Trait: platelet count

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004309
Description The number of PLATELETS per unit volume in a sample of venous BLOOD.
Trait category
Hematological measurement
Synonym blood platelet number
Mapped terms 4 mapped terms
  • MeSH:D010976
  • MedDRA:10035525
  • NCIt:C51951
  • SNOMEDCT:61928009

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
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000109
(plt)
PGP000051 |
Xu Y et al. Cell Genom (2022)
Platelet count platelet count 26,683
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000109/ScoringFiles/PGS000109.txt.gz
PGS000186
(plt)
PGP000078 |
Vuckovic D et al. Cell (2020)
Platelet count platelet count 739
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000186/ScoringFiles/PGS000186.txt.gz
PGS001238
(GBE_INI30080)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Platelet count platelet count 24,893
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001238/ScoringFiles/PGS001238.txt.gz
PGS001973
(portability-PLR_log_platelet)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Platelet count platelet count 60,665
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001973/ScoringFiles/PGS001973.txt.gz
PGS002191
(portability-ldpred2_log_platelet)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Platelet count platelet count 663,591
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002191/ScoringFiles/PGS002191.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
PPM000250 PGS000109
(plt)
PSS000174|
European Ancestry|
78,246 individuals
PGP000051 |
Xu Y et al. Cell Genom (2022)
Reported Trait: Platelet count Pearson correlation coefficent (r): 0.52039 age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment) UKB Testing Set - these samples were held out from Score Development (regression training) but overlap with the samples used for variant selection (GWAS)
PPM000251 PGS000109
(plt)
PSS000148|
European Ancestry|
38,939 individuals
PGP000051 |
Xu Y et al. Cell Genom (2022)
Reported Trait: Platelet count Pearson correlation coefficent (r): 0.53746 age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment)
PPM001775 PGS000186
(plt)
PSS000911|
Greater Middle Eastern Ancestry|
13,989 individuals
PGP000147 |
Thareja G et al. Nat Commun (2021)
|Ext.
Reported Trait: Platelet count Pearson correlation coefficent (r): 0.35
PPM000557 PGS000186
(plt)
PSS000290|
European Ancestry|
2,314 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Platelet count : 0.16049 sex, age, 10 genetic PCs
PPM000540 PGS000186
(plt)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Platelet count : 0.19195 sex, age, 10 genetic PCs
PPM008699 PGS001238
(GBE_INI30080)
PSS006946|
African Ancestry|
6,139 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Platelet count : 0.13129 [0.11599, 0.14659]
Incremental R2 (full-covars): 0.04423
PGS R2 (no covariates): 0.04881 [0.03859, 0.05902]
age, sex, UKB array type, Genotype PCs
PPM008700 PGS001238
(GBE_INI30080)
PSS006947|
East Asian Ancestry|
1,655 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Platelet count : 0.14398 [0.1132, 0.17476]
Incremental R2 (full-covars): 0.09414
PGS R2 (no covariates): 0.09846 [0.07165, 0.12527]
age, sex, UKB array type, Genotype PCs
PPM008701 PGS001238
(GBE_INI30080)
PSS006948|
European Ancestry|
24,175 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Platelet count : 0.26403 [0.25464, 0.27343]
Incremental R2 (full-covars): 0.21574
PGS R2 (no covariates): 0.21973 [0.21064, 0.22881]
age, sex, UKB array type, Genotype PCs
PPM008702 PGS001238
(GBE_INI30080)
PSS006949|
South Asian Ancestry|
7,520 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Platelet count : 0.24088 [0.22438, 0.25738]
Incremental R2 (full-covars): 0.15169
PGS R2 (no covariates): 0.153 [0.13833, 0.16767]
age, sex, UKB array type, Genotype PCs
PPM008703 PGS001238
(GBE_INI30080)
PSS006950|
European Ancestry|
65,637 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Platelet count : 0.26678 [0.26106, 0.2725]
Incremental R2 (full-covars): 0.20845
PGS R2 (no covariates): 0.20987 [0.20441, 0.21533]
age, sex, UKB array type, Genotype PCs
PPM010666 PGS001973
(portability-PLR_log_platelet)
PSS009007|
African Ancestry|
3,711 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.2443 [0.2137, 0.2744] sex, age, birth date, deprivation index, 16 PCs
PPM010659 PGS001973
(portability-PLR_log_platelet)
PSS009459|
European Ancestry|
