FISH experiments and molecular characterization of fusion transcripts.

(Ai) FISH with probe D11Z1 (red) for the alpha satellite of centromere 11 and a mixture of BAC 118H17 and BAC 290A12 (green), to encompass theNUP98 gene at 11p15. Red signals are present on normal 11 and der(11), and green signals are present on normal 11, der(11) (arrow), and der(8) (arrowhead). (Aii) FISH with probe D8Z1 (red) for the alpha satellite of centromere 8 and BAC 350N15 (green), to encompass the FGFR1 and NSD3 genes at 8p11.2. Red signals are present on normal 8 and on der(8), and green signals are present on normal 8, der(8) (arrowhead), and der(11) (arrow). (Bi) Nested PCR detects NUP98-NSD3 short fusion transcripts. After primary amplification with primers NUP737F-FLJ3081Cr, diluted aliquots of PCR products were amplified with the following primers: lanes 1-2, NUP737F-FLJ2907Br (2477 base pair [bp]); lanes 3-4, NUP737F-FLJ1747Er (1317 bp); lanes 5-6, NUP1252F-FLJ3081Cr (2136 bp); lanes 7-8, NUP1252F- FLJ2907Br (1962 bp); lanes 9-10, NUP1252F- FLJ1747Er (802 bp). Lane M, molecular weight markers (lambda DNA digested with HindIII). Negative controls without cDNA are marked as (−). (Bii) Nucleotide and deduced amino acid sequences ofNUP98 and NSD3 cDNA at the fusion point. Sequence numbers refer to GenBank accession no. U41815 for NUP98 andAF332469 for NSD3.