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 J.C. Anderson, Magnus Manske, Gareth Maslen, Dominic P. Kwiatkowski, Michael T. Ferdig

    Research output: Contribution to journalArticle

    21 Scopus citations

    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.

    Original languageEnglish (US)
    Article numberR35
    JournalGenome biology
    Volume12
    Issue number4
    DOIs
    StatePublished - Apr 8 2011

    ASJC Scopus subject areas

    • Ecology, Evolution, Behavior and Systematics
    • Genetics
    • Cell Biology

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  • Cite this

    Tan, J. C., Miller, B. A., Tan, A., Patel, J. J., Cheeseman, I. H., Anderson, T. J. C., Manske, M., Maslen, G., Kwiatkowski, D. P., & Ferdig, M. T. (2011). An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations. Genome biology, 12(4), [R35]. https://doi.org/10.1186/gb-2011-12-4-r35