Related Experiment Video
Updated: Jul 15, 2025
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
A Method for Extending Target Regions of Genomic Profiling by Combining a Custom Probe Pool with a Commercial
Yoji Kukita1, Kei Kunimasa2, Takashi Akazawa3
1Laboratory of Genomic Pathology, Research Center, Osaka International Cancer Institute, Osaka, Japan.
Background:
Next-generation sequencing (NGS)-based genomic profiling is becoming widespread in determining treatment policies for patients with tumors. Commercially available gene panels for pan-tumor targets comprise hundreds of tumor-related genes but frequently lack genes of interest in specific tumor types. In this study, we demonstrate a method for extending target regions of genomic profiling by combining a custom probe pool with a commercial targeted panel.
Methods:
We used TruSight Oncology 500 (TSO500) as a commercial targeted panel and a custom probe pool designed for all exons of the SMARCA2 gene. Sequencing libraries of custom targets were constructed using a portion of the TSO500 library solution before the hybridization-capture process. After hybridization capture, both libraries were combined and sequenced using a next-generation sequencer.
Results:
Sequencing results showed that >96.8% and 100% of the target exons were covered at a depth of over 100× using the TSO500 and custom panels, respectively. The custom panels had slightly better median exon coverage than the TSO500. The combined libraries of the custom and TSO500 panels showed a mapped read ratio close to the mixing ratio. Analysis of mutation-free regions showed similar accuracies between the TSO500 and custom panels regarding variant calling.
Conclusions:
Our devised method easily and affordably extends the targets beyond a ready-made panel. This method provides a valuable solution until the widespread adoption of whole-exome sequencing, which is costly for large target sizes.
Insights
This study presents a cost-effective method to expand genomic profiling targets by combining custom probes with commercial panels. This approach enhances tumor gene analysis, offering a practical alternative to expensive whole-exome sequencing.
Area of Science:
- Genomics
- Molecular Biology
- Oncology
Background:
- Next-generation sequencing (NGS) is crucial for tumor treatment decisions.
- Commercial gene panels often miss specific tumor-related genes.
- Extending genomic profiling targets is needed for comprehensive analysis.
Purpose of the Study:
- To develop a method for extending genomic profiling targets.
- To combine a custom probe pool with a commercial targeted panel.
- To enhance the analysis of specific tumor types.
Main Methods:
- Utilized the TruSight Oncology 500 (TSO500) commercial panel.
- Designed a custom probe pool for all SMARCA2 gene exons.
- Integrated custom target libraries with TSO500 libraries before sequencing.
Main Results:
- Achieved >96.8% exon coverage at 100× depth with TSO500 and 100% with custom panels.
- Custom panels showed slightly better median exon coverage.
- Variant calling accuracy was similar between TSO500 and custom panels.
Conclusions:
- The devised method affordably extends genomic profiling targets beyond commercial panels.
- This offers a valuable solution for comprehensive tumor gene analysis.
- Provides an alternative to costly whole-exome sequencing for large target sizes.
More Related Videos
05:53Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
13:24Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
