Open Access Method

An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations

John C Tan1, Becky A Miller1, Asako Tan1, Jigar J Patel12, Ian H Cheeseman3, Tim JC Anderson3, Magnus Manske4, Gareth Maslen4, Dominic P Kwiatkowski4 and Michael T Ferdig15*

  • * Corresponding author: Michael T Ferdig ferdig.1@nd.edu

  • † Equal contributors

Author Affiliations

1 The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA

2 Roche NimbleGen Inc., 504 South Rosa Road, Madison, WI 53719, USA

3 Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78245, USA

4 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

5 Current address: 100 Galvin Life Sciences, Notre Dame, IN 46556, USA

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Genome Biology 2011, 12:R35  doi:10.1186/gb-2011-12-4-r35

Published: 8 April 2011

Additional files

Additional file 1:

Supplementary Figures S1 to S3. Figure S1: pptimal probe melting temperature is consistent in exons, introns, and intergenic regions. Mean Dscore is plotted by probe melting temperature in exons, introns, and intergenic regions; vertical lines indicate 95% confidence intervals. Probes with approximately 66°C melting temperature consistently provided the best performance. Figure S2: CGH data reproducibility. CGH scatterplots for individual CNV events are displayed for replicate hybridizations from independent labeling reactions demonstrating data reproducibility. CNV events from three separate parasite clones are displayed: (a) Dd2; (b) HB3; (c) SC05. The CNV breakpoints are precisely identified between hybridizations. Figure S3: CNV detection in a WGA field sample. CGH scatterplot for a CNV event detected in a WGA field sample, M1064. Four genes (PFE1150w, PFE1155c, PFE1160w, and PFE1165c) are affected by this CNV, including the P. falciparum multidrug resistance gene, pfmdr1.

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