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PROBER: oligonucleotide FISH probe design software.

Nicholas Navin1, Vladimir Grubor, Jim Hicks

  • 1Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA. navin@cshl.edu

Bioinformatics (Oxford, England)
|June 3, 2006
PubMed
Summary
This summary is machine-generated.

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PROBER software designs oligonucleotide primer pairs for PCR probes, creating Tiling Oligonucleotide Probes (TOPs) for fluorescence in situ hybridization (FISH). This method offers a stable alternative to BACs for precise genomic region analysis.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Fluorescence in situ hybridization (FISH) is a cytogenetic technique used to detect and localize the presence or absence of specific DNA sequences on chromosomes.
  • Bacterial artificial chromosomes (BACs) are commonly used for FISH but can be unstable, unavailable, chimeric, or non-specific for small genomic regions.
  • PROBER software addresses these limitations by designing Tiling Oligonucleotide Probes (TOPs).

Purpose of the Study:

  • To introduce PROBER, a novel software application for designing oligonucleotide primer pairs.
  • To generate PCR probes for fluorescence in situ hybridization (FISH) applications.
  • To provide an alternative to BACs for analyzing small genomic regions.

Main Methods:

  • PROBER masks repetitive genomic sequences to identify unique regions.

Related Experiment Videos

  • It designs primer pairs to amplify these unique regions into small DNA probes (100-2000 bp).
  • These probes, termed Tiling Oligonucleotide Probes (TOPs), aggregate to generate a single fluorescent signal.

    • Main Results:

    • PROBER successfully designed probes for genomic amplifications and hemizygous deletions.
    • These probes were validated using breast cancer tumor samples initially analyzed by Representational Oligonucleotide Microarray Analysis.
    • The designed TOPs provide a strong fluorescent signal for regions as small as a single gene.

    Conclusions:

    • PROBER is an effective tool for designing Tiling Oligonucleotide Probes (TOPs) for FISH.
    • TOPs offer a reliable and specific alternative to BACs for analyzing genomic regions.
    • The software can be applied to any genomic locus with at least 10 kb of unique sequence blocks.