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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, Amar BS Sidhu3,2, María B Cassera4, Scott J Westenberger1, Selina ER Bopp1, Rich T Eastman2, David Plouffe5, Serge Batalov5, Daniel J Park6, Sarah K Volkman7,8, Dyann F Wirth7,6, Yingyao Zhou5, David A Fidock9,2 and Elizabeth A Winzeler1,5*

Author Affiliations

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

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

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

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

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

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

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

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

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

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Genome Biology 2009, 10:R21 doi:10.1186/gb-2009-10-2-r21

Published: 13 February 2009

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

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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

Open Data

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

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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

Open Data