The goal of Project 2 is to develop a high resolution sequence tagged site (STS) content based map of chromosome 12. We propose a program to build this map in close association with Dr. Daniel Cohen and his colleagues at CEPH in Paris who are developing a low resolution physical map for the entire human genome. We will obtain a chromosome 12 specific sublibrary of the large insert yeast artificial chromosome (YAC) libraries recently constructed in Paris. In addition, Dr. Cohen will provide us with information about those YACs in the chromosome 12 sublibrary which have been assembled into contigs by the fingerprinting methods they employ. We will ascertain the size of the individual YACs in these contigs generate end-specific sequences from each of the YACs. All end sequences which are determined to be derived from chromosome 12 will be sequenced, at least in part, to generate STSs. Each of the YACs within the contig will be screened for the presence or absence of each STSs. The binary information obtained will be used to construct an STS- content based map. We propose to utilize homologous recombination methods to construct an extremely high resolution map in which the precise order and distance between STSs will be deduced. We propose a combination of methods to identify gaps and to fill them to complete the physical map of chromosome 12. In addition to the YAC-end specific STS, we will use all of the genetic markers that have been utilized and that are being developed by several groups in constructing the chromosome 12 physical map. This procedure enables us to integrate the genetic maps being constructed elsewhere with the physical maps we will construct. The genetic distances between pairs of markers can be compared with precise physical distances that we will obtain to identify regions of high or low recombination. To fill in the gaps in the genetic map, we propose a directed effort to isolate microsatellite-containing sequences from specific YACs and use them to type the CEPH pedigrees. Our physical mapping effort will complement and build upon the global efforts at CEPH and other institutions and could provide a new paradigm for constructing high resolution maps of individual human chromosomes.
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