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Related Concept Videos

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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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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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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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Related Experiment Video

Updated: Sep 15, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Gene fusion detection in long-read transcriptome sequencing data with GFvoter.

Xiaolan Zhao1,2, Zitong Ren1, Junhai Qi1

  • 1Research Center for Mathematics and Interdisciplinary Sciences, Frontiers Science Center for Nonlinear Expectations (Ministry of Education), Shandong University, Qingdao, 266237, China.

BMC Genomics
|July 17, 2025
PubMed
Summary

GFvoter is a new method for detecting gene fusions using long-read RNA sequencing. This tool accurately identifies gene fusions, improving cancer diagnosis and treatment strategies.

Keywords:
Gene fusion detectionLong-read transcriptome sequencingMultivotingScoring mechanism

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Gene fusions are common in cancer and serve as important diagnostic biomarkers and therapeutic targets.
  • Long-read transcriptome sequencing offers advanced capabilities for detecting gene fusions.

Purpose of the Study:

  • To develop GFvoter, a novel method for accurate gene fusion detection using long-read RNA sequencing data.
  • To evaluate GFvoter's performance against existing methods in identifying gene fusions.

Main Methods:

  • GFvoter utilizes a multivoting strategy, integrating outputs from two RNA-seq aligners and two fusion detection tools.
  • A custom scoring mechanism is employed within the voting process to enhance fusion identification accuracy.
  • The method was validated using simulated and real cell line datasets from PacBio and Nanopore sequencing platforms.

Main Results:

  • GFvoter demonstrated significantly superior performance compared to alternative gene fusion detection methods.
  • The tool successfully identified the RPS6KB1:VMP1 gene fusion in MCF-7 cell lines, a fusion missed by other tested tools.
  • Validation on both simulated and real datasets confirmed GFvoter's high accuracy and reliability.

Conclusions:

  • GFvoter accurately detects gene fusions from long-read RNA sequencing data.
  • This method has the potential to enhance cancer diagnosis and guide therapeutic strategies.
  • GFvoter is publicly available for research use.