| 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. |
| 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 |
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 | — | — | R²: 0.06335555804809 | sex, age, 10 genetic PCs | — |
| PPM000559 | PGS000188 (rdw) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Red cell distribution width | — | — | R²: 0.07408984583025 | sex, age, 10 genetic PCs | — |
| PPM000558 | PGS000187 (rbc) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Red blood cell count | — | — | R²: 0.06797507483209 | sex, age, 10 genetic PCs | — |
| PPM000557 | PGS000186 (plt) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Platelet count | — | — | R²: 0.16048845222201 | sex, age, 10 genetic PCs | — |
| PPM000556 | PGS000182 (neut) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Neutrophil count | — | — | R²: 0.06858574356544 | sex, age, 10 genetic PCs | — |
| PPM000555 | PGS000179 (mpv) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Mean platelet volume | — | — | R²: 0.19379488101796 | sex, age, 10 genetic PCs | — |
| PPM000554 | PGS000177 (mono) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Monocyte count | — | — | R²: 0.09473720799481 | sex, age, 10 genetic PCs | — |
| PPM000553 | PGS000176 (mcv) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Mean corpuscular volume | — | — | R²: 0.166499089849 | sex, age, 10 genetic PCs | — |
| PPM000552 | PGS000174 (mch) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Mean corpuscular hemoglobin | — | — | R²: 0.17482726125225 | sex, age, 10 genetic PCs | — |
| PPM000551 | PGS000175 (mchc) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Mean corpuscular hemoglobin concentration | — | — | R²: 0.04795587553689 | sex, age, 10 genetic PCs | — |
| PPM000550 | PGS000172 (lymph) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Lymphocyte count | — | — | R²: 0.03216861060721 | sex, age, 10 genetic PCs | — |
| PPM000549 | PGS000168 (hgb) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Hemoglobin concentration | — | — | R²: 0.064603405584 | sex, age, 10 genetic PCs | — |
| PPM000548 | PGS000167 (hct) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Hematocrit | — | — | R²: 0.05146781897104 | sex, age, 10 genetic PCs | — |
| PPM000547 | PGS000165 (eo) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Eosinophil count | — | — | R²: 0.06931277783824 | sex, age, 10 genetic PCs | — |
| PPM000546 | PGS000163 (baso) | PSS000290 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Basophil count | — | — | R²: 0.0088977112141824 | sex, age, 10 genetic PCs | — |
| PPM000545 | PGS000191 (wbc) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: White blood cell count | — | — | R²: 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 | — | — | R²: 0.15022055905487 | sex, age, 10 genetic PCs | — |
| PPM000543 | PGS000189 (ret) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Reticulocyte count | — | — | R²: 0.141416096085758 | sex, age, 10 genetic PCs | — |
| PPM000542 | PGS000188 (rdw) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Red cell distribution width | — | — | R²: 0.0951892957157087 | sex, age, 10 genetic PCs | — |
| PPM000541 | PGS000187 (rbc) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Red blood cell count | — | — | R²: 0.117645844622335 | sex, age, 10 genetic PCs | — |
| PPM000540 | PGS000186 (plt) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Platelet count | — | — | R²: 0.191945878303405 | sex, age, 10 genetic PCs | — |
| PPM000539 | PGS000185 (pdw) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Platelet distribution width | — | — | R²: 0.0599616972316209 | sex, age, 10 genetic PCs | — |
| PPM000538 | PGS000184 (pct) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Plateletcrit | — | — | R²: 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 | — | — | R²: 0.064323704790284 | sex, age, 10 genetic PCs | — |
| PPM000536 | PGS000182 (neut) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Neutrophil count | — | — | R²: 0.0800863609061118 | sex, age, 10 genetic PCs | — |
| PPM000535 | PGS000179 (mpv) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Mean platelet volume | — | — | R²: 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 | — | — | R²: 0.144611250849609 | sex, age, 10 genetic PCs | — |
| PPM000533 | PGS000177 (mono) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Monocyte count | — | — | R²: 0.158586241573177 | sex, age, 10 genetic PCs | — |
| PPM000532 | PGS000176 (mcv) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Mean corpuscular volume | — | — | R²: 0.159305126007935 | sex, age, 10 genetic PCs | — |
| PPM000531 | PGS000175 (mchc) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Mean corpuscular hemoglobin concentration | — | — | R²: 0.0515942741395813 | sex, age, 10 genetic PCs | — |
| PPM000530 | PGS000174 (mch) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Mean corpuscular hemoglobin | — | — | R²: 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 | — | — | R²: 0.0696499739813752 | sex, age, 10 genetic PCs | — |
| PPM000528 | PGS000172 (lymph) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Lymphocyte count | — | — | R²: 0.105545616995283 | sex, age, 10 genetic PCs | — |
| PPM000527 | PGS000171 (irf) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Immature fraction of reticulocytes | — | — | R²: 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 | — | — | R²: 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 | — | — | R²: 0.118962528574492 | sex, age, 10 genetic PCs | — |
| PPM000524 | PGS000168 (hgb) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Hemoglobin concentration | — | — | R²: 0.0569660767976807 | sex, age, 10 genetic PCs | — |
| PPM000523 | PGS000167 (hct) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Hematocrit | — | — | R²: 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 | — | — | R²: 0.0978959437205518 | sex, age, 10 genetic PCs | — |
| PPM000521 | PGS000165 (eo) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Eosinophil count | — | — | R²: 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 | — | — | R²: 0.0254422491452189 | sex, age, 10 genetic PCs | — |
| PPM000519 | PGS000163 (baso) | PSS000291 | PGP000078 Vuckovic D et al. (2020) Pre |
Reported Trait: Basophil count | — | — | R²: 0.0269108302450236 | sex, age, 10 genetic PCs | — |
|
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 | — |