Exploratory Whole Transcriptome Sequencing Reveals Ancillary Fusion Transcripts in Driver-Positive Tumors

Nikkan Chakraborty; Raja  Kumar; Rajan Kumar Singh; Spandan Chaudhary; Naman Mangukia

doi:10.31557/APJCB.2026.11.4.1101

Authors

Nikkan Chakraborty Faculty of Applied Science, Parul University, Waghodia, Vadodara, Gujrat, 391760, India. Unipath Specialty laboratory Ltd. Ahmedabad, Gujarat, 380015, India.
Raja Kumar Faculty of Applied Science, Parul University, Waghodia, Vadodara, Gujrat, 391760, India. Unipath Specialty laboratory Ltd. Ahmedabad, Gujarat, 380015, India.
Rajan Kumar Singh Department of Biotechnology, Parul Institute of Technology, Faculty of Engineering and Technology, Parul University, Waghodia, Vadodara, Gujrat, 391760, India.
Spandan Chaudhary Unipath Specialty laboratory Ltd. Ahmedabad, Gujarat, 380015, India.
Naman Mangukia Unipath Specialty laboratory Ltd. Ahmedabad, Gujarat, 380015, India.

DOI:

https://doi.org/10.31557/APJCB.2026.11.4.1101

Keywords:

Whole transcriptome sequencing, Gene fusions, RNA sequencing, Fusion landscape, Tumor heterogeneity, Chimeric Transcripts, Ancillary fusion transcripts

Abstract

Background: Gene fusions are important oncogenic drivers and therapeutic biomarkers across multiple malignancies. While targeted RNA sequencing panels reliably detect established rearrangements, the broader landscape of ancillary fusion transcripts remains incompletely characterized. This exploratory study aimed to characterize ancillary fusion transcripts identified by whole transcriptome sequencing (WTS) in tumors harbouring known driver fusions.

Materials and Methods: WTS was performed on nine FFPE tumor samples with known ALK, RET, ROS1, or FGFR rearrangements. Fusion detection employed a consensus pipeline integrating STAR-Fusion, Arriba, and FusionCatcher, and high-confidence candidate fusions were prioritized using concordant junction and spanning read support.

Results: Thirty-one candidate ancillary fusion transcripts were identified, demonstrating substantial inter-sample heterogeneity. Several involved genes associated with mTOR, MAPK, and calcium signalling pathways, although their functional significance remains uncertain. Within this limited cohort, FGFR-rearranged tumors exhibited a relatively higher ancillary fusion burden; however, no statistical comparisons were performed.

Conclusion: WTS enabled exploratory characterization of transcriptomic fusion complexity beyond canonical driver events. Given the limited sample size, absence of orthogonal validation, and methodological differences between sequencing workflows, these findings should be considered hypothesisgenerating and require confirmation in larger independent cohorts.