The identification of the molecular events that underlie the development of human tumors is a major challenge in the design of improved strategies in the prevention, management and cure of these diseases. High resolution cytogenetic studies to map recurrent chromosome abnormalities are expected to expedite the identification of protooncogenes or tumor suppressor genes involved in cancer development. These studies will be greatly facilitated by an ordered array of mapped BACs that cover the human genome at high density. Jointly with Dr. Heinz-Ulrich Weier at E.O. Lawrence Berkeley National Laboratory, we propose to develop a high resolution BAC map coupled with an arrayed BAC resource that covers the whole human genome intervals of 1 Mb or less. For this purpose, 6,000-8,000 BACs will be isolated by using mapped markers and screening the NHGRI-DOE approved Caltech BAC library D, which was constructed from human sperm samples. High resolution physical maps already available for several chromosomes and an emerging genome wide BAC map based on more than 20,000 mapped Unigene probes will provide rich sources from which ideally spaced markers and BACs will be selected. Initially, we will perform high throughput BAC library screening with sets of precisely mapped markers from chromosomes for which high resolution maps are available. In collaboration with TIGR and the Los Alamos National Laboratory, we have constructed a BAC based physical map for most of chromosome 16, so that at we will be able to immediately select optimally spaced library D clones for this chromosome. To cover chromosomes for which high resolution maps are not yet available, we will select BACs from our BAC-EST map available at the beginning of the proposed research. Prior to distribution, we will perform clone validation by sizing and fingerprinting. We estimate that up to 1,000 BACs selected in this process will not by associated with precisely mapped STSs or ESTs, or belong to regions that are difficult to map such as heterochromatic regions and satellite DNA. We will employ high resolution FISH analysis using DNA and chromatic fibers to determine the order and distance of such BAC clones and to devise strategies to fill lager gaps in the map.
