | null | ERSPC | null |
PSS000070 | PGS000001, PGS000002, PGS000003, PGS000045, PGS000046, PGS000047 | 15,252 | 7,797 | 7,455 | 0 | null | European | null | NR | Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry | BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. | null | null | null | null | CIMBA | Median censoring age (cases) = 40 |
PSS000071 | PGS000001, PGS000002, PGS000003, PGS000045, PGS000046, PGS000047 | 8,211 | 4,330 | 3,881 | 0 | null | European | null | NR | Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry | BRCA2 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. | null | null | null | null | CIMBA | Median censoring age (cases) = 43 |
PSS000072 | PGS000048 | 15,252 | 2,462 | 12,790 | 0 | null | European | null | NR | Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry | BRCA1 mutation carriers were followed until the age of ovarian cancer diagnosis, age at risk-reducing salpingo-oophorectomy (RRSO) or age at last observation. Breast cancer diagnosis was not considered as a censoring event in the ovarian cancer analysis | null | null | null | null | CIMBA | Median censoring age (cases) = 50 |
PSS000073 | PGS000048 | 8,211 | 631 | 7,580 | 0 | null | European | null | NR | Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry | BRCA2 mutation carriers were followed until the age of ovarian cancer diagnosis, age at risk-reducing salpingo-oophorectomy (RRSO) or age at last observation. Breast cancer diagnosis was not considered as a censoring event in the ovarian cancer analysis | null | null | null | null | CIMBA | Median censoring age (cases) = 57 |
PSS000074 | PGS000045, PGS000046, PGS000047 | 1,590 | 277 | 1,313 | 100 | null | European | null | Australia, Austria, Belgium, Canada, Denmark, Finland, France, Germany, Greece, Hungary, Iceland, Italy, Lithuania, Netherlands, Portugal, Spain, Sweden, UK, USA | Self-reported European ancestry | Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. | null | null | null | null | DEMOKRITOS|CNIO|CONSIT|DKFZ|FCCC|G-FaST|HVH|IOVHBOCS|kConFab|MAYO|NCI|OSU|UPITT|CBCS|BCFR|ILUH|SWE-BRCA|Chicago|GC-HBOC|HEBCS|MSKCC|PBCS|BRICOH|CIMBA|EMBRACE|GEMO|HCSC|HEBON|HUNBOCS|ICO|IPOBCS|MUV|OCGN|OUH|UPENN|VFCTG|BFBOCC | null |
PSS000075 | PGS000049 | 1,525 | 212 | 1,313 | 100 | null | European | null | Australia, Austria, Belgium, Canada, Denmark, Finland, France, Germany, Greece, Hungary, Iceland, Italy, Lithuania, Netherlands, Portugal, Spain, Sweden, UK, USA | Self-reported European ancestry | Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. | null | null | null | null | DEMOKRITOS|CNIO|CONSIT|DKFZ|FCCC|G-FaST|HVH|IOVHBOCS|kConFab|BRICOH|EMBRACE|HEBON|HUNBOCS|ICO|IPOBCS|MAYO|NCI|OSU|UPITT|CBCS|BCFR|ILUH|SWE-BRCA|Chicago|GC-HBOC|HEBCS|MSKCC|PBCS|CIMBA|HCSC|MUV|OCGN|OUH|UPENN|VFCTG|BFBOCC|GEMO | null |
PSS000076 | PGS000049 | 3,325 | 2,012 | 1,313 | 100 | null | European | null | Australia, Austria, Belgium, Canada, Denmark, Finland, France, Germany, Greece, Hungary, Iceland, Italy, Lithuania, Netherlands, Portugal, Spain, Sweden, UK, USA | Self-reported European ancestry | null | null | null | null | null | DEMOKRITOS|CNIO|CONSIT|DKFZ|FCCC|G-FaST|HVH|IOVHBOCS|kConFab|MAYO|NCI|OSU|UPITT|CBCS|BCFR|ILUH|SWE-BRCA|Chicago|GC-HBOC|HEBCS|MSKCC|PBCS|BRICOH|CIMBA|EMBRACE|GEMO|HCSC|HEBON|HUNBOCS|ICO|IPOBCS|MUV|OCGN|OUH|UPENN|VFCTG|BFBOCC | null |
PSS000077 | PGS000049 | 1,366 | 53 | 1,313 | 100 | null | European | null | Australia, Austria, Belgium, Canada, Denmark, Finland, France, Germany, Greece, Hungary, Iceland, Italy, Lithuania, Netherlands, Portugal, Spain, Sweden, UK, USA | Self-reported European ancestry | null | null | null | null | null | DEMOKRITOS|CNIO|CONSIT|DKFZ|FCCC|G-FaST|HVH|IOVHBOCS|kConFab|MAYO|NCI|OSU|UPITT|CBCS|BCFR|ILUH|SWE-BRCA|Chicago|GC-HBOC|HEBCS|MSKCC|PBCS|BRICOH|EMBRACE|GEMO|HEBON|HUNBOCS|ICO|IPOBCS|OCGN|OUH|VFCTG|BFBOCC|CIMBA|HCSC|MUV|UPENN | null |
PSS000078 | PGS000050 | 23,567 | 11,905 | 11,662 | 0 | null | East Asian | null | Thaiand, Japan, China, Korea, Malaysia | null | null | null | null | null | null | BCAC|ACP|HERPACC|LAABC|MYBRCA|SBCGS|SEBCS|SGBCC|TBCS|TWBCS|SGWAS | null |
PSS000079 | PGS000050 | 5,152 | 2,867 | 2,285 | 0 | null | East Asian | Chinese | China | null | null | null | null | 19,219,042 | null | SGWAS | SGWAS (Stage 1). Smaller set of the larger test set from this study. |
