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An optimized microarray platform for assaying genomic variation in |
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| Authors: | John C Tan Becky A Miller Asako Tan Jigar J Patel Ian H Cheeseman Tim JC Anderson Magnus Manske Gareth Maslen Dominic P Kwiatkowski Michael T Ferdig |
| Affiliation: | (1) The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA;(2) Roche NimbleGen Inc., 504 South Rosa Road, Madison, WI 53719, USA;(3) Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78245, USA;(4) Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK;(5) 100 Galvin Life Sciences, Notre Dame, IN 46556, USA |
| 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. |
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