PGS Publication: PGP000271

Publication Information (EuropePMC)
Title Genome-wide risk prediction of common diseases across ancestries in one million people.
PubMed ID 35591975(Europe PMC)
doi 10.1016/j.xgen.2022.100118
Publication Date April 13, 2022
Journal Cell Genom
Author(s) Mars N, Kerminen S, Feng YA, Kanai M, Läll K, Thomas LF, Skogholt AH, Della Briotta Parolo P, Biobank Japan Project, FinnGen, Neale BM, Smoller JW, Gabrielsen ME, Hveem K, Mägi R, Matsuda K, Okada Y, Pirinen M, Palotie A, Ganna A, Martin AR, Ripatti S.
Released in PGS Catalog: April 13, 2022

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

PGS Developed By This Publication

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)
PGS002240
(prscs_prostatecancer)
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Prostate cancer prostate carcinoma 1,092,093
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002240/ScoringFiles/PGS002240.txt.gz
PGS002241
(ldpred_prostatecancer)
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Prostate cancer prostate carcinoma 6,497,734
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002241/ScoringFiles/PGS002241.txt.gz
PGS002244
(ldpred_cad)
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Coronary artery disease coronary artery disorder 6,576,338
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002244/ScoringFiles/PGS002244.txt.gz
PGS002243
(ldpred_t2d)
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 6,431,973
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002243/ScoringFiles/PGS002243.txt.gz
PGS002242
(ldpred_breastcancer)
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Breast cancer breast carcinoma 6,494,889
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002242/ScoringFiles/PGS002242.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
PPM012733 PGS002243
(ldpred_t2d)
 PSS009522|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.58 [1.56, 1.6] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012734 PGS002242
(ldpred_breastcancer)
 PSS009523|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.48 [1.45, 1.51] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012736 PGS002244
(ldpred_cad)
 PSS009517|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.47 [1.43, 1.52] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012737 PGS002243
(ldpred_t2d)
 PSS009518|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.55 [1.51, 1.59] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012738 PGS002242
(ldpred_breastcancer)
 PSS009519|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.45 [1.37, 1.53] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012739 PGS002241
(ldpred_prostatecancer)
 PSS009520|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.79 [1.68, 1.91] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012740 PGS002244
(ldpred_cad)
 PSS009513|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.32 [1.3, 1.34] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012741 PGS002243
(ldpred_t2d)
 PSS009514|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.37 [1.36, 1.39] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012742 PGS002242
(ldpred_breastcancer)
 PSS009515|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.25 [1.21, 1.28] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012743 PGS002241
(ldpred_prostatecancer)
 PSS009516|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.69 [1.64, 1.74] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012744 PGS002244
(ldpred_cad)
 PSS009525|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.44 [1.4, 1.48] — — birth year, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012745 PGS002243
(ldpred_t2d)
 PSS009526|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.64 [1.6, 1.69] — — birth year, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012746 PGS002242
(ldpred_breastcancer)
 PSS009527|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.5 [1.43, 1.58] — — birth year, 10 PCs (+/- dataset-specific technical covariates) —
PPM012747 PGS002241
(ldpred_prostatecancer)
 PSS009528|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.8 [1.72, 1.88] — — birth year, 10 PCs (+/- dataset-specific technical covariates) —
PPM012749 PGS002243
(ldpred_t2d)
 PSS009534|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.46 [1.41, 1.51] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012750 PGS002242
(ldpred_breastcancer)
 PSS009535|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.45 [1.38, 1.54] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012751 PGS002241
(ldpred_prostatecancer)
 PSS009536|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.66 [1.57, 1.76] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012752 PGS002244
(ldpred_cad)
 PSS009529|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.1 [0.96, 1.26] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012753 PGS002243
(ldpred_t2d)
 PSS009530|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.24 [1.09, 1.42] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012754 PGS002242
(ldpred_breastcancer)
 PSS009531|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 0.9 [0.69, 1.17] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012755 PGS002241
(ldpred_prostatecancer)
 PSS009532|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.19 [0.91, 1.55] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012756 PGS002244
(ldpred_cad)
 PSS009541|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.64 [1.61, 1.67] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012757 PGS002243
(ldpred_t2d)
 PSS009542|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.78 [1.75, 1.81] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012758 PGS002242
(ldpred_breastcancer)
 PSS009543|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.5 [1.47, 1.53] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012759 PGS002241
(ldpred_prostatecancer)
 PSS009544|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.91 [1.86, 1.96] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012760 PGS002240
(prscs_prostatecancer)
 PSS009544|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 2.14 [2.09, 2.19] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012761 PGS002244
(ldpred_cad)
 PSS009537|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.32 [1.13, 1.54] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012762 PGS002243
(ldpred_t2d)
 PSS009538|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.46 [1.32, 1.62] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012763 PGS002242
(ldpred_breastcancer)
 PSS009539|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.12 [0.93, 1.35] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012764 PGS002241
(ldpred_prostatecancer)
 PSS009540|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.35 [1.14, 1.61] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012766 PGS002244
(ldpred_cad)
 PSS009545|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.41 [1.3, 1.53] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012767 PGS002243
(ldpred_t2d)
 PSS009546|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.66 [1.55, 1.79] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012768 PGS002242
(ldpred_breastcancer)
 PSS009547|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Breast cancer OR: 1.47 [1.23, 1.75] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012769 PGS002241
(ldpred_prostatecancer)
 PSS009548|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 2.21 [1.73, 2.81] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012770 PGS002240
(prscs_prostatecancer)
 PSS009548|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 2.54 [1.98, 3.26] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012732 PGS002244
(ldpred_cad)
 PSS009521|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.53 [1.5, 1.55] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012735 PGS002241
(ldpred_prostatecancer)
 PSS009524|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.96 [1.91, 2.01] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012748 PGS002244
(ldpred_cad)
 PSS009533|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Coronary artery disease OR: 1.35 [1.29, 1.4] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012765 PGS002240
(prscs_prostatecancer)
 PSS009540|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.43 [1.21, 1.69] — — age, 10 PCs (+/- dataset-specific technical covariates) —