PSS000080 | PGS000051 | 11,880 | 4,006 | 7,874 | 0 | mean:53.7;range:[34.0,70.0];sd:8.0;unit:years | European, NR | null | USA | null | Questionnaires were mailed to women biennially to collect information on breast cancer risk factors, including age at menarche, age at first birth, parity, family history of breast cancer, height, weight, physical activity, menopausal status, age at menopause, and HT use. Incident breast cancer cases up to 1 June 2010 were also identified through biennial questionnaires. Diagnoses were confirmed with the participants (or next of kin), and permission was obtained to collect relevant medical or pathology reports. Analysis was restricted to invasive breast cancer. | mean:26.54;unit:years | null | null | null | NHS|NHS2 | Performance metrics are reported for the "All women" results of Table 2 |
PSS000081 | PGS000051 | 8,160 | 2,676 | 5,484 | 0 | mean:53.7;range:[34.0,70.0];sd:8.0;unit:years | European, NR | null | USA | null | Questionnaires were mailed to women biennially to collect information on breast cancer risk factors, including age at menarche, age at first birth, parity, family history of breast cancer, height, weight, physical activity, menopausal status, age at menopause, and HT use. Incident breast cancer cases up to 1 June 2010 were also identified through biennial questionnaires. Diagnoses were confirmed with the participants (or next of kin), and permission was obtained to collect relevant medical or pathology reports. Analysis was restricted to invasive breast cancer. | mean:23.08;unit:years | null | null | null | NHS|NHS2 | Performance metrics are reported for the "All women" results of Table 3 |
PSS000082 | PGS000052 | 585 | 323 | 262 | 0 | mean (cases):51.0;sd (cases):11.0;unit:years | European | null | Netherlands, Hungary | null | A family-based cohort including 323 breast cancer cases and 262 unaffected relatives from 101 families. Unaffected relatives derived from 49 out of 101 families. | null | null | null | null | null | null |
PSS000083 | PGS000021 | 1,963 | 1,963 | 0 | null | null | European | null | UK | null | Cases were clinically diagnosed with T1D before 17 years of age and treated with insulin from diagnosis. Patients with known MODY or NDM were excluded. | null | null | null | null | WTCCC | Cases with Type 1 Diabetes |
PSS000083 | PGS000021 | 805 | 805 | 0 | 33.913043 | null | European | null | UK | null | MODY patients with a confirmed monogenic etiology on genetic testing (415 patients with HNF1A MODY, 346 with GCK MODY, 42 with HNF4A MODY, and 2 with HNF1B MODY). The median age of diagnosis was 20 years (interquartile range 15, 30), and 532 patients were female. | null | null | null | null | null | Maturity-onset diabetes of young (MODY) cases ascertained from the Genetic Βeta Cell Research Bank, Exeter, U.K. |
PSS000084 | PGS000054 | 3,324 | 2,155 | 1,169 | 34 | null | Hispanic or Latin American | null | USA, Dominican Republic | Samples are described as "Carribbean Hispanic" | EFIGA recruited patients from families multiply affected by LOAD, but of Caribbean Hispanic ancestry from the Dominican Republic and New York. Families were recruited after confirming diagnoses in the probands. Family members with dementia were also interviewed and neurologically evaluated. Clinical diagnoses were made in a consensus diagnostic conference by a panel of neurologists, neuropsychologists, and psychiatrists. Detailed description is available elsewhere.14 For these family-based studies, we included data from families for which their members (1) were 60 years or older at the time of enrollment; (2) had a diagnosis of probable or possible LOAD according to National Institute of Neurological and Communicative Disorders and Stroke–Alzheimer’s Disease and Related Disorders Association (NINDS-ADRDA) criteria; (3) had available pedigree information and covariates. | null | null | null | null | EFIGA | null |
