Fully integrated SNV, fusion, and isoform analysis of cancer drivers with FLAIR3 for improved functional interpretation

FLAIR3 integrates long-read RNA-seq to phase SNVs, fusions, and isoforms, capturing full-length molecules and revealing fusion splicing in osteosarcoma driver genes like TP53.

• Why it matters: Variant effects and transcript regulation are often analyzed separately, but their interaction is key for interpreting oncogenic drivers.
• What they did: The method was applied to lrRNA-seq datasets from osteosarcoma and lung adenocarcinoma, using integrated SNV/indel, fusion, and alternative splicing analysis with amino-acid impact prediction.
• The result: In osteosarcoma, it identified alternative splicing of gene fusions in known driver genes, and in lung adenocarcinoma it showed isoform-biased expression of oncogenic SNVs including BRAF, CDKN2A, and TP53.

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