MalHaploFreq : A computer programme for estimating malaria haplotype frequencies from blood samples
Abstract Background Molecular markers, particularly those associated with drug resistance, are important surveillance tools that can inform policy choice. People infected with falciparum malaria often contain several genetically-distinct clones of the parasite; genotyping the patients' blood re...
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ftdoajarticles:oai:doaj.org/article:28f939be9a104cbd83c6df3c1e7b1abe 2023-05-15T15:12:11+02:00 MalHaploFreq : A computer programme for estimating malaria haplotype frequencies from blood samples Smith Thomas A Hastings Ian M 2008-07-01T00:00:00Z https://doi.org/10.1186/1475-2875-7-130 https://doaj.org/article/28f939be9a104cbd83c6df3c1e7b1abe EN eng BMC http://www.malariajournal.com/content/7/1/130 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-7-130 1475-2875 https://doaj.org/article/28f939be9a104cbd83c6df3c1e7b1abe Malaria Journal, Vol 7, Iss 1, p 130 (2008) Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2008 ftdoajarticles https://doi.org/10.1186/1475-2875-7-130 2022-12-31T13:51:50Z Abstract Background Molecular markers, particularly those associated with drug resistance, are important surveillance tools that can inform policy choice. People infected with falciparum malaria often contain several genetically-distinct clones of the parasite; genotyping the patients' blood reveals whether or not the marker is present (i.e. its prevalence), but does not reveal its frequency. For example a person with four malaria clones may contain both mutant and wildtype forms of a marker but it is not possible to distinguish the relative frequencies of the mutant and wildtypes i.e. 1:3, 2:2 or 3:1. Methods An appropriate method for obtaining frequencies from prevalence data is by Maximum Likelihood analysis. A computer programme has been developed that allows the frequency of markers, and haplotypes defined by up to three codons, to be estimated from blood phenotype data. Results The programme has been fully documented [see Additional File 1 ] and provided with a user-friendly interface suitable for large scale analyses. It returns accurate frequencies and 95% confidence intervals from simulated dataset sets and has been extensively tested on field data sets. Additional File 1 User manual for MalHaploFreq. <file name="1475-2875-7-130-S1.pdf"> Click here for file </file> Conclusion The programme is included [see Additional File 2 ] and/or may be freely downloaded from 1 . It can then be used to extract molecular marker and haplotype frequencies from their prevalence in human blood samples. This should enhance the use of frequency data to inform antimalarial drug policy choice. Additional File 2 executable programme compiled for use on DOS or windows <file name="1475-2875-7-130-S2.exe"> Click here for file </file> Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 7 1 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Smith Thomas A Hastings Ian M MalHaploFreq : A computer programme for estimating malaria haplotype frequencies from blood samples |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
Abstract Background Molecular markers, particularly those associated with drug resistance, are important surveillance tools that can inform policy choice. People infected with falciparum malaria often contain several genetically-distinct clones of the parasite; genotyping the patients' blood reveals whether or not the marker is present (i.e. its prevalence), but does not reveal its frequency. For example a person with four malaria clones may contain both mutant and wildtype forms of a marker but it is not possible to distinguish the relative frequencies of the mutant and wildtypes i.e. 1:3, 2:2 or 3:1. Methods An appropriate method for obtaining frequencies from prevalence data is by Maximum Likelihood analysis. A computer programme has been developed that allows the frequency of markers, and haplotypes defined by up to three codons, to be estimated from blood phenotype data. Results The programme has been fully documented [see Additional File 1 ] and provided with a user-friendly interface suitable for large scale analyses. It returns accurate frequencies and 95% confidence intervals from simulated dataset sets and has been extensively tested on field data sets. Additional File 1 User manual for MalHaploFreq. <file name="1475-2875-7-130-S1.pdf"> Click here for file </file> Conclusion The programme is included [see Additional File 2 ] and/or may be freely downloaded from 1 . It can then be used to extract molecular marker and haplotype frequencies from their prevalence in human blood samples. This should enhance the use of frequency data to inform antimalarial drug policy choice. Additional File 2 executable programme compiled for use on DOS or windows <file name="1475-2875-7-130-S2.exe"> Click here for file </file> |
format |
Article in Journal/Newspaper |
author |
Smith Thomas A Hastings Ian M |
author_facet |
Smith Thomas A Hastings Ian M |
author_sort |
Smith Thomas A |
title |
MalHaploFreq : A computer programme for estimating malaria haplotype frequencies from blood samples |
title_short |
MalHaploFreq : A computer programme for estimating malaria haplotype frequencies from blood samples |
title_full |
MalHaploFreq : A computer programme for estimating malaria haplotype frequencies from blood samples |
title_fullStr |
MalHaploFreq : A computer programme for estimating malaria haplotype frequencies from blood samples |
title_full_unstemmed |
MalHaploFreq : A computer programme for estimating malaria haplotype frequencies from blood samples |
title_sort |
malhaplofreq : a computer programme for estimating malaria haplotype frequencies from blood samples |
publisher |
BMC |
publishDate |
2008 |
url |
https://doi.org/10.1186/1475-2875-7-130 https://doaj.org/article/28f939be9a104cbd83c6df3c1e7b1abe |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 7, Iss 1, p 130 (2008) |
op_relation |
http://www.malariajournal.com/content/7/1/130 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-7-130 1475-2875 https://doaj.org/article/28f939be9a104cbd83c6df3c1e7b1abe |
op_doi |
https://doi.org/10.1186/1475-2875-7-130 |
container_title |
Malaria Journal |
container_volume |
7 |
container_issue |
1 |
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1766342913621491712 |