Overview of treatments and PacBio results for patient 6. A)BCR-ABL1 IS% values measured by routine quantitative RT-PCR are shown in open circles. The sensitivity of this assay was measured for the BGUS reference gene and depicted by gray squares. The samples that were analyzed by PacBio sequencing are indicated by black arrows. The vertical line indicates the treatment period. B) This panel shows BCR-ABL1 isoforms in patient 6. At 7 months post diagnosis four different splice isoforms were identified. The most common isoform was the ‘wild type’ (WT) BCR-ABL1 transcript isoform, i.e. identical to the reference sequence used for mapping, present in 80% of the molecules. Two other isoforms contained insertions of entire exons, of lengths 35 bp and 154 bp, respectively and one contained a partial deletion of exon 7 of ABL1. At 13 months post diagnosis the WT isoform was present in 54% of the molecules whereas isoforms containing the 35 bp insertion between exon 8 and 9 in ABL1 was present in the other two isoforms.