Publication: FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance
Issued Date
2009-11-30
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ISSN
14752875
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2-s2.0-70450257755
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Mahidol University
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SCOPUS
Bibliographic Citation
Malaria Journal. Vol.8, No.1 (2009)
Suggested Citation
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 FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance. Malaria Journal. Vol.8, No.1 (2009). doi:10.1186/1475-2875-8-229 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/27630
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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
Other Contributor(s)
Institut Pasteur du Cambodge
Institut Pasteur, Paris
Amunix, Inc.
GENOPOLE
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
Institut Pasteur, Paris
Amunix, Inc.
GENOPOLE
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
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.