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

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 effec...

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Bibliographic Details
Published in:	Genome biology Vol. 12; no. 4; p. R35
Main Authors:	Tan, John C, Miller, Becky A, Tan, Asako, Patel, Jigar J, Cheeseman, Ian H, Anderson, Tim J C, Manske, Magnus, Maslen, Gareth, Kwiatkowski, Dominic P, Ferdig, Michael T
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 08-04-2011 BioMed Central
Subjects:	Animals DNA Contamination DNA Copy Number Variations - genetics Genotyping Techniques Humans Method Oligonucleotide Array Sequence Analysis - methods Plasmodium falciparum - genetics Polymorphism, Single Nucleotide
Online Access:	Get full text
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1474-760X 1465-6906 1474-760X 1465-6914
DOI:	10.1186/gb-2011-12-4-r35