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)
Pre
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)
Pre
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)
Pre
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)
Pre
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 572 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000112/ScoringFiles/PGS000112.txt.gz
PGS000169 hlr PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
High light scatter 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. medRxiv (2020)
Pre
High light scatter reticulocyte percentage of red cells 566 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000170/ScoringFiles/PGS000170.txt.gz
PGS000171 irf PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Immature fraction of reticulocytes 372 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000171/ScoringFiles/PGS000171.txt.gz
PGS000189 ret PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
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. medRxiv (2020)
Pre
Reticulocyte fraction of red cells 537 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000190/ScoringFiles/PGS000190.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 the Model PGS Performance: Other Relevant Information
PPM000543 PGS000189 (ret) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Reticulocyte count : 0.141416096085758 sex, age, 10 genetic PCs
PPM000220 PGS000094 (hlr) PSS000159 PGP000051
Xu Y et al. (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)
PPM000221 PGS000094 (hlr) PSS000133 PGP000051
Xu Y et al. (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)
PPM000254 PGS000111 (ret) PSS000176 PGP000051
Xu Y et al. (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)
PPM000255 PGS000111 (ret) PSS000150 PGP000051
Xu Y et al. (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)
PPM000527 PGS000171 (irf) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Immature fraction of reticulocytes : 0.0916443198384835 sex, age, 10 genetic PCs
PPM000224 PGS000096 (irf) PSS000161 PGP000051
Xu Y et al. (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)
PPM000225 PGS000096 (irf) PSS000135 PGP000051
Xu Y et al. (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)
PPM000526 PGS000170 (hlr_p) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: High light scatter reticulocyte percentage of red cells : 0.127990430729481 sex, age, 10 genetic PCs
PPM000256 PGS000112 (ret_p) PSS000177 PGP000051
Xu Y et al. (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)
PPM000257 PGS000112 (ret_p) PSS000151 PGP000051
Xu Y et al. (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 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Reticulocyte fraction of red cells : 0.15022055905487 sex, age, 10 genetic PCs
PPM000222 PGS000095 (hlr_p) PSS000160 PGP000051
Xu Y et al. (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)
PPM000223 PGS000095 (hlr_p) PSS000134 PGP000051
Xu Y et al. (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)
PPM000525 PGS000169 (hlr) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: High light scatter reticulocyte count : 0.118962528574492 sex, age, 10 genetic PCs

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
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