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
PSS009513 — —
[
  • 29,080 cases
  • , 149,646 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS009514 — —
[
  • 40,121 cases
  • , 138,605 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS009515 — —
[
  • 5,316 cases
  • , 173,410 controls
]
,
0.0 % Male samples
 — East Asian
(Japanese)		 — BBJ —
PSS009516 — —
[
  • 5,192 cases
  • , 173,534 controls
]
,
100.0 % Male samples
 — East Asian
(Japanese)		 — BBJ —
PSS009517 — —
[
  • 5,064 cases
  • , 105,533 controls
]
 — European
(Estonian)		 — EB —
PSS009518 — —
[
  • 7,066 cases
  • , 103,531 controls
]
 — European
(Estonian)		 — EB —
PSS009519 — —
[
  • 1,379 cases
  • , 109,218 controls
]
,
0.0 % Male samples
 — European
(Estonian)		 — EB —
PSS009520 — —
[
  • 1,202 cases
  • , 109,395 controls
]
,
100.0 % Male samples
 — European
(Estonian)		 — EB —
PSS009521 — —
[
  • 25,706 cases
  • , 232,696 controls
]
 — European
(Finnish)		 — FinnGen —
PSS009522 — —
[
  • 37,001 cases
  • , 221,401 controls
]
 — European
(Finnish)		 — FinnGen —
PSS009523 — —
[
  • 11,573 cases
  • , 246,829 controls
]
,
0.0 % Male samples
 — European
(Finnish)		 — FinnGen —
PSS009524 — —
[
  • 8,709 cases
  • , 249,693 controls
]
,
100.0 % Male samples
 — European
(Finnish)		 — FinnGen —
PSS009525 — —
[
  • 6,594 cases
  • , 62,828 controls
]
 — European Norwegian HUNT —
PSS009526 — —
[
  • 5,228 cases
  • , 64,194 controls
]
 — European Norwegian HUNT —
PSS009527 — —
[
  • 1,731 cases
  • , 67,691 controls
]
,
0.0 % Male samples
 — European Norwegian HUNT —
PSS009528 — —
[
  • 2,224 cases
  • , 67,198 controls
]
,
100.0 % Male samples
 — European Norwegian HUNT —
PSS009529 — —
[
  • 285 cases
  • , 1,250 controls
]
 — African American or Afro-Caribbean — MGBB —
PSS009530 — —
[
  • 660 cases
  • , 875 controls
]
 — African American or Afro-Caribbean — MGBB —
PSS009531 — —
[
  • 64 cases
  • , 1,471 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean — MGBB —
PSS009532 — —
[
  • 80 cases
  • , 1,455 controls
]
,
100.0 % Male samples
 — African American or Afro-Caribbean — MGBB —
PSS009533 — —
[
  • 3,206 cases
  • , 22,490 controls
]
 — European — MGBB —
PSS009534 — —
[
  • 5,182 cases
  • , 20,514 controls
]
 — European — MGBB —
PSS009535 — —
[
  • 1,513 cases
  • , 24,183 controls
]
,
0.0 % Male samples
 — European — MGBB —
PSS009536 — —
[
  • 1,593 cases
  • , 24,103 controls
]
,
100.0 % Male samples
 — European — MGBB —
PSS009537 — —
[
  • 169 cases
  • , 7,449 controls
]
 — African unspecified — UKB —
PSS009538 — —
[
  • 691 cases
  • , 6,927 controls
]
 — African unspecified — UKB —
PSS009539 — —
[
  • 132 cases
  • , 7,486 controls
]
,
0.0 % Male samples
 — African unspecified — UKB —
PSS009540 — —
[
  • 199 cases
  • , 7,419 controls
]
,
100.0 % Male samples
 — African unspecified — UKB —
PSS009541 — —
[
  • 17,986 cases
  • , 325,690 controls
]
 — European British UKB —
PSS009542 — —
[
  • 13,616 cases
  • , 330,060 controls
]
 — European British UKB —
PSS009543 — —
[
  • 11,075 cases
  • , 332,601 controls
]
,
0.0 % Male samples
 — European British UKB —
PSS009544 — —
[
  • 7,429 cases
  • , 336,247 controls
]
,
100.0 % Male samples
 — European British UKB —
PSS009545 — —
[
  • 740 cases
  • , 6,888 controls
]
 — South Asian — UKB —
PSS009546 — —
[
  • 1,120 cases
  • , 6,508 controls
]
 — South Asian — UKB —
PSS009547 — —
[
  • 139 cases
  • , 7,489 controls
]
,
0.0 % Male samples
 — South Asian — UKB —
PSS009548 — —
[
  • 72 cases
  • , 7,556 controls
]
,
100.0 % Male samples
 — South Asian — UKB —