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...
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th-mahidol.276302018-09-13T13:51:21Z FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance 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. 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 Immunology and Microbiology Medicine 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. 2018-09-13T06:40:02Z 2018-09-13T06:40:02Z 2009-11-30 Article Malaria Journal. Vol.8, No.1 (2009) 10.1186/1475-2875-8-229 14752875 2-s2.0-70450257755 https://repository.li.mahidol.ac.th/handle/123456789/27630 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=70450257755&origin=inward |
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Immunology and Microbiology Medicine 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 |
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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. |
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Institut Pasteur du Cambodge |
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Institut Pasteur du Cambodge 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 |
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Article |
author |
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 |
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Nicolas Steenkeste |
title |
FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance |
title_short |
FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance |
title_full |
FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance |
title_fullStr |
FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance |
title_full_unstemmed |
FlexiChip package: An universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance |
title_sort |
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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2018 |
url |
https://repository.li.mahidol.ac.th/handle/123456789/27630 |
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1763488089191219200 |