Nanopore Flongle sequencing as a rapid, single specimen clinical test for fusion detection

The identification of gene fusions is a cornerstone of diagnosis and treatment decision making for tumors of many forms and primary sites. Diverse molecular approaches are currently used for the molecular diagnosis of fusions, but few permit broad, partner agnostic detection of fusions over multiple potential targets. We previously described the combination of nanopore sequencing with the anchored multiplex PCR technique to permit a rapid testing paradigm.

Recently, a new platform for Nanopore sequencing has become publicly available, the Flongle flow cell from Oxford Nanopore Technologies (ONT), that offers lower throughput, but lower price testing. In this report, we describe the results of retesting of 15 specimens previously tested with both Illumina and ONT MinION sequencing. Further, we additionally blindly tested 13 specimens that had undergone clinical Illumina based sequencing.

We find that our Flongle sequencing pipeline removes key complexities of a multiplexed nanopore sequencing protocol, reduces sequencing turnaround time, and shows excellent concordance with Illumina results, and is particularly strong in identifying notoriously difficult to detect CIC-DUX4 translocations. We propose that features of the reported assay may make it of substantial interest for deployment in small to medium size molecular laboratories.