title: An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations.
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.
authors.affiliation: The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Tan
authors.forename: Becky A
authors.initials: BA
authors.lastname: Miller
authors.forename: Asako
authors.initials: A
authors.lastname: Tan
authors.forename: Jigar J
authors.initials: JJ
authors.lastname: Patel
authors.forename: Ian H
authors.initials: IH
authors.lastname: Cheeseman
authors.forename: Tim J C
authors.initials: TJ
authors.lastname: Anderson
authors.forename: Magnus
authors.initials: M
authors.lastname: Manske
authors.forename: Gareth
authors.initials: G
authors.lastname: Maslen
authors.forename: Dominic P
authors.initials: DP
authors.lastname: Kwiatkowski
authors.forename: Michael T
authors.initials: MT
authors.lastname: Ferdig
mesh_terms: D000818:Animals; D059018:DNA Contamination; D056915:DNA Copy Number Variations / Q000235:genetics*; D060005:Genotyping Techniques; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010963:Plasmodium falciparum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide