The pipeline proposed was tested on a cell line (K562) and on 16 multiplexed specimens (14 clinical samples and two control analytes) for the identification of BCR-ABL1, PML-RARA, CBFB-MYH11, KMT2A-MLLT3, PAX5-AUTS2 and other gene fusions involved in solid tumors such as sarcomas or lung cancers. Here, AUTS2 is linked to lung carcinoma.