Trait: reticulocyte count

Experimental Factor Ontology (EFO) Information
Identifier EFO_0007986
Description
  • The number of reticulocytes per unit volume of blood. Reticulocytes are immature red blood cells and typically compose aoubt 1% of red blood cells in the human body.
Trait category
Hematological measurement

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 PGS Scoring File (FTP Link)
PGS000094
(hlr)
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
High light scatter reticulocyte count reticulocyte count 605
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000094/ScoringFiles/PGS000094.txt.gz
PGS000095
(hlr_p)
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
High light scatter reticulocyte percentage of red cells reticulocyte count 594
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000095/ScoringFiles/PGS000095.txt.gz
PGS000096
(irf)
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Immature fraction of reticulocytes reticulocyte count 390
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000096/ScoringFiles/PGS000096.txt.gz
PGS000111
(ret)
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reticulocyte count reticulocyte count 590
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000111/ScoringFiles/PGS000111.txt.gz
PGS000112
(ret_p)
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reticulocyte fraction of red cells reticulocyte count 572
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000112/ScoringFiles/PGS000112.txt.gz
PGS000169
(hlr)
PGP000078 |
Vuckovic D et al. Cell (2020)
High light scatter reticulocyte count reticulocyte count 570
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000169/ScoringFiles/PGS000169.txt.gz
PGS000170
(hlr_p)
PGP000078 |
Vuckovic D et al. Cell (2020)
High light scatter reticulocyte percentage of red cells reticulocyte count 566
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000170/ScoringFiles/PGS000170.txt.gz
PGS000171
(irf)
PGP000078 |
Vuckovic D et al. Cell (2020)
Immature fraction of reticulocytes reticulocyte count 372
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000171/ScoringFiles/PGS000171.txt.gz
PGS000189
(ret)
PGP000078 |
Vuckovic D et al. Cell (2020)
Reticulocyte count reticulocyte count 555
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000189/ScoringFiles/PGS000189.txt.gz
PGS000190
(ret_p)
PGP000078 |
Vuckovic D et al. Cell (2020)
Reticulocyte fraction of red cells reticulocyte count 537
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000190/ScoringFiles/PGS000190.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
PPM000220 PGS000094
(hlr)
PSS000159|
European Ancestry|
80,067 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: High light scatter reticulocyte count Pearson correlation coefficent (r): 0.4294 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)
PPM000222 PGS000095
(hlr_p)
PSS000160|
European Ancestry|
80,088 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: High light scatter reticulocyte percentage of red cells Pearson correlation coefficent (r): 0.4385 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)
PPM000224 PGS000096
(irf)
PSS000161|
European Ancestry|
79,282 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Immature fraction of reticulocytes Pearson correlation coefficent (r): 0.3512 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)
PPM000254 PGS000111
(ret)
PSS000176|
European Ancestry|
79,344 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Reticulocyte count Pearson correlation coefficent (r): 0.4241 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)
PPM000256 PGS000112
(ret_p)
PSS000177|
European Ancestry|
79,362 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Reticulocyte fraction of red cells Pearson correlation coefficent (r): 0.4316 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)
PPM000221 PGS000094
(hlr)
PSS000133|
European Ancestry|
40,244 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: High light scatter reticulocyte count Pearson correlation coefficent (r): 0.363 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)
PPM000223 PGS000095
(hlr_p)
PSS000134|
European Ancestry|
40,225 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: High light scatter reticulocyte percentage of red cells Pearson correlation coefficent (r): 0.3687 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)
PPM000225 PGS000096
(irf)
PSS000135|
European Ancestry|
40,227 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Immature fraction of reticulocytes Pearson correlation coefficent (r): 0.3367 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)
PPM000255 PGS000111
(ret)
PSS000150|
European Ancestry|
40,253 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Reticulocyte count Pearson correlation coefficent (r): 0.4069 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)
PPM000257 PGS000112
(ret_p)
PSS000151|
European Ancestry|
40,286 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Reticulocyte fraction of red cells Pearson correlation coefficent (r): 0.423 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)
PPM000544 PGS000190
(ret_p)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Reticulocyte fraction of red cells : 0.15022 sex, age, 10 genetic PCs
PPM000543 PGS000189
(ret)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Reticulocyte count : 0.14142 sex, age, 10 genetic PCs
PPM000527 PGS000171
(irf)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Immature fraction of reticulocytes : 0.09164 sex, age, 10 genetic PCs
PPM000526 PGS000170
(hlr_p)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: High light scatter reticulocyte percentage of red cells : 0.12799 sex, age, 10 genetic PCs
PPM000525 PGS000169
(hlr)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: High light scatter reticulocyte count : 0.11896 sex, age, 10 genetic 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
PSS000133 40,244 individuals,
49.0 % Male samples
Mean = 43.84 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000134 40,225 individuals,
49.0 % Male samples
Mean = 43.84 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000135 40,227 individuals,
49.0 % Male samples
Mean = 43.85 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000291 39,260 individuals European INTERVAL
PSS000176 79,344 individuals,
46.0 % Male samples
Mean = 57.29 years
Range = [39.66, 72.91] years
European UKB
PSS000177 79,362 individuals,
46.0 % Male samples
Mean = 57.22 years
Range = [39.66, 72.91] years
European UKB
PSS000150 40,253 individuals,
49.0 % Male samples
Mean = 43.84 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000151 40,286 individuals,
49.0 % Male samples
Mean = 43.84 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000159 80,067 individuals,
46.0 % Male samples
Mean = 57.2 years
Range = [39.91, 70.52] years
European UKB
PSS000160 80,088 individuals,
46.0 % Male samples
Mean = 57.19 years
Range = [39.66, 72.91] years
European UKB
PSS000161 79,282 individuals,
46.0 % Male samples
Mean = 57.28 years
Range = [39.91, 70.99] years
European UKB