Replication Data for: Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision

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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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Description	This is a replication dataset for the manuscript titled: "Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision." 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. Variable Description: 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) platelets: number of platelets x1000 per uL of blood wbc: number of white blood cells x1000 per uL of blood pfhrp2: PfHRP2 concentration in plasma (ng/mL) age: years HbAS: sickle trait genotype (0: not sickle trait; 1: sickle trait) outcome: in hospital survival (0: survived; 1: died) parasitaemia: parasite density per uL of blood. The package presented contains data and replication code. The code is also available on github repo: code is on this github repo: https://github.com/jwatowatson/Kenyan_phenotypic_accuracy
Subject	Medicine, Health and Life Sciences
Keyword	Severe malaria, diagnostic biomarkers
Related Publication	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.
Notes	Data Access: Open License: Creative Commons Attribution 4.0 International
License/Data Use Agreement	Custom Dataset Terms

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	Watson_SevereMalaria_Data_Readme.txt Plain Text - 10.3 KB Published Jul 5, 2021 5 Downloads MD5: b5806fd18ee7d13846294edeb066c27d DocumentationData Readme	Preview "Watson_SevereMalaria_Data_Readme.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	KWTRP_Dataverse_dataset.tab Tabular Data - 171.2 KB Published Jul 5, 2021 16 Downloads 8 Variables, 4374 Observations UNF:6:mwwyTYMcojPhaZDP4PlXAA== DataCSV	Preview "KWTRP_Dataverse_dataset.tab" Preview "KWTRP_Dataverse_dataset.tab" Access File File Access Public Download Options Comma Separated Values (Original File Format) Tab-Delimited RData Download Metadata DDI Codebook v2 Data File Citation Download EndNote XML Download RIS Download BibTeX Explore Options Data Explorer v2
	Kenyan_phenotypic_accuracy-main.zip ZIP Archive - 28.8 MB Published Jul 5, 2021 11 Downloads MD5: 826f57194feca597660b82a4eca88ced Source: https://github.com/jwatowatson/Kenyan_phenotypic_accuracy CodeRMarkdown and R scripts	Preview "Kenyan_phenotypic_accuracy-main.zip" Access File File Access Public Download Options ZIP Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX

Citation Metadata

Persistent Identifier	doi:10.7910/DVN/TH8WAW
Publication Date	2021-07-05
Title	Replication Data for: Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision
Author	Mahidol Oxford Tropical Medicine Research Unit0000-0001-5524-0325 KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya0000-0002-0007-0645 Williams, Thomas N.KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya Mahidol Oxford Tropical Medicine Research Unit0000-0002-1897-1978
Point of Contact	Use email button above to contact. Watson, James A. (Mahidol Oxford Tropical Medicine Research Unit)
Description	This is a replication dataset for the manuscript titled: "Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision." 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. Variable Description: 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) platelets: number of platelets x1000 per uL of blood wbc: number of white blood cells x1000 per uL of blood pfhrp2: PfHRP2 concentration in plasma (ng/mL) age: years HbAS: sickle trait genotype (0: not sickle trait; 1: sickle trait) outcome: in hospital survival (0: survived; 1: died) parasitaemia: parasite density per uL of blood. The package presented contains data and replication code. The code is also available on github repo: code is on this github repo: https://github.com/jwatowatson/Kenyan_phenotypic_accuracy
Subject	Medicine, Health and Life Sciences
Keyword	Severe malaria diagnostic biomarkers
Related Publication	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. 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. 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. 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. 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). 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. The Malaria Genomic Epidemiology Network. Reappraisal of known malaria resistance loci in a large multi center study. Nature Genetics. 2014; 46(11):1197.
Notes	Data Access: Open License: Creative Commons Attribution 4.0 International
Depositor	Watson, James A.
Deposit Date	2021-07-05
Related Dataset	https://github.com/jwatowatson/Kenyan_phenotypic_accuracy

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