Methods for partner agnostic gene fusion detection

A system for detecting a gene fusion, comprising:

• a machine-readable memory;
• and
• a processor in communication with the memory, wherein the processor is configured to execute machine-readable instructions, which, when executed by the processor, cause the system to perform a method, comprising:
• receiving, at the processor, a plurality of nucleic acid sequence reads for a plurality of amplicons produced by amplification of a nucleic acid sample a presence of a primer pool, the primer pool including primers targeting a plurality of exon-exon junctions of a driver gene, wherein the amplicons correspond to the exon-exon junctions;
• aligning the reads to a reference sequence, the reference sequence including nucleic acid sequences of the amplicons corresponding to the targeted exon-exon junctions of the driver gene;
• determining a number of reads for each amplicon corresponding to each targeted exon-exon junction;
• dividing the number of reads for each amplicon by a maximum number of reads among the amplicons of the driver gene to give a normalized read count for each amplicon;
• applying a baseline correction to the normalized read counts for the amplicons to form corrected read counts, wherein the baseline correction uses baseline values based on read counts for amplicons of a plurality of normal samples;
• determining an imbalance between the corrected read counts for the amplicons corresponding to a 5′ end of the driver gene and the corrected read counts for the amplicons corresponding to a 3′end of the driver gene;
• and
• detecting the gene fusion in the driver gene based on the imbalance.