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

John C Tan, Becky A Miller, Asako Tan, Jigar J Patel, Ian H Cheeseman, Tim JC Anderson, Magnus Manske, Gareth Maslen, Dominic P Kwiatkowski and Michael T Ferdig
Genome Biology 12.4 (2011): R35.
Publication Date: 
April, 2011

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.