19,422 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.4839 [0.473, 0.4946] sex, age, birth date, deprivation index, 16 PCs
PPM010660 PGS001973
(portability-PLR_log_platelet)
PSS009233|
European Ancestry|
4,002 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.4742 [0.4498, 0.498] sex, age, birth date, deprivation index, 16 PCs
PPM010661 PGS001973
(portability-PLR_log_platelet)
PSS008787|
European Ancestry|
6,436 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.4739 [0.4547, 0.4927] sex, age, birth date, deprivation index, 16 PCs
PPM010662 PGS001973
(portability-PLR_log_platelet)
PSS008561|
Greater Middle Eastern Ancestry|
1,153 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.4562 [0.4088, 0.5011] sex, age, birth date, deprivation index, 16 PCs
PPM010663 PGS001973
(portability-PLR_log_platelet)
PSS008339|
South Asian Ancestry|
6,076 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.4242 [0.4034, 0.4447] sex, age, birth date, deprivation index, 16 PCs
PPM010664 PGS001973
(portability-PLR_log_platelet)
PSS008116|
East Asian Ancestry|
1,762 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.3503 [0.3084, 0.3908] sex, age, birth date, deprivation index, 16 PCs
PPM010665 PGS001973
(portability-PLR_log_platelet)
PSS007903|
African Ancestry|
2,343 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.2414 [0.2028, 0.2794] sex, age, birth date, deprivation index, 16 PCs
PPM012376 PGS002191
(portability-ldpred2_log_platelet)
PSS009233|
European Ancestry|
4,002 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.469 [0.4444, 0.4929] sex, age, birth date, deprivation index, 16 PCs
PPM012377 PGS002191
(portability-ldpred2_log_platelet)
PSS008787|
European Ancestry|
6,436 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.468 [0.4487, 0.4869] sex, age, birth date, deprivation index, 16 PCs
PPM012378 PGS002191
(portability-ldpred2_log_platelet)
PSS008561|
Greater Middle Eastern Ancestry|
1,153 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.4476 [0.3998, 0.493] sex, age, birth date, deprivation index, 16 PCs
PPM012379 PGS002191
(portability-ldpred2_log_platelet)
PSS008339|
South Asian Ancestry|
6,076 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.4155 [0.3944, 0.4361] sex, age, birth date, deprivation index, 16 PCs
PPM012375 PGS002191
(portability-ldpred2_log_platelet)
PSS009459|
European Ancestry|
19,422 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.4757 [0.4648, 0.4866] sex, age, birth date, deprivation index, 16 PCs
PPM012380 PGS002191
(portability-ldpred2_log_platelet)
PSS008116|
East Asian Ancestry|
1,762 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.3472 [0.3052, 0.3878] sex, age, birth date, deprivation index, 16 PCs
PPM012381 PGS002191
(portability-ldpred2_log_platelet)
PSS007903|
African Ancestry|
2,343 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.2554 [0.217, 0.293] sex, age, birth date, deprivation index, 16 PCs
PPM012382 PGS002191
(portability-ldpred2_log_platelet)
PSS009007|
African Ancestry|
3,711 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Platelet count Partial Correlation (partial-r): 0.2355 [0.2048, 0.2658] sex, age, birth date, deprivation index, 16 PCs

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
PSS000290 2,314 individuals European
(French Canadian)
CARTaGENE
PSS000291 39,260 individuals European INTERVAL
PSS006946 6,139 individuals African unspecified UKB
PSS006947 1,655 individuals East Asian UKB
PSS000174 78,246 individuals,
46.0 % Male samples
Mean = 57.23 years
Range = [39.98, 70.43] years
European UKB
PSS006948 24,175 individuals European non-white British ancestry UKB
PSS006949 7,520 individuals South Asian UKB
PSS006950 65,637 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS009007 3,711 individuals African unspecified Nigeria (West Africa) UKB
PSS009459 19,422 individuals European UK (+ Ireland) UKB
PSS000148 38,939 individuals,
49.0 % Male samples
Mean = 43.75 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000911 13,989 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
(Qatari)
QBB
PSS009233 4,002 individuals European Poland (NE Europe) UKB
PSS008787 6,436 individuals European Italy (South Europe) UKB
PSS008561 1,153 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008339 6,076 individuals South Asian India (South Asia) UKB
PSS008116 1,762 individuals East Asian China (East Asia) UKB
PSS007903 2,343 individuals African American or Afro-Caribbean Carribean UKB