Datasets Affected by Aneuploidy

An investigation of the strains used in more than 100 published microarray datasets revealed that some of the mutant strains that were constructed for the analyses had acquired chromosomal abnormalities. The presence of additional, or fewer, copies of some chromosomes leads to biases in gene expression profiles.

In this study, the datasets from the publications listed below were identified as having been generated using aneuploid strains. However, note that since aneuploidy is common and occurs frequently during the routine handling of C. albicans strains, it should always be considered as a possible complication unless its presence has been specifically investigated. The authors of this study present a rapid method of testing for aneuploidy.

For more details, please see the original publication:
Arbour M, Epp E, Hogues H, Sellam A, Lacroix C, Rauceo J, Mitchell A, Whiteway M, Nantel A (2009) Widespread occurrence of chromosomal aneuploidy following the routine production of Candida albicans mutants. FEMS Yeast Res  

Datasets known to be affected:

• Dignard D and Whiteway M (2006) SST2, a Regulator of G-Protein Signaling for the Candida albicans Mating Response Pathway. Eukaryot Cell 5(1):192-202.
     
• Oberholzer U, et al. (2006) Transcript Profiles of Candida albicans Cortical Actin Patch Mutants Reflect Their Cellular Defects: Contribution of the Hog1p and Mkc1p Signaling Pathways. Eukaryot Cell 5(8):1252-65.
     
• Garcia-Sanchez S, et al. (2005) Global Roles of Ssn6 in Tup1- and Nrg1-dependent Gene Regulation in the Fungal Pathogen, Candida albicans. Mol Biol Cell 16(6):2913-25. Courtesy of the Galar Fungail Consortium; study supported by the European Commission, The Wellcome Trust, and the UK Biotechnology and Biological Sciences Research Council.
     
• Harcus D, et al. (2004) Transcription profiling of cyclic AMP signaling in Candida albicans. Mol Biol Cell 15(10):4490-9
     
• Cowen LE, et al. (2002) Population genomics of drug resistance in Candida albicans. Proc Natl Acad Sci U S A 99(14):9284-9.
     
• Nantel A, et al. (2002) Transcription profiling of Candida albicans cells undergoing the yeast-to-hyphal transition. Mol Biol Cell 13(10):3452-65.
     

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