A sequence-ready map for human chromosome 12q15-21

Construction of sequence-ready clone map is an essential step toward sequen cing the human genome. We chose a region that is frequently amplified in Li posarcoma between D12S350 and D12S106 in chromosome 12q15-21 to build a PAC /BAG clone contig map. This region was spanned by 4 YACs and contained 30 S TS on the YAC and radiation hybrid (RH) framework maps, providing an averag e STS spacing of 160 kb if each YAC is approximately 1.2 Mb in size. To con vert a STS-based YAC map to a STS-based contig map of bacterial clones, 22 non-polymorphic STS markers were used as probes to screen the high density gridded arrays of PAC and BAC clones by filter hybridizations, followed by assembly of clones into contigs by marker content. Contigs have been extend ed and joined by direct end sequencing of appropriate clones, generating ne w STSs and rescreening the library as necessary. Using these approaches, we have constructed 5 contigs covering the region with the largest single con tig being 1.4 Mb and a final size estimation of 3.6 Mb. The map is comprise d of 17 YACs, 187 PACs, 160 BACs, and 17 cosmids; onto this, 6 polymorphic, 97 non-polymorphic, 24 ESTs, and 4 gene-based markers are now placed in a unique order, providing an average resolution of similar to 28 kb. Of a tot al of 131 markers, 97 were developed in the present study. The sequence-rea dy map should provide a framework to generate complete DNA sequence and ult imately gene map of this segment of chromosome 12.