We propose to develop a comprehensive physical map for human chromosome 3 consisting of YAC contigs and molecular probes ordered by pulsed field gel (PFG) electrophoresis. This competing renewal represents the fusion of two independent R01s, and reflects a long-standing and extremely productive corroboration between the laboratories. Our initial studies have resulted in the isolation of over 500 probes from NotI and random libraries, their localization using an extensive somatic cell hybrid mapping panel containing many of the known chromosome 3 specific rearrangements associated with malignant and developmental disorders, and the development of PFG maps for several regions of the chromosome. We have developed a rapid and economical method for screening YAC libraries which greatly facilitates the isolation of those YACs which correspond to regionally localized probes. Additional compartmentalization is provided by a set of single and two-fragment radiation reduction hybrids that will permit high resolution regional mapping to the 5-Mb level. A subset of highly polymorphic (CA)n containing probes, defining sequence-tagged sites (STS), will also be integrated into the developing physical map and contigs. