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Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
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Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
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Related Experiment Video

Updated: Jan 3, 2026

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
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Gene Fusion Discovery with INTEGRATE.

Jin Zhang1, Christopher A Maher2,3

  • 1Department of Radiation Oncology, Siteman Cancer Center, Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 16, 2019
PubMed
Summary

INTEGRATE is a gene fusion discovery tool that uses next-generation sequencing (NGS) data. It reconstructs gene fusions and genomic breakpoints from both whole transcriptome sequencing (RNA-seq) and whole genome sequencing (WGS) data.

Keywords:
CancerChimerasGene fusionNext-generation sequencingRNA-seqStructural variationWhole transcriptome sequencingWhole-genome sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Next-generation sequencing (NGS) is crucial for identifying gene fusions.
  • Declining NGS costs increase the availability of whole transcriptome sequencing (RNA-seq) and whole genome sequencing (WGS) data for patient studies.

Purpose of the Study:

  • To introduce INTEGRATE, a novel computational tool for gene fusion discovery.
  • To detail the methodology and application of INTEGRATE for analyzing NGS data.

Main Methods:

  • Developed INTEGRATE, a tool leveraging both RNA-seq and WGS data.
  • Utilized split-read alignment to reconstruct gene fusion junctions and genomic breakpoints.
  • Demonstrated application for combined RNA-seq and WGS data, as well as RNA-seq only data.

Main Results:

  • INTEGRATE effectively reconstructs gene fusion junctions and genomic breakpoints.
  • The tool has been widely adopted within the cancer research community.
  • Successful application in discovering biologically and clinically relevant gene fusions.

Conclusions:

  • INTEGRATE provides a robust method for gene fusion discovery using NGS data.
  • The tool's flexibility allows application to combined or RNA-seq only datasets.
  • INTEGRATE aids in identifying clinically relevant gene fusions for cancer research.