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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

INTEGRATE: gene fusion discovery using whole genome and transcriptome data.

Jin Zhang¹, Nicole M White², Heather K Schmidt³

¹McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, USA;

Genome Research

|November 12, 2015

Summary

We developed INTEGRATE, a new tool that combines whole genome and RNA sequencing data to accurately detect gene fusions. This approach improves sensitivity and specificity, identifying novel fusions in cancer patients.

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Area of Science:

Genomics
Bioinformatics
Cancer Research

Background:

Next-generation sequencing (NGS) is key for gene fusion discovery, but challenges remain in accuracy and minimizing false positives.
Current tools analyze whole genome sequencing (WGS) and RNA sequencing (RNA-seq) data independently, each with limitations.
Integrating WGS and RNA-seq offers orthogonal validation for sensitive and specific gene fusion detection.

Purpose of the Study:

To develop and evaluate a novel computational tool, INTEGRATE, for high-confidence gene fusion prediction.
To leverage the combined power of RNA-seq and WGS data for improved gene fusion discovery.
To assess the performance of INTEGRATE against existing gene fusion detection tools.

Main Methods:

Developed INTEGRATE, a tool that reconstructs gene fusion junctions and genomic breakpoints using split-read mapping from both RNA-seq and WGS data.
Compared INTEGRATE with eight other gene fusion discovery tools using HCC1395 cell line and HCC1395BL samples.
Performed targeted validation on predicted fusions to assess accuracy and identify novel events.

Main Results:

INTEGRATE demonstrated high accuracy, missing only 6 out of 138 validated fusions and outperforming eight other tools.
Identified 131 novel gene fusions, in addition to 7 previously reported fusions, in the validation set.
Applied INTEGRATE to 62 breast cancer patients (TCGA), revealing recurrent gene fusions, including those involving the estrogen receptor.

Conclusions:

INTEGRATE is a highly sensitive and accurate tool for gene fusion discovery by integrating RNA-seq and WGS data.
The combined data approach significantly enhances the reliability of gene fusion predictions.
INTEGRATE offers a valuable, freely available resource for academic research in cancer genomics.