PGS Publication: PGP000078

Publication Information (EuropePMC)
Title The Polygenic and Monogenic Basis of Blood Traits and Diseases.
PubMed ID 32888494(Europe PMC)
doi 10.1016/j.cell.2020.08.008
Publication Date Sept. 1, 2020
Journal Cell
Author(s) Vuckovic D, Bao EL, Akbari P, Lareau CA, Mousas A, Jiang T, Chen MH, 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 FJA, Chitrala KN, Wilson PWF, 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 MH, Guo Q, Greinacher A, Haessler J, Hansen T, Howson JMM, 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 LP, Manichaikul A, Matsuda K, Mohlke KL, Mononen N, Murakami Y, Nadkarni GN, Nikus K, Pankratz N, Pedersen O, Preuss M, Psaty BM, Raitakari OT, Rich SS, Rodriguez BAT, Rosen JD, Rotter JI, Schubert P, Spracklen CN, Surendran P, Tang H, Tardif JC, Ghanbari M, Völker U, Völzke H, Watkins NA, Weiss S, VA Million Veteran Program, Cai N, Kundu K, Watt SB, Walter K, Zonderman AB, Cho K, Li Y, Loos RJF, 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.
Released in PGS Catalog: 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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
PGS000180 mrv PGP000078 Vuckovic D et al. Cell (2020) Mean reticulocyte volume mean reticulocyte volume 629 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000180/ScoringFiles/PGS000180.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
PGS000172 lymph PGP000078 Vuckovic D et al. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) Mean platelet volume mean platelet volume 654 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000179/ScoringFiles/PGS000179.txt.gz
PGS000181 mscv PGP000078 Vuckovic D et al. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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. 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
PGS000191 wbc PGP000078 Vuckovic D et al. Cell (2020) 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. Cell (2020) 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. Cell (2020) 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
PPM000547 PGS000165
(eo)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Eosinophil count — — R²: 0.06931 sex, age, 10 genetic PCs —
PPM000560 PGS000191
(wbc)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: White blood cell count — — R²: 0.06336 sex, age, 10 genetic PCs —
PPM000559 PGS000188
(rdw)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Red cell distribution width — — R²: 0.07409 sex, age, 10 genetic PCs —
PPM000558 PGS000187
(rbc)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Red blood cell count — — R²: 0.06798 sex, age, 10 genetic PCs —
PPM000557 PGS000186
(plt)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Platelet count — — R²: 0.16049 sex, age, 10 genetic PCs —
PPM000556 PGS000182
(neut)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Neutrophil count — — R²: 0.06859 sex, age, 10 genetic PCs —
PPM000555 PGS000179
(mpv)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Mean platelet volume — — R²: 0.19379 sex, age, 10 genetic PCs —
PPM000554 PGS000177
(mono)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Monocyte count — — R²: 0.09474 sex, age, 10 genetic PCs —
PPM000553 PGS000176
(mcv)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Mean corpuscular volume — — R²: 0.1665 sex, age, 10 genetic PCs —
PPM000552 PGS000174
(mch)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Mean corpuscular hemoglobin — — R²: 0.17483 sex, age, 10 genetic PCs —
PPM000551 PGS000175
(mchc)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Mean corpuscular hemoglobin concentration — — R²: 0.04796 sex, age, 10 genetic PCs —
PPM000550 PGS000172
(lymph)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Lymphocyte count — — R²: 0.03217 sex, age, 10 genetic PCs —
PPM000549 PGS000168
(hgb)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Hemoglobin concentration — — R²: 0.0646 sex, age, 10 genetic PCs —
PPM000548 PGS000167
(hct)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Hematocrit — — R²: 0.05147 sex, age, 10 genetic PCs —
PPM000546 PGS000163
(baso)
 PSS000290 PGP000078 Vuckovic D et al. (2020) Reported Trait: Basophil count — — R²: 0.0089 sex, age, 10 genetic PCs —
