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Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum

Neekesh V Dharia1 email, Amar Bir Singh Sidhu2,3 email, María Belén Cassera4 email, Scott J Westenberger1 email, Selina ER Bopp1 email, Rich T Eastman2 email, David Plouffe5 email, Serge Batalov5 email, Daniel J Park6 email, Sarah K Volkman7,8 email, Dyann F Wirth6,7 email, Yingyao Zhou5 email, David A Fidock2,9 email and Elizabeth A Winzeler1,5 email

Department of Cell Biology, ICND 202, The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA

Department of Microbiology, Columbia University College of Physicians and Surgeons, West 186th Street, New York, NY 10032, USA

The Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA 02142, USA

Department of Biochemistry, Albert Einstein College of Medicine at Yeshiva University, Morris Park Avenue, Bronx, NY 10461, USA

Genomics Institute of the Novartis Research Foundation, John Jay Hopkins Drive, San Diego, CA 92121, USA

The Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, MA 02142, USA

Department of Immunology and Infectious Diseases, Harvard School of Public Health, Huntington Avenue, Boston, MA 02115, USA

School for Health Studies, Simmons College, The Fenway, Boston, MA 02115, USA

Department of Medicine, Columbia University College of Physicians and Surgeons, West 186th Street, New York, NY 10032, USA

author email corresponding author email

Genome Biology 2009, 10:R21doi:10.1186/gb-2009-10-2-r21

Published: 13 February 2009

Subject areas: Drug discovery, Medicine, Microbiology and parasitology


Additional files

Additional data file 1:

Presented is a table listing MOID gene present calls and average log2 ratios for Dd2, HB3, 3D7attB and FOS-RDd2-CL1

Format: XLS Size: 1.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 2:

Presented is a table listing CNVs predicted by our algorithm in Dd2, HB3, 3D7attB and FOS-RDd2-CL1.

Format: XLS Size: 43KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 3:

Table S1 contains SNP prediction results for Dd2. Table S2 contains SNP test set filtering information. Figure S1 is the probe behavior based on SNP position. Figure S2 is a genome-wide view of polymorphisms detected by microarray and sequencing in Dd2 relative to 3D7. Figure S3 contains control experiments for fosmidomycin resistance metabolite profiling.

Format: DOC Size: 1.7MB Download file

This file can be viewed with: Microsoft Word Viewer

Additional data file 4:

Presented is a table listing polymorphisms predicted by our algorithm in Dd2, HB3, 3D7attB, and FOR-RDd2-Cl1.

Format: XLS Size: 11.2MB Download file

This file can be viewed with: Microsoft Excel Viewer


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