A New Approach of Detecting ALK Fusion Oncogenes by RNA Sequencing Exon Coverage Analysis

Area of Science:

• Oncology
• Genomics
• Bioinformatics

Background:

• Traditional methods for detecting anaplastic lymphoma kinase (ALK) gene rearrangements include IHC, FISH, and RT-qPCR.
• Whole transcriptome sequencing (WTS, RNAseq) offers broad analysis but faces analytical and bioinformatic challenges.
• Existing RNAseq fusion detection methods are limited by low sensitivity due to insufficient chimeric reads.

Purpose of the Study:

• To evaluate the accuracy of ALK fusion detection using RNAseq exon coverage analysis.
• To investigate the asymmetry in RNAseq exon coverage of ALK gene partners.
• To explore RNAseq as a sensitive method for identifying ALK rearrangements.

Main Methods:

• Analyzed 906 human cancer biosamples using experimental RNAseq data.
• Focused on 50 samples: 13 with predicted ALK fusions and 37 without.
• Utilized targeted sequencing with TruSight RNA Fusion and OncoFu Elite panels for validation.

Main Results:

• Achieved 96% overall accuracy in confirming ALK fusions (11 out of 13 predicted cases).
• Demonstrated 100% sensitivity and 94.9% specificity.
• Identified low coverage depth and antisense transcripts as factors affecting accuracy, suggesting algorithmic solutions.

Conclusions:

• RNAseq exon coverage analysis is a viable and effective method for detecting ALK rearrangements.
• This approach holds potential for improving diagnostic accuracy in oncology.
• The study highlights the utility of RNAseq beyond targeted gene panels.