Svetlana Nikic: Promise for Faster, More Comprehensive Gene Fusion Detection in Cancer
Svetlana Nikic, Founder at Precision Oncology Consulting, shared on LinkedIn about a recent paper by Karleena Rybacki et al. published on Cell Reports Methods:
“A recent study aimed to develop and validate a comprehensive gene fusion detection workflow using Oxford Nanopore Technologies (ONT) long-read sequencing.
The goal was to overcome the limitations of conventional Illumina-based short-read targeted NGS, such as limited fusion discovery and long turnaround times, by leveraging long-read NGS’ faster and more comprehensive detection of known and novel gene fusions in cancer diagnostics.
I list here some of the key findings of this study:
- Panel-positive samples sequenced on ONT successfully detected known fusions with faster turnaround times.
- In 24 panel-negative glioma samples that were sequenced using ONT’s PromethION, 20 candidate novel gene fusions were identified and experimentally validated.
- PromethION detected expected fusions in 19 of 22 panel-positive samples missed by Flongle due to coverage limitations.
- Flongle flow cell sequencing enabled 1-day fusion detection, offering significant advantages over traditional methods (which take ~14–21 days) being higly relevant for clinical implementation from practical standpoint.
This study highlights a valuable clinical application of long-read NGS in oncology. I anticipate that additional research on gene fusion detection using this technology will follow soon.
One consideration: a more appropriate comparator might have been whole-transcriptome analysis via short-read NGS, which also has a higher capacity in detecting novel gene fusions in comparison to targeted aproaches.”
Title: Combining panel-based and whole-transcriptome-based gene fusion detection by long-read sequencing
Authors: Karleena Rybacki, Feng Xu, Hannah M. Deutsch, Mian Umair Ahsan, Joe Chan, Zizhuo Liang, Yuanquan Song, Marilyn Li, Kai Wang
More posts featuring Svetlana Nikic.
-
Challenging the Status Quo in Colorectal Cancer 2024
December 6-8, 2024
-
ESMO 2024 Congress
September 13-17, 2024
-
ASCO Annual Meeting
May 30 - June 4, 2024
-
Yvonne Award 2024
May 31, 2024
-
OncoThon 2024, Online
Feb. 15, 2024
-
Global Summit on War & Cancer 2023, Online
Dec. 14-16, 2023