Methodology

FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance

Nicolas Steenkeste^1* , Marie-Agnès Dillies^2* , Nimol Khim¹ , Odile Sismeiro² , Sophy Chy¹ , Pharath Lim¹ , Andreas Crameri³ , Christiane Bouchier⁴ , Odile Mercereau-Puijalon⁵ , Hans-Peter Beck⁶ , Mallika Imwong^7,8 , Arjen M Dondorp^7,8 , Duong Socheat⁹ , Christophe Rogier¹⁰ , Jean-Yves Coppée² and Frédéric Ariey¹

¹  Laboratoire d'épidémiologie moléculaire, Institut Pasteur du Cambodge, 5 bd Monivong, BP 983, Phnom Penh, Cambodia

²  Institut Pasteur, Génopole, Plate-forme Puces à ADN, F-75015 Paris, France

³  Amunix, 500 Ellis Street, Mountain View, CA 94043, USA

⁴  Institut Pasteur, Génopole, Plate-forme Génomique, F-75015 Paris, France

⁵  Immunologie Moléculaire des Parasites, Institut Pasteur de Paris, Paris, France

⁶  Swiss Tropical Institute, Socinstrasse 57, CH 4002 Basel, Switzerland

⁷  Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand

⁸  Center for Clinical Vaccinology and Tropical Medicine, Oxford, UK

⁹  National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia

¹⁰  IMTSSA, Unité de Recherche en Biologie et Epidémiologie Parasitaires (URBEP), Marseille, France

author email corresponding author email* Contributed equally

Malaria Journal 2009, 8:229doi:10.1186/1475-2875-8-229

Published:	15 October 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.