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Title: FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance
Authors: Nicolas Steenkeste
Marie Agnès Dillies
Nimol Khim
Odile Sismeiro
Sophy Chy
Pharath Lim
Andreas Crameri
Christiane Bouchier
Odile Mercereau-Puijalon
Hans Peter Beck
Mallika Imwong
Arjen M. Dondorp
Duong Socheat
Christophe Rogier
Jean Yves Coppée
Frédéric Ariey
Institut Pasteur du Cambodge
Institut Pasteur, Paris
Amunix, Inc.
Swiss Tropical and Public Health Institute (Swiss TPH)
Mahidol University
Centre for Clinical Vaccinology and Tropical Medicine
National Center for Parasitology, Entomology and Malaria Control
IMTSSA Institut de Medecine Tropicale du Service de Sante des Armees
Keywords: Immunology and Microbiology;Medicine
Issue Date: 30-Nov-2009
Citation: Malaria Journal. Vol.8, No.1 (2009)
Abstract: 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). Conclusion. 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.
ISSN: 14752875
Appears in Collections:Scopus 2006-2010

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