PGS Preprint: PGP000078

Publication Information (EuropePMC)
Title The Polygenic and Monogenic Basis of Blood Traits and Diseases
doi 10.1101/2020.02.02.20020065
Publication Date Feb. 3, 2020
Journal medRxiv Preprint
Author(s) Vuckovic D, Bao EL, Akbari P, Lareau CA, Mousas A, Jiang T, Chen M, Raffield LM, Tardaguila M, Huffman JE, Ritchie SC, Megy K, Ponstingl H, Penkett CJ, Albers PK, Wigdor EM, Sakaue S, Moscati A, Manansala R, Lo KS, Qian H, Akiyama M, Bartz TM, Ben-Shlomo Y, Beswick A, Bork-Jensen J, Bottinger EP, Brody JA, van Rooij FJ, Chitrala KN, Cho K, Choquet H, Danesh J, Di Angelantonio E, Dimou N, Ding J, Elliott P, Esko T, Evans MK, Felix SB, Floyd JS, Broer L, Grarup N, Guo M, Greinacher A, Haessler J, Hansen T, Howson J, Huang W, Jorgenson E, Kacprowski T, Kähönen M, Kamatani Y, Kanai M, Karthikeyan S, Koskeridis F, Lange LA, Lehtimäki T, Linneberg A, Liu Y, Lyytikäinen L, Manichaikul A, Matsuda K, Mohlke KL, Mononen N, Murakami Y, Nadkarni G, Nikus K, Pankratz N, Pedersen O, Preuss M, Psaty BM, Raitakari OT, Rich SS, Rodriguez BA, Rosen JD, Rotter JI, Schubert P, Spracklen CN, Surendran P, Tang H, Tardif J, Ghanbari M, Völker U, Völzke H, Watkins NA, Weiss S, Cai N, Kundu K, Watt S, Walter K, Zonderman AB, Wilson PW, Li Y, Loos RJ, Knight JC, Georges M, Stegle O, Evangelou E, Okada Y, Roberts DJ, Inouye M, Johnson AD, Auer PL, Astle WJ, Reiner AP, Butterworth AS, Ouwehand WH, Lettre G, Sankaran VG, Soranzo N, VA Million Veteran Program.
Released in PGS: April 29, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000163 baso PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Basophil count basophil count 185 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000163/ScoringFiles/PGS000163.txt.gz
PGS000164 baso_p PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Basophil percentage of white cells basophil percentage of leukocytes 150 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000164/ScoringFiles/PGS000164.txt.gz
PGS000165 eo PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Eosinophil count eosinophil count 607 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000165/ScoringFiles/PGS000165.txt.gz
PGS000166 eo_p PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Eosinophil percentage of white cells eosinophil percentage of leukocytes 571 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000166/ScoringFiles/PGS000166.txt.gz
PGS000169 hlr PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
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. medRxiv (2020)
Pre
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. medRxiv (2020)
Pre
Immature fraction of reticulocytes reticulocyte count 372 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000171/ScoringFiles/PGS000171.txt.gz
PGS000172 lymph PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Lymphocyte count lymphocyte count 621 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000172/ScoringFiles/PGS000172.txt.gz
PGS000173 lymph_p PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Lymphocyte percentage of white cells lymphocyte percentage of leukocytes 472 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000173/ScoringFiles/PGS000173.txt.gz
PGS000174 mch PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Mean corpuscular hemoglobin mean corpuscular hemoglobin 628 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000174/ScoringFiles/PGS000174.txt.gz
PGS000175 mchc PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Mean corpuscular hemoglobin concentration mean corpuscular hemoglobin concentration 224 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000175/ScoringFiles/PGS000175.txt.gz
PGS000176 mcv PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Mean corpuscular volume mean corpuscular volume 685 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000176/ScoringFiles/PGS000176.txt.gz
PGS000177 mono PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Monocyte count monocyte count 638 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000177/ScoringFiles/PGS000177.txt.gz
PGS000178 mono_p PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Monocyte percentage of white cells monocyte percentage of leukocytes 549 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000178/ScoringFiles/PGS000178.txt.gz
PGS000179 mpv PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Mean platelet volume mean platelet volume 654 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000179/ScoringFiles/PGS000179.txt.gz
PGS000180 mrv PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Mean reticulocyte volume hematological measurement 629 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000180/ScoringFiles/PGS000180.txt.gz
PGS000181 mscv PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Mean sphered corpuscular volume mean corpuscular volume 761 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000181/ScoringFiles/PGS000181.txt.gz
PGS000182 neut PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Neutrophil count neutrophil count 492 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000182/ScoringFiles/PGS000182.txt.gz
PGS000183 neut_p PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Neutrophil percentage of white cells neutrophil percentage of leukocytes 437 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000183/ScoringFiles/PGS000183.txt.gz
PGS000184 pct PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Plateletcrit platelet crit 700 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000184/ScoringFiles/PGS000184.txt.gz
PGS000185 pdw PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Platelet distribution width platelet component distribution width 555 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000185/ScoringFiles/PGS000185.txt.gz
PGS000186 plt PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Platelet count platelet count 739 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000186/ScoringFiles/PGS000186.txt.gz
PGS000187 rbc PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Red blood cell count erythrocyte count 678 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000187/ScoringFiles/PGS000187.txt.gz
PGS000188 rdw PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Red cell distribution width red blood cell distribution width 546 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000188/ScoringFiles/PGS000188.txt.gz
PGS000189 ret PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
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. medRxiv (2020)
Pre
Reticulocyte fraction of red cells reticulocyte count 537 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000190/ScoringFiles/PGS000190.txt.gz
