Tool Development

Microarray

To get as useful data as we can, we have developed multiple microarray designs on Roche-Nimblegen platform and Agilent platform

CGH Microarray (385K)

- High resolution comparative genomic hybridization (CGH) microarray with 385,585 probes representing the entire P. falciparum 3D7 reference genome
- Probe length adjusted for isothermal balance for optimal hybridization
- Probe length averages 56 base pairs (bp) and are spaced at a median of 21 bp across the genome

CNV-SNP Array (3-Plex 720K)

- High resolution microarray capable of simultaneously assaying copy number variation (CNV) and genotyping single nucleotide polymorphisms (SNPs)
- CNV interrogated by 355,803 CGH probes with a median spacing of 52 bp across the genome
- 45,524 SNP loci interrogated by 364,192 resequencing probes capable of making base calls and adjusted for isothermal balance for optimal hybridization; Averages 36,948 base calls with 94.6% accuracy
- Low DNA requirement of 250 ng of parasite DNA
- Robust up to 92% human DNA contamination

Southeast Asia SNP Array (12-Plex 135K)

- Interrogates 16,875 SNP loci tailored to Southeast Asia samples
- Probe length adjusted for isothermal balance for optimal hybridization
- Averages 10,136 usable SNPs with 97% accuracy
- Low DNA requirement of less than 30 ng of parasite DNA
- Robust to <99% human DNA contamination