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Related Experiment Videos

Widespread aneuploidy revealed by DNA microarray expression profiling.

T R Hughes1, C J Roberts, H Dai

  • 1Rosetta Inpharmatics, Inc., Kirkland, Washington, USA.

Nature Genetics
|July 11, 2000
PubMed
Summary
This summary is machine-generated.

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DNA microarrays reveal that many yeast deletion mutants are aneuploid, causing inaccurate gene expression profiles. This highlights the need to validate genomic stability when analyzing expression data.

Area of Science:

  • Genomics
  • Molecular Biology
  • Yeast Genetics

Background:

  • DNA microarrays are valuable for gene expression profiling and characterizing novel genes.
  • Systematic analysis of gene deletion mutants is crucial for understanding gene function.

Purpose of the Study:

  • To assess the utility of DNA microarrays for expression profiling in Saccharomyces cerevisiae deletion mutants.
  • To identify potential issues affecting the accuracy of expression data in mutant strains.

Main Methods:

  • Expression profiling of nearly 300 Saccharomyces cerevisiae deletion mutants using DNA microarrays.
  • Competitive hybridization of genomic DNA from mutant and wild-type strains to detect aneuploidy.
  • Analysis of published expression data for evidence of aneuploid strains.

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Main Results:

  • Approximately 8% of profiled mutants showed chromosome-wide expression biases, indicative of aneuploidy.
  • Aneuploidy was confirmed through genomic DNA hybridization, involving whole chromosomes or segments.
  • Analysis of other studies revealed similar instances of aneuploid strains in expression profiling experiments.
  • In some cases, extra chromosomes contained homologous genes to the deleted ones, conferring a growth advantage.

Conclusions:

  • Aneuploidy is a significant factor that can lead to spurious correlations in gene expression profiles.
  • Genomic instability, such as aneuploidy, must be considered when interpreting whole-genome expression data, especially in malignant or immortalized cells.
  • The findings emphasize the importance of quality control for genomic stability in gene expression studies.