PROBER: Oligonucleotide FISH probe design software

Nicholas Navin*, Vladimir Grubor, Jim Hicks, Evan Leibu, Elizabeth Thomas, Jennifer Troge, Michael Riggs, Pär Lundin, Susanne Månér, Jonathan Sebat, Anders Zetterberg, Michael Wigler

*Corresponding author for this work

Research output: Contribution to journalArticle

21 Scopus citations

Abstract

PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100-2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10-100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors.

Original languageEnglish (US)
Pages (from-to)2437-2438
Number of pages2
JournalBioinformatics
Volume22
Issue number19
DOIs
StatePublished - Oct 1 2006

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ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Navin, N., Grubor, V., Hicks, J., Leibu, E., Thomas, E., Troge, J., Riggs, M., Lundin, P., Månér, S., Sebat, J., Zetterberg, A., & Wigler, M. (2006). PROBER: Oligonucleotide FISH probe design software. Bioinformatics, 22(19), 2437-2438. https://doi.org/10.1093/bioinformatics/btl273