FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance.
BACKGROUND
A number of molecular tools have been developed to monitor the emergence and spread of anti-malarial drug resistance to Plasmodium falciparum. One of the major obstacles to the wider implementation of these tools is the absence of practical methods enabling high throughput analysis. Here a new Zip-code array is described, called FlexiChip, linked to a dedicated software program, which largely overcomes this problem.


METHODS
Previously published microarray probes detecting single-nucleotide polymorphisms (SNP) associated with parasite resistance to anti-malarial drugs (ResMalChip) were adapted for a universal microarray FlexiChip format. To evaluate the overall sensitivity of the FlexiChip package (microarray + software), the results of FlexiChip were compared to ResMalChip microarray, using the same extension probes and with the same PCR products. In both cases, sequence results were used as gold standard to calculate sensitivity and specificity. FlexiChip results obtained with a set of field isolates were then compared to those assessed in an independent reference laboratory.


RESULTS
The FlexiChip package gave results identical to the ResMalChip results in 92.7% of samples (kappa coefficient 0.8491, with a standard error 0.021) and had a sensitivity of 95.88% and a specificity of 97.68% compared to the sequencing as the reference method. Moreover the method performed well compared to the results obtained in the reference laboratories, with 99.7% of identical results (kappa coefficient 0.9923, S.E. 0.0523).


CONCLUSIONS
Microarrays could be employed to monitor P. falciparum drug resistance markers with greater cost effectiveness and the possibility for high throughput analysis. The FlexiChip package is a promising tool for use in poor resource settings of malaria endemic countries.
Steenkeste
Nicolas
N
Laboratoire d'épidémiologie moléculaire, Institut Pasteur du Cambodge, 5 bd Monivong, BP 983, Phnom Penh, Cambodia. nicolas@pasteur-kh.org
Dillies
Marie-Agnès
MA
Khim
Nimol
N
Sismeiro
Odile
O
Chy
Sophy
S
Lim
Pharath
P
Crameri
Andreas
A
Bouchier
Christiane
C
Mercereau-Puijalon
Odile
O
Beck
Hans-Peter
HP
Imwong
Mallika
M
Dondorp
Arjen M
AM
Socheat
Duong
D
Rogier
Christophe
C
Coppée
Jean-Yves
JY
Ariey
Frédéric
F
D000818:Animals; D004351:Drug Resistance; D006801:Humans; D008288:Malaria / Q000469:parasitology; D046228:Microarray Analysis / Q000379:methods*; D021261:Parasitic Sensitivity Tests / Q000379:methods*; D010963:Plasmodium falciparum / Q000187:drug effects* / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D012984:Software