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Leukemic cells often carry chromosome aberrations which generate chimeric genes of pathogenetic, diagnostic, and prognostic importance. New rearrangements giving rise to novel fusion genes define hitherto unrecognized genetic leukemia subgroups. G-banding, fluorescence in situ hybridization (FISH), and molecular genetic analyses were done on bone marrow cells from a patient with chronic lymphocytic leukemia (CLL) and secondary myelodysplasia. The G-banding analysis revealed the karyotype 46,XX,del(21)(q22)[9]/46,XX[2]. FISH on metaphase spreads with a  RUNX1  break apart probe demonstrated that part of  RUNX1  (from 21q22) had moved to chromosome band 5p15. RNA sequencing showed in-frame fusion of  RUNX1  with  PDCD6  (from 5p15), something that was verified by RT-PCR together with Sanger sequencing. Further FISH analyses with  PDCD6  and  RUNX1  home-made break apart/double fusion probes showed a red signal ( PDCD6 ) on chromosome 5, a green signal on chromosome 21 ( RUNX1 ), and two yellow fusion signals, one on der(5) and the other on der(21). Reassessment of the G-banding preparations in light of the FISH and RNA-sequencing data thus yielded the karyotype 46,XX,t(5;21)(p15;q22)[9]/46,XX[2]. The t(5;21)(p15;q22)/ RUNX1-PDCD6  was detected only by performing molecular studies of the leukemic cells, but should be sought after also in other leukemic/myelodysplastic cases with del(21q).

plos one

RUNX1-PDCD6 fusion resulting from a novel t(5;21)(p15;q22) chromosome translocation in myelodysplastic syndrome secondary to chronic lymphocytic leukemia