PSS000085 | PGS000053 | 4,792 | 2,128 | 2,664 | 38 | null | European | null | USA | null | Selection criteria included (1) a proband who received a dianosis of definite or probable late onset Alzheimer's Disease (LOAD) with age at onset of at least 60 years; (2) a full sibling with definite, probable, or possible LOAD with age at onset after 60 years; (3) a related family member (first-,second-,or third-degree relative) of theaffected sibling pair and 60 years or older if unaffected, or 50 years or older if dianosed with LOAD or mild cognitive impairment (MCI) | null | null | null | null | NIA-LOAD | null |
PSS000086 | PGS000055 | 21,630 | 8,580 | 13,050 | null | null | East Asian | null | China, Japan, Korea, Taiwan | null | null | null | null | null | null | EPIC|NHS|UKB|HPFS|MGI|CORSA|DACHS|COLON | null |
PSS000087 | PGS000055 | 61,335 | 12,952 | 48,383 | null | null | European | null | USA, Europe | null | null | null | null | null | null | HPFS3|NHS3|EPIC|UKB|MGI|CORSA|COLON|DACHS | null |
PSS000088 | PGS000056 | 285 | 285 | 0 | 56.140351 | mean:69.1;sd:10.4;unit:years | European | null | USA | null | Parkinson Disease symptom progression was assessed during 1 to 3 follow-up examinations by a movement disorder team (June 1, 2007, to August 31, 2013; mean [SD] time from disease onset, 7.3 [2.8] years) using the following methods: - Cognitive decline was determined with the Mini-Mental State Examination (MMSE; range, 0-30, with lower scores indicating worse cognitive function). Cognitive decline was defined as a 4-point decrease from baseline MMSE score and time to event as the time from the baseline to follow-up examinations in which a 4-point decrease was first measured - Motor decline was defined as a 20-point increase in Unified Parkinson’s Disease Rating Scale part III (UPDRS-III) score, and time to event as the time from the baseline to follow-up examinations in which a 20-point increase was first measured. - Motor decline was also measured by assessing conversion to stage 3 or higher of the Hoehn & Yahr (H&Y) scale. Time to conversion to H&Y stage 3 was defined as the time from the baseline to first follow-up examinations in which the patient scored at least stage 3. | mean:5.3;sd:2.1;unit:years | null | 29,340,614 | null | PEG | Patients with idiopathic PD diagnosed less than 3 years previously were recruited from June 1, 2001, through November 31, 2007. Patients were confirmed as having clinically probable or possible Parkinson Disease by a team of movement disorder specialists |
PSS000089 | PGS000057 | 4,392 | null | null | null | range:[55.0,80.0];unit:years | NR | null | null | null | Total carotid plaque burden (mm2) | null | null | null | null | BioImage | null |
PSS000090 | PGS000057 | 1,154 | null | null | null | range:[32.0,47.0];unit:years | NR | null | null | null | Total coronary arterial clacification (CAC) was coded as a a dichotomous outcome variable (CAC>0 versus CAC=0), and quantified by the Agatston method | mean:15.0;unit:years | null | null | null | CARDIA | null |
PSS000091 | PGS000057 | 2,440 | null | null | 100 | mean:55.1;sd:5.5;unit:years | NR | null | null | null | Nonfatal myocardial infarction or death from CHD | mean:13.5;sd:2.8;unit:years | null | null | null | null | Participants were all men hypercholesterolemia but without a history of myocardial infarction, allocated to the placebo group |
PSS000092 | PGS000058 | 5,360 | 675 | 4,685 | 64.8 | mean:62.8;unit:years | European | null | Canada, USA | Self reported white | Incident Major coronary events (MCE) are defined as: fatal or nonfatal coronary artery disease (CAD) events, nonfatal myocardial infarction, or unstable angina | median:4.7;unit:years | null | null | null | ACCORD | Type 2 Diabetes patients |
PSS000093 | PGS000058 | 1,931 | 163 | 1,768 | null | null | European | null | null | Self reported white | Incident Major coronary events (MCE) are defined as: fatal or nonfatal coronary artery disease (CAD) events, nonfatal myocardial infarction, or unstable angina | median:6.2;unit:years | null | null | null | ORIGIN | Participants are from the Outcome Reduction With Initial Glargine Intervention (ORIGIN) trial and were enrolled based on having some combination of impaired fasting glucose, impaired glucose tolerance or type 2 diabetes, and high cardiovascular risk |
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PGS Catalog — Scoring Files & Cleaned Metadata
Complete mirror of PGS Catalog scoring files converted to Apache Parquet format, together with cleaned and normalised metadata tables.
