PMC5859504_01
G-banding, molecular, and FISH analyses. a Partial karyotype showing the der(7) t(7;13)(p14;q12) and der(13)t(7;13)(p14;q12) together with the corresponding normal chromosome homologs. Breakpoint positions are indicated by arrows. b Gel electrophoresis showing the amplified cDNA fragments. c Partial sequence chromatogram of the amplified cDNA fragment showing the junction point of exon 6 of the PAN3 gene with exon 2 of PSMA2. d Deduced amino acid sequence of the PAN3-PSMA2 fusion transcript. The out-of-frame sequence from PSMA2 is in bold. The asterisk indicates the TAG termination codon. e Ideogram of chromosome 7 showing the mapping position of the PSMA2 gene (vertical red line). f Diagram showing the FISH probe for PSMA2. Additional genes in this region are also shown. g Ideogram of chromosome 13 showing the mapping position of the PAN3 gene (vertical green line). h Diagram showing the FISH probe for PAN3. Additional genes in this region are also shown. i FISH on interphase nucleus showing a red PSMA2 signal, a green PAN3 signal, and two yellow fusion signals
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PMC5859504_01_40164_2018_99_Fig1_HTML.jpg
Fig1
G-banding analysis of the bone marrow cells at diagnosis of MDS-EB2 yielded a karyotype with a single clonal abnormality: 46,XX,t(7;13)(p14;q12)[2]/46,XX[23] (Fig. 1a). PCR with the primer combinations PAN3-957F1/PSMA2-206R1 and PAN3-1005F1/PSMA2-168R1 amplified 337 and 250 bp long cDNA fragments, respectively (Fig. 1b). Direct sequencing of the PCR products verified the presence of PAN3-PSMA2 (Fig. 1c). The fusion point was identical to that found by analysis of RNA sequencing data using FusionCatcher software (Fig. 1c). In the PAN3-PSMA2 transcript, exon 6 of PAN3 (nt 1152 in sequence with accession number NM_175854 version 7) was fused out-of-frame to exon 2 of PSMA2 (nt 90 in NM_002787 version 4) (Fig. 1c, d). No cDNA amplified product was obtained when PSMA2 forward and PAN3 reverse primers (primer set PSMA2-21F1/PAN3-1241R1) were used, suggesting that the PSMA2-PAN3 fusion transcript was absent or not expressed (Fig. 1b). Both normal PAN3 (primer set PAN3-957F1/PAN3-1241R1) and PSMA2 (primer set PSMA2-21F1/PSMA2-206R1) cDNA fragments were amplified from the cDNAs of the patient suggesting that both genes are expressed in the bone marrow (Fig. 1b).