Figure 5.
Figure 5. Ph translocation–associated fusions and rearrangement. Chromosomes 9q (A) and 22q (B) are shown along with the location of genes involved in the fusions. Pink arrows indicate transcription from the plus strand and blue arrows from the minus strand. Green bars indicate the relative location of deletions detected in 4 patients: patients 4, 8, 11, and 26. These align with the fusion partners in some cases. Sequence inversions brought some genes into the same transcriptional orientation. Fusion partners were located upstream and downstream of ABL1 and BCR, indicating the complex nature of the rearrangements. Fusion partners were also located on other chromosomes in 3 patients with variant Ph translocations. Listed are fusion transcripts and the genomic fusions where no corresponding fusion transcript was identified. Superscripts indicate the patient number. Two fusions involved intragenic sequence inversions: BCR sequence inversion (NUP214-BCR) and GGT1 sequence inversion (URM1-GGT1). Some fusions involving an intergenic sequence also contained an inverted sequence. (C) RNA-Seq aligned sequencing reads that mapped to the ABL1 gene for a representative patient at diagnosis (patient 3) viewed in the Integrative Genomics Viewer. Reads are colored by first-of-pair strand. A large number of reads were evident in intronic regions because the protocol sequenced total RNA, including intron-retaining primary RNA transcripts. ABL1 is transcribed on the plus strand, and reads are colored pink. (D) Patient 8 had a large ∼93-Kb inversion within ABL1 intron 1, as indicated by the reads colored blue, which specify antisense transcription. A genomic break was evident at the distal end of the antisense transcripts, which was an ABL1-BCR genomic fusion inversion. The BCR-ABL1 genomic breakpoint was located 224 bp upstream in the correct transcriptional orientation. The patient also had a 13-Mb deletion between BCR and the MYH9 gene on chromosome 22 (shown in panel B), plus an inversion that brought MYH9 into the same transcriptional orientation as BCR and generated an MYH9-BCR fusion transcript.

Ph translocation–associated fusions and rearrangement. Chromosomes 9q (A) and 22q (B) are shown along with the location of genes involved in the fusions. Pink arrows indicate transcription from the plus strand and blue arrows from the minus strand. Green bars indicate the relative location of deletions detected in 4 patients: patients 4, 8, 11, and 26. These align with the fusion partners in some cases. Sequence inversions brought some genes into the same transcriptional orientation. Fusion partners were located upstream and downstream of ABL1 and BCR, indicating the complex nature of the rearrangements. Fusion partners were also located on other chromosomes in 3 patients with variant Ph translocations. Listed are fusion transcripts and the genomic fusions where no corresponding fusion transcript was identified. Superscripts indicate the patient number. Two fusions involved intragenic sequence inversions: BCR sequence inversion (NUP214-BCR) and GGT1 sequence inversion (URM1-GGT1). Some fusions involving an intergenic sequence also contained an inverted sequence. (C) RNA-Seq aligned sequencing reads that mapped to the ABL1 gene for a representative patient at diagnosis (patient 3) viewed in the Integrative Genomics Viewer. Reads are colored by first-of-pair strand. A large number of reads were evident in intronic regions because the protocol sequenced total RNA, including intron-retaining primary RNA transcripts. ABL1 is transcribed on the plus strand, and reads are colored pink. (D) Patient 8 had a large ∼93-Kb inversion within ABL1 intron 1, as indicated by the reads colored blue, which specify antisense transcription. A genomic break was evident at the distal end of the antisense transcripts, which was an ABL1-BCR genomic fusion inversion. The BCR-ABL1 genomic breakpoint was located 224 bp upstream in the correct transcriptional orientation. The patient also had a 13-Mb deletion between BCR and the MYH9 gene on chromosome 22 (shown in panel B), plus an inversion that brought MYH9 into the same transcriptional orientation as BCR and generated an MYH9-BCR fusion transcript.

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