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Open Access Methodology article

A microarray platform and novel SNP calling algorithm to evaluate Plasmodium falciparum field samples of low DNA quantity

Christopher G Jacob1, John C Tan23, Becky A Miller34, Asako Tan3, Shannon Takala-Harrison1, Michael T Ferdig3 and Christopher V Plowe1*

Author Affiliations

1 Malaria Group, Howard Hughes Medical Institute / Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA

2 Research and Development, Roche NimbleGen, Inc., Madison, WI 53719, USA

3 Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA

4 Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA

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BMC Genomics 2014, 15:719  doi:10.1186/1471-2164-15-719

Published: 26 August 2014

Abstract

Background

Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In areas with adequate cold chain facilities, large volumes of leukocyte-depleted patient blood can be frozen for use in parasite genomic analyses. In more remote endemic areas smaller volumes of infected blood are taken by finger prick, and dried and stored on filter paper. These dried blood spots do not generally yield enough concentrated parasite DNA for whole-genome sequencing.

Results

A DNA microarray was designed for use on field samples to type a genome-wide set of SNPs which prior sequencing had shown to be variable in Africa, Southeast Asia, and Papua New Guinea. An algorithm was designed to call SNPs in samples with low parasite DNA. With this new algorithm SNP-calling accuracy of 98% was measured by hybridizing purified DNA from malaria lab strains and comparing calls with SNPs called from full genome sequences. An average accuracy of >98% was likewise obtained for DNA extracted from malaria field samples collected in studies in Southeast Asia, with an average call rate of > 82%.

Conclusion

This new high-density microarray provided high quality SNP calls from a wide range of parasite DNA quantities, and represents a robust tool for genome-wide analysis of malaria parasites in diverse settings.

Keywords:
Plasmodium falciparum; Malaria; Microarray