Built automatically by the just-prs pipeline.
Last updated: 2026-03-04 20:08 UTC
Release Statistics
| Metric | Value |
|---|---|
| Scoring file parquets | 5,268 |
| Unique PGS IDs (metadata) | 5,251 |
| Genome build | GRCh38 |
| Total scoring data size | 51.6 GB |
| Release timestamp | 2026-03-04T20:08:14Z |
Files
Metadata (data/metadata/)
Cleaned and normalised PGS Catalog metadata tables.
| File | Rows | Columns | Key columns |
|---|---|---|---|
metadata/scores.parquet |
5,251 | 12 | pgs_id, name, trait_reported, trait_efo, trait_efo_id, genome_build, n_variants, weight_type, ... (12 total) |
metadata/performance.parquet |
20,788 | 30 | ppm_id, pgs_id, pss_id, pgp_id, trait_reported, covariates, pmid, doi, ... (30 total) |
metadata/best_performance.parquet |
5,233 | 30 | pgs_id, ppm_id, pss_id, pgp_id, trait_reported, covariates, pmid, doi, ... (30 total) |
Scoring files (data/scores/)
Individual scoring weight files, one parquet per PGS ID. Each file contains variant-level effect weights with harmonised positions.
| Info | Value |
|---|---|
| Total files | 5,268 |
| Naming pattern | {PGS_ID}_hmPOS_GRCh38.parquet |
| Compression | zstd (level 9) |
| Examples | PGS000001_hmPOS_GRCh38.parquet, PGS000002_hmPOS_GRCh38.parquet, PGS000003_hmPOS_GRCh38.parquet, ... (5,268 files total) |
Metadata Cleanup Pipeline
The raw PGS Catalog CSVs undergo several transformations:
- Column renaming — verbose PGS column names (e.g.
Polygenic Score (PGS) ID) are mapped to shortsnake_caseequivalents (pgs_id). - Genome build normalization — 9 raw build variants (
hg19,hg37,hg38,NCBI36,hg18,NCBI35,GRCh37,GRCh38,NR) are mapped to canonical values:GRCh37,GRCh38,GRCh36, orNR. - Metric string parsing — performance metrics stored as strings like
"1.55 [1.52,1.58]"or"-0.7 (0.15)"are parsed into structured numeric columns (*_estimate,*_ci_lower,*_ci_upper,*_se) for OR, HR, Beta, AUROC, and C-index. - Performance flattening — performance metrics are joined with evaluation sample sets to include
sample size (
n_individuals) and ancestry (ancestry_broad). - Best performance selection —
best_performance.parquetcontains one row per PGS ID, selecting the evaluation with the largest sample size (with a preference for European-ancestry cohorts).
Scoring File Schema
Each scoring parquet contains variant-level data from the PGS Catalog harmonised files:
rsID— dbSNP rsIDchr_name/chr_position— chromosome and position (original)effect_allele/other_allele— alleleseffect_weight— variant weight (beta, log-OR, etc.)hm_chr/hm_pos— harmonised chromosome and position (GRCh38)hm_inferOtherAllele— inferred other allele during harmonisation- PGS header metadata is embedded as file-level Parquet metadata under the key
pgs_catalog_header.
Usage
Load metadata with polars
import polars as pl
from huggingface_hub import hf_hub_download
path = hf_hub_download(
repo_id="just-dna-seq/pgs-catalog",
filename="data/metadata/scores.parquet",
repo_type="dataset",
)
scores = pl.read_parquet(path)
print(scores.head())
Load a scoring file
path = hf_hub_download(
repo_id="just-dna-seq/pgs-catalog",
filename="data/scores/PGS000001_hmPOS_GRCh38.parquet",
repo_type="dataset",
)
weights = pl.read_parquet(path)
print(weights.head())
Source & License
- Source: PGS Catalog (EBI / NHGRI)
- License: CC BY 4.0
- Citation: Lambert, S.A. et al. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics 53, 420-425 (2021). doi:10.1038/s41588-021-00783-5
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