PPM000545 PGS000191
(wbc)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: White blood cell count — — R²: 0.08672 sex, age, 10 genetic PCs —
PPM000544 PGS000190
(ret_p)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Reticulocyte fraction of red cells — — R²: 0.15022 sex, age, 10 genetic PCs —
PPM000543 PGS000189
(ret)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Reticulocyte count — — R²: 0.14142 sex, age, 10 genetic PCs —
PPM000542 PGS000188
(rdw)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Red cell distribution width — — R²: 0.09519 sex, age, 10 genetic PCs —
PPM000541 PGS000187
(rbc)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Red blood cell count — — R²: 0.11765 sex, age, 10 genetic PCs —
PPM000540 PGS000186
(plt)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Platelet count — — R²: 0.19195 sex, age, 10 genetic PCs —
PPM000539 PGS000185
(pdw)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Platelet distribution width — — R²: 0.05996 sex, age, 10 genetic PCs —
PPM000538 PGS000184
(pct)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Plateletcrit — — R²: 0.1555 sex, age, 10 genetic PCs —
PPM000537 PGS000183
(neut_p)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Neutrophil percentage of white cells — — R²: 0.06432 sex, age, 10 genetic PCs —
PPM000536 PGS000182
(neut)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Neutrophil count — — R²: 0.08009 sex, age, 10 genetic PCs —
PPM000535 PGS000179
(mpv)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Mean platelet volume — — R²: 0.27306 sex, age, 10 genetic PCs —
PPM000534 PGS000178
(mono_p)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Monocyte percentage of white cells — — R²: 0.14461 sex, age, 10 genetic PCs —
PPM000533 PGS000177
(mono)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Monocyte count — — R²: 0.15859 sex, age, 10 genetic PCs —
PPM000532 PGS000176
(mcv)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Mean corpuscular volume — — R²: 0.15931 sex, age, 10 genetic PCs —
PPM000531 PGS000175
(mchc)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Mean corpuscular hemoglobin concentration — — R²: 0.05159 sex, age, 10 genetic PCs —
PPM000530 PGS000174
(mch)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Mean corpuscular hemoglobin — — R²: 0.18282 sex, age, 10 genetic PCs —
PPM000529 PGS000173
(lymph_p)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Lymphocyte percentage of white cells — — R²: 0.06965 sex, age, 10 genetic PCs —
PPM000528 PGS000172
(lymph)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Lymphocyte count — — R²: 0.10555 sex, age, 10 genetic PCs —
PPM000527 PGS000171
(irf)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Immature fraction of reticulocytes — — R²: 0.09164 sex, age, 10 genetic PCs —
PPM000526 PGS000170
(hlr_p)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: High light scatter reticulocyte percentage of red cells — — R²: 0.12799 sex, age, 10 genetic PCs —
PPM000525 PGS000169
(hlr)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: High light scatter reticulocyte count — — R²: 0.11896 sex, age, 10 genetic PCs —
PPM000524 PGS000168
(hgb)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Hemoglobin concentration — — R²: 0.05697 sex, age, 10 genetic PCs —
PPM000523 PGS000167
(hct)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Hematocrit — — R²: 0.04931 sex, age, 10 genetic PCs —
PPM000522 PGS000166
(eo_p)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Eosinophil percentage of white cells — — R²: 0.0979 sex, age, 10 genetic PCs —
PPM000521 PGS000165
(eo)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Eosinophil count — — R²: 0.11155 sex, age, 10 genetic PCs —
PPM000520 PGS000164
(baso_p)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Basophil percentage of white cells — — R²: 0.02544 sex, age, 10 genetic PCs —
PPM000519 PGS000163
(baso)
 PSS000291 PGP000078 Vuckovic D et al. (2020) Reported Trait: Basophil count — — R²: 0.02691 sex, age, 10 genetic PCs —

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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 —