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, Bioban... k 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.Show more
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

JSONXMLCSVTXTMS-Excel
Loading, please wait
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 cancerprostate carcinoma1,092,093
G
D
E
 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 cancerprostate carcinoma6,497,734
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002241/ScoringFiles/PGS002241.txt.gz
PGS002242
(ldpred_breastcancer)
PGP000271 |
Mars N et al. Cell Genom (2022)
Breast cancerbreast carcinoma6,494,889
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002242/ScoringFiles/PGS002242.txt.gz
PGS002243
(ldpred_t2d)
PGP000271 |
Mars N et al. Cell Genom (2022)
Type 2 diabetes (T2D)type 2 diabetes mellitus6,431,973
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002243/ScoringFiles/PGS002243.txt.gz
PGS002244
(ldpred_cad)
PGP000271 |
Mars N et al. Cell Genom (2022)
Coronary artery diseasecoronary artery disease6,576,338
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002244/ScoringFiles/PGS002244.txt.gz
Showing 1 to 5 of 5 rows

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.

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PPM012732PGS002244
(ldpred_cad)
PSS009521|
European Ancestry|
258,402 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Coronary artery diseaseOR: 1.53 [1.5, 1.55]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012733PGS002243
(ldpred_t2d)
PSS009522|
European Ancestry|
258,402 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.58 [1.56, 1.6]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012734PGS002242
(ldpred_breastcancer)
PSS009523|
European Ancestry|
258,402 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Breast cancerOR: 1.48 [1.45, 1.51]——age, 10 PCs (+/- dataset-specific technical covariates)—
PPM012735PGS002241
(ldpred_prostatecancer)
PSS009524|
European Ancestry|
258,402 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Prostate cancerOR: 1.96 [1.91, 2.01]——age, 10 PCs (+/- dataset-specific technical covariates)—
PPM012736PGS002244
(ldpred_cad)
PSS009517|
European Ancestry|
110,597 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Coronary artery diseaseOR: 1.47 [1.43, 1.52]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012737PGS002243
(ldpred_t2d)
PSS009518|
European Ancestry|
110,597 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.55 [1.51, 1.59]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012738PGS002242
(ldpred_breastcancer)
PSS009519|
European Ancestry|
110,597 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Breast cancerOR: 1.45 [1.37, 1.53]——age, 10 PCs (+/- dataset-specific technical covariates)—
PPM012739PGS002241
(ldpred_prostatecancer)
PSS009520|
European Ancestry|
110,597 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Prostate cancerOR: 1.79 [1.68, 1.91]——age, 10 PCs (+/- dataset-specific technical covariates)—
PPM012740PGS002244
(ldpred_cad)
PSS009513|
East Asian Ancestry|
178,726 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Coronary artery diseaseOR: 1.32 [1.3, 1.34]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012741PGS002243
(ldpred_t2d)
PSS009514|
East Asian Ancestry|
178,726 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.37 [1.36, 1.39]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012742PGS002242
(ldpred_breastcancer)
PSS009515|
East Asian Ancestry|
178,726 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Breast cancerOR: 1.25 [1.21, 1.28]——age, 10 PCs (+/- dataset-specific technical covariates)—
PPM012743PGS002241
(ldpred_prostatecancer)
PSS009516|
East Asian Ancestry|
178,726 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Prostate cancerOR: 1.69 [1.64, 1.74]——age, 10 PCs (+/- dataset-specific technical covariates)—
PPM012744PGS002244
(ldpred_cad)
PSS009525|
European Ancestry|
69,422 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Coronary artery diseaseOR: 1.44 [1.4, 1.48]——birth year, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012745PGS002243
(ldpred_t2d)
PSS009526|
European Ancestry|
69,422 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.64 [1.6, 1.69]——birth year, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012746PGS002242
(ldpred_breastcancer)
PSS009527|
European Ancestry|
69,422 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Breast cancerOR: 1.5 [1.43, 1.58]——birth year, 10 PCs (+/- dataset-specific technical covariates)—
Showing 1 to 15 of 39 rows
152550All
rows per page

Evaluated Samples

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
]
—EuropeanNorwegianHUNT—
PSS009526——
[
  • 5,228 cases
  • , 64,194 controls
]
—EuropeanNorwegianHUNT—
PSS009527——
[
  • 1,731 cases
  • , 67,691 controls
]
,
0.0 % Male samples
—EuropeanNorwegianHUNT—
Showing 1 to 15 of 36 rows
152550All
rows per page