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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Detalles Bibliográficos
Autores principales: Tan, John C, Miller, Becky A, Tan, Asako, Patel, Jigar J, Cheeseman, Ian H, Anderson, Tim JC, Manske, Magnus, Maslen, Gareth, Kwiatkowski, Dominic P, Ferdig, Michael T
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218861/
https://www.ncbi.nlm.nih.gov/pubmed/21477297
http://dx.doi.org/10.1186/gb-2011-12-4-r35
Descripción
Sumario: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.

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