PGS000191 wbc PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
White blood cell count leukocyte count 636 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000191/ScoringFiles/PGS000191.txt.gz
PGS000167 hct PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Hematocrit hematocrit 502 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000167/ScoringFiles/PGS000167.txt.gz
PGS000168 hgb PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Hemoglobin concentration hemoglobin measurement 515 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000168/ScoringFiles/PGS000168.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
PPM000560 PGS000191 (wbc) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: White blood cell count : 0.06335555804809 sex, age, 10 genetic PCs
PPM000559 PGS000188 (rdw) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Red cell distribution width : 0.07408984583025 sex, age, 10 genetic PCs
PPM000558 PGS000187 (rbc) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Red blood cell count : 0.06797507483209 sex, age, 10 genetic PCs
PPM000557 PGS000186 (plt) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Platelet count : 0.16048845222201 sex, age, 10 genetic PCs
PPM000556 PGS000182 (neut) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Neutrophil count : 0.06858574356544 sex, age, 10 genetic PCs
PPM000555 PGS000179 (mpv) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Mean platelet volume : 0.19379488101796 sex, age, 10 genetic PCs
PPM000554 PGS000177 (mono) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Monocyte count : 0.09473720799481 sex, age, 10 genetic PCs
PPM000553 PGS000176 (mcv) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Mean corpuscular volume : 0.166499089849 sex, age, 10 genetic PCs
PPM000552 PGS000174 (mch) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Mean corpuscular hemoglobin : 0.17482726125225 sex, age, 10 genetic PCs
PPM000551 PGS000175 (mchc) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Mean corpuscular hemoglobin concentration : 0.04795587553689 sex, age, 10 genetic PCs
PPM000550 PGS000172 (lymph) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Lymphocyte count : 0.03216861060721 sex, age, 10 genetic PCs
PPM000549 PGS000168 (hgb) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Hemoglobin concentration : 0.064603405584 sex, age, 10 genetic PCs
PPM000548 PGS000167 (hct) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Hematocrit : 0.05146781897104 sex, age, 10 genetic PCs
PPM000547 PGS000165 (eo) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Eosinophil count : 0.06931277783824 sex, age, 10 genetic PCs
PPM000546 PGS000163 (baso) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Basophil count : 0.0088977112141824 sex, age, 10 genetic PCs
PPM000545 PGS000191 (wbc) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: White blood cell count : 0.0867179367384127 sex, age, 10 genetic PCs
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
PPM000543 PGS000189 (ret) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Reticulocyte count : 0.141416096085758 sex, age, 10 genetic PCs
PPM000542 PGS000188 (rdw) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Red cell distribution width : 0.0951892957157087 sex, age, 10 genetic PCs
PPM000541 PGS000187 (rbc) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Red blood cell count : 0.117645844622335 sex, age, 10 genetic PCs
PPM000540 PGS000186 (plt) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Platelet count : 0.191945878303405 sex, age, 10 genetic PCs
PPM000539 PGS000185 (pdw) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Platelet distribution width : 0.0599616972316209 sex, age, 10 genetic PCs
PPM000538 PGS000184 (pct) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Plateletcrit : 0.155504415400892 sex, age, 10 genetic PCs
PPM000537 PGS000183 (neut_p) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Neutrophil percentage of white cells : 0.064323704790284 sex, age, 10 genetic PCs
PPM000536 PGS000182 (neut) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Neutrophil count : 0.0800863609061118 sex, age, 10 genetic PCs
PPM000535 PGS000179 (mpv) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Mean platelet volume : 0.273060063873527 sex, age, 10 genetic PCs
PPM000534 PGS000178 (mono_p) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Monocyte percentage of white cells : 0.144611250849609 sex, age, 10 genetic PCs
PPM000533 PGS000177 (mono) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Monocyte count : 0.158586241573177 sex, age, 10 genetic PCs
PPM000532 PGS000176 (mcv) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Mean corpuscular volume : 0.159305126007935 sex, age, 10 genetic PCs
PPM000531 PGS000175 (mchc) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Mean corpuscular hemoglobin concentration : 0.0515942741395813 sex, age, 10 genetic PCs
PPM000530 PGS000174 (mch) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Mean corpuscular hemoglobin : 0.182817764969849 sex, age, 10 genetic PCs
PPM000529 PGS000173 (lymph_p) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Lymphocyte percentage of white cells : 0.0696499739813752 sex, age, 10 genetic PCs
PPM000528 PGS000172 (lymph) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Lymphocyte count : 0.105545616995283 sex, age, 10 genetic PCs
PPM000527 PGS000171 (irf) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Immature fraction of reticulocytes : 0.0916443198384835 sex, age, 10 genetic PCs
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
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
PPM000524 PGS000168 (hgb) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Hemoglobin concentration : 0.0569660767976807 sex, age, 10 genetic PCs
PPM000523 PGS000167 (hct) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Hematocrit : 0.0493128145200219 sex, age, 10 genetic PCs
PPM000522 PGS000166 (eo_p) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Eosinophil percentage of white cells : 0.0978959437205518 sex, age, 10 genetic PCs
PPM000521 PGS000165 (eo) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Eosinophil count : 0.111546932492314 sex, age, 10 genetic PCs
PPM000520 PGS000164 (baso_p) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Basophil percentage of white cells : 0.0254422491452189 sex, age, 10 genetic PCs
PPM000519 PGS000163 (baso) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Basophil count : 0.0269108302450236 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
PSS000290 2,314 individuals European
(French Canadian)
CARTaGENE
PSS000291 39,260 individuals European INTERVAL