Open Access Method

An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations

John C Tan1†, Becky A Miller1†, Asako Tan1, Jigar J Patel12, Ian H Cheeseman3, Tim JC Anderson3, Magnus Manske4, Gareth Maslen4, Dominic P Kwiatkowski4 and Michael T Ferdig15*

  • * Corresponding author: Michael T Ferdig ferdig.1@nd.edu

  • † Equal contributors

Author Affiliations

1 The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA

2 Roche NimbleGen Inc., 504 South Rosa Road, Madison, WI 53719, USA

3 Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78245, USA

4 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

5 Current address: 100 Galvin Life Sciences, Notre Dame, IN 46556, USA

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Genome Biology 2011, 12:R35 doi:10.1186/gb-2011-12-4-r35

Published: 8 April 2011

Abstract

We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.