Publication: FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance.
Accepted Date
2009-10-15
Issued Date
2009-10-15
Copyright Date
2009
Resource Type
Language
eng
ISSN
1475-2875 (electronic)
Rights
Mahidol University
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BioMed Central
Bibliographic Citation
Steenkeste N, Dillies MA, Khim N, Sismeiro O, Chy S, Lim P, et al. FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance. Malar J. 2009 Oct 15;8:229.
Suggested Citation
Steenkeste, Nicolas, Dillies, Marie-Agnès, Khim, Nimol, Sismeiro, Odile, Chy, Sophy, Lim, Pharath, Crameri, Andreas, Bouchier, Christiane, Mercereau-Puijalon, Odile, Beck, Hans-Peter, Mallika Imwong, มัลลิกา อิ่มวงศ์, Dondorp, Arjen M., Socheat, Duong, Rogier, Christophe, Coppée, Jean- Yves, Ariey, Frédéric FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance.. Steenkeste N, Dillies MA, Khim N, Sismeiro O, Chy S, Lim P, et al. FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance. Malar J. 2009 Oct 15;8:229.. doi:10.1186/1475-2875-8-229 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/723
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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.
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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.