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. 2013;16(1-2):37-43.
doi: 10.1159/000345607. Epub 2013 Mar 18.

Malaria diagnostics and surveillance in the post-genomic era

N W Lucchi  1 , J Oberstaller, J C Kissinger, V Udhayakumar
Affiliations

Malaria diagnostics and surveillance in the post-genomic era

N W Lucchi et al. Public Health Genomics. 2013.

Abstract

Genome sequences are available for 3 human-infecting malaria parasites, Plasmodium falciparum, P. vivax and P. knowlesi, and population genomics data are available for many endemic regions. This review summarizes how genomic data have been used to develop new, species-specific molecular targets for better malaria diagnosis. The combination of bioinformatics and genomics has been used to identify new sequence targets suitable for diagnostic applications and assess their viability within the context of global Plasmodium sequence variation. The selection criteria maximized the sensitivity and specificity of the novel targets. At least one target from each species was found to be suitable for molecular diagnosis of malaria with some advantages over existing molecular methods. The promise of using genome sequence data to develop sensitive, genus- or species-specific diagnostic methods for other pathogens of public health interest is strong. This undertaking together with what we envision as the future of malaria diagnosis in the 'omic' era is discussed.

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Figures

Fig. 1
Fig. 1
Schematic of diagnostic target screening and development pipeline. Genomic sequences for P. falciparum (Pf), P. vivax (Pv), and P. knowlesi (Pk) were downloaded from PlasmoDB. Data were mined for repeats using the RepeatScout algorithm to construct consensus repeat sequences (CRSs) for each identified repeat family. We identified 418 CRSs for Pf, 428 CRSs for Pv and 423 CRSs for Pk. CRSs were then screened in parallel for tandem repeats, similarity to human sequences and vector sequences. Pf, Pv and Pk CRSs passing these screens and proceeding to the next steps are indicated in parentheses. Any CRSs failing these screens were removed from further consideration. CRSs that were not species-specific or less than 300 bp long were eliminated. Family copy numbers for the remaining candidates were determined via comparison of the CRSs against the appropriate genome sequences. Candidate repeat families containing six or more copies and separated by at least 100 bp were considered for further testing.
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