Identification of a BAC clone overlapping the t(6p12.3) breakpoint in the cell line ESS-1 derived from an endometrial stromal sarcoma

A major subgroup of endometrial stromal sarcomas (ESS) is characterized by translocations involving chromosome 6 with consistent breakpoints at 6p11 approximately p21. As part of an ongoing positional cloning effort to identify the genes affected by these translocations, this article reports on the delineation of the 6p breakpoint in the cell line ESS-1 derived from an ESS. The G- and 4',6-diamidino-2-phenylindole-banded karyotypes showed an unbalanced translocation described originally as der(3)t(3;6) (q29;p21.1). Fluorescence in situ hybridization using probes derived from contigous yeast artificial chromosome, bacterial artificial chromosome (BAC), and P1-derived artificial chromosome clones specific to 6p12.3 approximately p21.1 located the breakpoint at 6p to the BAC clone RP11-337K13 mapping to 6p12.3. The DNA sequence of the breakpoint region contained in RP11-337K13 will serve as a candidate locus for further molecular genetic analyses to isolate the gene(s) altered in ESS with 6p rearrangement.