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Related Experiment Videos

Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach.

Yi-Shin Pan1, Yun-Shien Lee, Yung-Lin Lee

  • 1Liver Research Unit, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan. extraganoderma@yahoo.com.tw

BMC Genomics
|June 2, 2006
PubMed
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This study introduces a modified SSH/microarray technique to efficiently profile low-expression genes. The new method significantly improves the detection of differentially expressed genes in hepatocarcinoma, aiding functional genomic studies.

Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Assaying low-expression genes is a major challenge in genome-wide gene-expression profiling.
  • High-throughput, high-sensitivity methods are needed for functional genomic studies.
  • Previous SSH and microarray combinations were inefficient due to extensive sequencing.

Purpose of the Study:

  • To develop a more efficient and sensitive method for profiling low-expression transcriptomes.
  • To improve the identification of differentially expressed genes, especially those with low expression.
  • To enhance functional genomic studies by overcoming limitations of existing techniques.

Main Methods:

  • Modified a combined SSH (suppressive subtractive hybridization) and microarray approach.

Related Experiment Videos

  • Directly used subtracted amplicons as targets for pre-made cDNA microarrays (SSH/microarray).
  • Applied the SSH/microarray assay to hepatoma and non-hepatoma liver tissue samples.

    • Main Results:

    • The modified SSH/microarray simplified gene identification without tedious sequencing.
    • 5015 low-expression genes, previously unanalyzable, became detectable.
    • Detected ~10 times more differentially expressed genes in HCC (701 vs. 69), including rare transcripts.

    Conclusions:

    • The modified SSH/microarray approach is a simple, sensitive, and efficient tool for low-expression transcriptome profiling.
    • This method is highly suitable for functional genomic studies.
    • Identified genes involved in cell cycle, cell death, signal transduction, and morphogenesis in hepatocarcinogenesis.