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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision |
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Identification Number: |
doi:10.7910/DVN/TH8WAW |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2021-07-05 |
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Version: |
1 |
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Bibliographic Citation: |
Watson, James A.; Maitland, Kathryn; Williams, Thomas N.; White, Nicholas J., 2021, "Replication Data for: Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision", https://doi.org/10.7910/DVN/TH8WAW, Harvard Dataverse, V1, UNF:6:mwwyTYMcojPhaZDP4PlXAA== [fileUNF] |
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Citation |
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Title: |
Replication Data for: Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision |
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Identification Number: |
doi:10.7910/DVN/TH8WAW |
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Authoring Entity: |
Watson, James A. (Mahidol Oxford Tropical Medicine Research Unit) |
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Maitland, Kathryn (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Williams, Thomas N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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White, Nicholas J. (Mahidol Oxford Tropical Medicine Research Unit) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Watson, James A. |
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Depositor: |
Watson, James A. |
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Date of Deposit: |
2021-07-05 |
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Holdings Information: |
https://doi.org/10.7910/DVN/TH8WAW |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, Severe malaria, diagnostic biomarkers |
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Abstract: |
<p>This is a replication dataset for the manuscript titled: "<a href="">Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision</a>." </p> <p>This dataset contains complete blood count data (platelet counts and total white blood cell counts) for severely ill patients enrolled in either studies of severe malaria or general severe febrile illness in Africa and Asia. For reproducibility of analyses we also provide parasite densities; hospital outcome; sickle trait status for the Kenyan children; plasma PfHRP2 for FEAST and Bangladesh adults; age.</p> <p>Variable Description: <br> study: Vietnam (2 randomized trials in severe malaria: Hien et al; Phu et al); Bangladesh/Thailand (observational studies in severe malaria); FEAST (Maitland et); Kenya (KEMRI severe malaria cohort) <br> platelets: number of platelets x1000 per uL of blood <br> wbc: number of white blood cells x1000 per uL of blood <br> pfhrp2: PfHRP2 concentration in plasma (ng/mL) <br> age: years <br> HbAS: sickle trait genotype (0: not sickle trait; 1: sickle trait) <br> outcome: in hospital survival (0: survived; 1: died) <br> parasitaemia: parasite density per uL of blood. </p> <p>The package presented contains data and replication code. The code is also available on github repo: <a href="https://github.com/jwatowatson/Kenyan_phenotypic_accuracy">code is on this github repo: https://github.com/jwatowatson/Kenyan_phenotypic_accuracy</a> </p> |
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Notes: |
<p><strong>Data Access: </strong>Open</p> <p><strong>License: </strong><a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a> </p> |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Citation Requirement: |
<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p> |
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Notes: |
<p>This data is licensed under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a> </p> |
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Other Study Description Materials |
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Related Studies |
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https://github.com/jwatowatson/Kenyan_phenotypic_accuracy |
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Related Publications |
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Citation |
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Title: |
Ndila CM, Uyoga S, Macharia AW, Nyutu G, Peshu N, Ojal J, Shebe M, Awuondo KO, Mturi N, Tsofa B, et al. Human candidate gene polymorphisms and risk of severe malaria in children in Kili , Kenya: a case-control association study. The Lancet Haematology. 2018; 5(8):e333–e345. |
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Bibliographic Citation: |
Ndila CM, Uyoga S, Macharia AW, Nyutu G, Peshu N, Ojal J, Shebe M, Awuondo KO, Mturi N, Tsofa B, et al. Human candidate gene polymorphisms and risk of severe malaria in children in Kili , Kenya: a case-control association study. The Lancet Haematology. 2018; 5(8):e333–e345. |
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Citation |
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Title: |
Maitland K, Kiguli S, Opoka RO, Engoru C, Olupot-Olupot P, Akech SO, Nyeko R, Mtove G, Reyburn H, Lang T et al. Mortality after uid bolus in African children with severe infection. New England Journal of Medicine. 2011; 364(26):2483–2495. |
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Bibliographic Citation: |
Maitland K, Kiguli S, Opoka RO, Engoru C, Olupot-Olupot P, Akech SO, Nyeko R, Mtove G, Reyburn H, Lang T et al. Mortality after uid bolus in African children with severe infection. New England Journal of Medicine. 2011; 364(26):2483–2495. |
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Citation |
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Title: |
Hien TT, Day NP, Phu NH, Mai NTH, Chau TTH, Loc PP, Sinh DX, Chuong LV, Vinh H, Waller D, et al. A controlled trial of artemether or quinine in Vietnamese adults with severe falciparum malaria. New England Journal of Medicine. 1996; 335(2):76–83. |
