ABNORMALITIES OF THE ETV6 GENE OCCUR IN THE MAJORITY OF PATIENTS WITHABERRATIONS OF THE SHORT ARM OF CHROMOSOME-12 - A COMBINED PCR AND SOUTHERN BLOTTING ANALYSIS

Involvement of the ETV6 gene, located at 12p13, has been investigated in 20 patients with an abnormality of the short arm of chromosome 12(a bn 12p) detected cytogenetically. Patients in the study had c/pre-B ac ute lymphoblastic leukemia (ALL) (nine children and three adults), T-A LL (three adults), acute myeloid leukemia (AML) (two adults), biphenot ypic acute leukemia (Bip-L) (one adult), myelodysplasia (MDS) (one adu lt) and chronic myelomonocytic leukemia (CMML) (one child). Abnormalit ies of 12p comprised deleted (del)(12p) alone (seven cases), add(12p) alone (seven cases), del(lap) and add(12p) (one case) and balanced tra nslocations of 12p to 1p13, 1q31, 10q11, 14q11 and 15q15 (one case of each). A novel, exon-specific RT-PCR assay identified breakpoints in E TV6 in nine of 19 cases, and showed breakpoints in intron 5 (seven cas es of children with c-ALL), in intron 4 (in one adult with Bip-L) and in intron 2 (in one adult with AML). RT-PCR for the ETV6/AMLI fusion ( tested in 19 cases) was positive using standard primers in five cases (four of which had shown rearrangements in intron 5) and occurred as a variant fusion in a sixth case (also positive for a rearrangement in intron 5) using 3' RACE PCR. Southern blotting confirmed rearrangement s in intron 5 in the five cases available for analysis and revealed a rearrangement in intron 5 in one of 10 cases with no evidence of intro n 5 involvement by RT-PCR. Rearrangements in intron 5 of ETV6 were fou nd in eight of nine cases of children with c-ALL of which six carried the ETV6/AMLI fusion. Heterozygosity within intron 5 (revealed by the genomic probe Bl)was found in seven of 11 cases tested. Deletion of on e allele was indicated in three cases with del(12p) and one case with add(12p). This study, using a combination of ETV6 exon-specific RT-PCR , RI-PCR for ETV6/AMLI and Southern blotting has shown that rearrangem ent and/or deletion of ETV6 may occur in up to 70% of patients with ab n 12p. Furthermore, 90% of children in this study with an abn 12p and c-ALL, carried a rearrangement of ETV6 in intron 5.