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Tagging and Fusion Proteins

Tagging and Fusion Proteins

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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Updated: Apr 11, 2026

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing

Published on: July 5, 2019

JAFFA: High sensitivity transcriptome-focused fusion gene detection.

Nadia M Davidson¹, Ian J Majewski², Alicia Oshlack³

¹Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia.

Genome Medicine

|May 29, 2015

Summary

This summary is machine-generated.

Genomic instability in cancer involves fusion genes. JAFFA, a RNA sequencing tool, accurately detects these fusion genes using long reads or assembled short reads for better cancer transcriptome profiling.

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Published on: October 18, 2013

Area of Science:

Oncology
Bioinformatics
Genomics

Background:

Genomic instability is a key characteristic of cancer, frequently leading to structural alterations and fusion genes.
RNA sequencing (RNA-Seq) is crucial for cancer profiling, but existing fusion gene detection methods are optimized for short reads.
Fusion genes play a significant role in cancer development and progression.

Purpose of the Study:

To introduce JAFFA, a novel method for sensitive fusion gene detection in cancer transcriptomes.
To demonstrate JAFFA's superior performance with longer sequencing reads (100 bp or greater).
To provide an alternative approach for fusion gene identification by analyzing the cancer transcriptome.

Main Methods:

JAFFA compares the cancer transcriptome to a reference transcriptome.
The cancer transcriptome is inferred either directly from long reads or by de novo assembly of short reads.
The method is optimized for RNA sequencing data with reads of 100 bp or greater.

Main Results:

JAFFA exhibits higher sensitivity in detecting fusion genes compared to existing methods, particularly with longer reads.
The tool effectively identifies fusion genes by analyzing transcriptomic data.
JAFFA's approach of transcriptome comparison aids in accurate fusion gene discovery.

Conclusions:

JAFFA is a sensitive and effective tool for detecting fusion genes in cancer.
The method offers improved performance for RNA sequencing data with longer reads.
JAFFA provides a valuable approach for cancer transcriptome profiling and understanding genomic alterations.