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Bibliographic Citation: |
Hien TT, Day NP, Phu NH, Mai NTH, Chau TTH, Loc PP, Sinh DX, Chuong LV, Vinh H, Waller D, et al. A controlled trial of artemether or quinine in Vietnamese adults with severe falciparum malaria. New England Journal of Medicine. 1996; 335(2):76–83. |
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Citation |
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Title: |
Phu NH, Tuan PQ, Day N, Mai NT, Chau TT, Chuong LV, Sinh DX, White NJ, Farrar J, Hien TT. Randomized controlled trial of artesunate or artemether in Vietnamese adults with severe falciparum malaria. Malaria Journal. 2010; 9(1):97. |
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Bibliographic Citation: |
Phu NH, Tuan PQ, Day N, Mai NT, Chau TT, Chuong LV, Sinh DX, White NJ, Farrar J, Hien TT. Randomized controlled trial of artesunate or artemether in Vietnamese adults with severe falciparum malaria. Malaria Journal. 2010; 9(1):97. |
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Citation |
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Title: |
Leopold SJ, Watson JA, Jeeyapant A, Simpson JA, Phu NH, Hien TT, Day NP, Dondorp AM, White NJ. Investigating causal pathways in severe falciparum malaria: A pooled retrospective analysis of clinical studies. PLoS Medicine. 2019; 16(8). |
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Bibliographic Citation: |
Leopold SJ, Watson JA, Jeeyapant A, Simpson JA, Phu NH, Hien TT, Day NP, Dondorp AM, White NJ. Investigating causal pathways in severe falciparum malaria: A pooled retrospective analysis of clinical studies. PLoS Medicine. 2019; 16(8). |
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Citation |
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Title: |
Band G, Le QS, Clarke GM, Kivinen K, Hubbart C, Jeffreys AE, Rowlands K, Le er EM, Jallow M, Conway DJ, Sisay-Joof F, Sirugo G, d’Alessandro U, ToureOB, TheraMA, Konate S, Sissoko S,Mangano VD, Bougouma EC, Sirima SB, et al. Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nature Communications. 2019; 10(1):5732. https://doi.org/10.1038/s41467-019-13480-z, doi:10.1038/s41467-019-13480-z. |
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Bibliographic Citation: |
Band G, Le QS, Clarke GM, Kivinen K, Hubbart C, Jeffreys AE, Rowlands K, Le er EM, Jallow M, Conway DJ, Sisay-Joof F, Sirugo G, d’Alessandro U, ToureOB, TheraMA, Konate S, Sissoko S,Mangano VD, Bougouma EC, Sirima SB, et al. Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nature Communications. 2019; 10(1):5732. https://doi.org/10.1038/s41467-019-13480-z, doi:10.1038/s41467-019-13480-z. |
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Citation |
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Title: |
The Malaria Genomic Epidemiology Network. Reappraisal of known malaria resistance loci in a large multi center study. Nature Genetics. 2014; 46(11):1197. |
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Bibliographic Citation: |
The Malaria Genomic Epidemiology Network. Reappraisal of known malaria resistance loci in a large multi center study. Nature Genetics. 2014; 46(11):1197. |
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File Description--f4876805 |
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File: KWTRP_Dataverse_dataset.tab |
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Notes: |
UNF:6:mwwyTYMcojPhaZDP4PlXAA== |
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List of Variables: | |
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Variables |
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f4876805 Location: |
Variable Format: character Notes: UNF:6:E8WFCMkMrwBRWd0CVOCPhw== |
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f4876805 Location: |
Summary Statistics: Mean 137.20927914125258; StDev 138.2152907053682; Valid 3912.0; Max. 1234.0; Min. 1.0 Variable Format: numeric Notes: UNF:6:qYeH1IBOBofnHi6vpC0WqA== |
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f4876805 Location: |
Summary Statistics: StDev 11.425762437034567; Min. 1.03; Valid 4330.0; Mean 14.130847576735349; Max. 152.0; Variable Format: numeric Notes: UNF:6:t0l3NyfdP1ir13SVTczHOA== |
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f4876805 Location: |
Summary Statistics: Mean 2662.612978075521; StDev 5753.593282575879; Valid 739.0; Min. 0.0; Max. 75118.1 Variable Format: numeric Notes: UNF:6:yqcbHovxCGuP4BCGSV8/3g== |
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f4876805 Location: |
Summary Statistics: Valid 4369.0; Max. 80.0; Min. 0.166666666666667; StDev 16.993312711299684; Mean 13.616388189517398 Variable Format: numeric Notes: UNF:6:pnjxL8aThmGl7RXDmoYIDQ== |
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f4876805 Location: |
Summary Statistics: Max. 1.0; Valid 2213.0; Mean 0.025756891098056876; Min. 0.0; StDev 0.15844499962352845 Variable Format: numeric Notes: UNF:6:RlIReyv3ECKgXo0QTcNKcQ== |
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f4876805 Location: |
Summary Statistics: Min. 0.0; Mean 0.1282404221151648; StDev 0.3343956773511135; Max. 1.0; Valid 4359.0 Variable Format: numeric Notes: UNF:6:lDA+TS5Bt9/iJRFoeK24ig== |
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f4876805 Location: |
Summary Statistics: Max. 5100000.0; Valid 4078.0; Mean 204189.6055847299; Min. 0.0; StDev 347633.98331081786 Variable Format: numeric Notes: UNF:6:XLAqkgMyShMR2NEPoBSTTw== |
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Label: |
Kenyan_phenotypic_accuracy-main.zip |
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Text: |
Source: https://github.com/jwatowatson/Kenyan_phenotypic_accuracy |
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Notes: |
application/zip |
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Label: |
Watson_SevereMalaria_Code_Readme.txt |
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Notes: |
text/plain |
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Label: |
Watson_SevereMalaria_Data_Readme.txt |
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Notes: |
text/plain |