FISH analysis of UPN2 at presentation, using the LSI TEL/AML1 ES Dual-Color translocation probe (Vysis) and CDKN2A probe. The red signal represents the RUNX1 probe; green, the ETV6 probe; yellow, the ETV6-RUNX1 fusion gene; and purple, the CDKN2A probe. This image represents 2 different leukemic cells at presentation. The cell in the right bottom corner represents the dominant leukemic clone (according to the SNP array data analysis), with duplicated fusion gene, loss of wild-type ETV6, 2 copies of CDKN2A, 1 normal RUNX1, and 1 ES (72% of total cells analyzed). In the left top corner FISH analysis identified a leukemic cell with a constellation of signals corresponding to the dominant relapse clone, that is, a duplicated fusion gene, loss of wild-type ETV6, 1 normal RUNX1, 1 ES, and complete loss of CDKN2A (0.4% of total cells analyzed). In control experiments with normal blood lymphocytes from 5 donors, using the same probe combination, this CNA pattern was not observed in any cells (< 0.2%).