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)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Number of Variants PGS Scoring File (FTP Link)
PGS000094 hlr PGP000051
Xu Y et al. bioRxiv (2020)
High light scatter 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)
High light scatter reticulocyte percentage of red cells 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)
Immature fraction of reticulocytes 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)
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)
Reticulocyte fraction of red cells 572 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000112/ScoringFiles/PGS000112.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000224 PGS000096 (irf) PSS000161 PGP000051
Xu Y et al. (2020)
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)
PPM000225 PGS000096 (irf) PSS000135 PGP000051
Xu Y et al. (2020)
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)
PPM000256 PGS000112 (ret_p) PSS000177 PGP000051
Xu Y et al. (2020)
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)
PPM000257 PGS000112 (ret_p) PSS000151 PGP000051
Xu Y et al. (2020)
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)
PPM000220 PGS000094 (hlr) PSS000159 PGP000051
Xu Y et al. (2020)
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)
PPM000221 PGS000094 (hlr) PSS000133 PGP000051
Xu Y et al. (2020)
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)
PPM000254 PGS000111 (ret) PSS000176 PGP000051
Xu Y et al. (2020)
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)
PPM000255 PGS000111 (ret) PSS000150 PGP000051
Xu Y et al. (2020)
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)
PPM000222 PGS000095 (hlr_p) PSS000160 PGP000051
Xu Y et al. (2020)
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)
PPM000223 PGS000095 (hlr_p) PSS000134 PGP000051
Xu Y et al. (2020)
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)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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
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