The goal of this project is to contribute to the determination of the accurate sequence of human chromosome 12. Towards this goal, we entered into a collaboration with the Baylor College of Medicine (BCM) Genome Center. We propose to generate a sequence ready map of chromosome 12 in the form of P1 artificial chromosome (PAC) and bacterial artificial chromosome (BAC) maps. During the first year of the proposed grant, we propose to construct a map for 20 Mbp of chromosome 12, implement a bioinformatics strategy and put in place a number of high throughput systems to reach a production level mapping. During years two and three, we propose to construct maps for 100 Mbp of chromosome 12 and provide them to the BCM Genome Center. Based on this throughput, the sequence ready maps of chromosome 12 will be completed by December 31, 2000 and the sequence will be completed shortly thereafter. The general approach to construct the maps is as follows. We will use the 100 Kbp resolution physical map of human chromosome 12 in the form of a YAC contig map that we constructed as the framework map. PCR products from ten to twelve consecutive non-polymorphic markers will be used to screen a 20X genomic PAC/BAC library. False positive will be eliminated by a PCR based screening assay and the clones will be assembled into contigs by STS-content. Marker density will be increased by sequencing ends of clones by a direct sequencing method we developed and developing new STSs. Gaps will be filled by screening libraries with end clones. Clones that can constitute minimal tiling paths will be identified by fingerprinting methods. All of the data and the minimal tiling path of clones will be electronically transmitted to the BCM Genome Center and made publicly available through a web site. A team of six mappers assisted by an Informatics team will produce 20 Mbp of maps during the first year. We will implement automated methods for several steps in the procedure and, during the second and third years, we propose to increase the throughput by 2X with only the addition of two FTEs to the overall team. During years 2 and 3, the cost of producing the maps is estimated to be no more than $.025/nucleotide.
| Lee, S G; Cho, K A; Choi, Y H et al. (2000) A sequence-ready map for human chromosome 12q15-21. DNA Seq 11:353-61 |
| Roda-Navarro, P; Arce, I; Renedo, M et al. (2000) Human KLRF1, a novel member of the killer cell lectin-like receptor gene family: molecular characterization, genomic structure, physical mapping to the NK gene complex and expression analysis. Eur J Immunol 30:568-76 |
