Characterization of a highly complex region in Xq13 and mapping of three isodicentric breakpoints associated with preleukemia

The chromosomal abnormality represented by an isodicentric X chromosome [id ic(X)(q13)] is associated with a subset of acute myeloid leukemia (ARIL) an d preleukemia observed in elderly females. A previous study localized the b reakpoints of two acquired isodicentric X chromosomes associated with myelo dysplasia to a 450-kb region proximal to the XIST gene. Here we report the construction and extensive characterization of a reliable 1-Mb P1 artificia l chromosome and bacterial artificial chromosome contig covering a highly p roblematic region in Xq13 that includes the previously described isodicentr ic breakpoint region. In addition to mapping of the brain-specific gene (NA P1L2) and the phosphoglyceryl kinase alpha subunit 1 gene (PHKA1) and gener ation and mapping of a large number of STSs throughout the contig, we have mapped a putative transcriptional regulatory protein (HDACL1), and 35 ESTs. Sequencing data, Southern blot analysis, and fiber-FISH analysis have perm itted characterization of extensive region-specific duplications and tripli cations in addition to an unusually high concentration of long interspersed repeat elements, both of which could be implicated in isodicentric chromos ome formation and other Xq13 chromosome aberrations. FISH analysis of metap hase chromosomes from two previously unpublished AML patients and one prele ukemic patient using cosmid clones and selected subclones allowed mapping o f the idic(X)(q13) breakpoints to a 100-kb interval, consistent with the in volvement of an X-linked gene in the genesis of this form of preleukemia, d isruption of which may represent a preliminary step in progression to AML. Assembly and physical mapping of this complex 1-Mb contig establish a found ation for ongoing sequencing and gene identification projects in the region . (C) 2000 Academic Press.