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

Genome Biol. 2011;12(4):R35. doi: 10.1186/gb-2011-12-4-r35. Epub 2011 Apr 8.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • DNA Contamination
  • DNA Copy Number Variations / genetics*
  • Genotyping Techniques*
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods*
  • Plasmodium falciparum / genetics*
  • Polymorphism, Single Nucleotide*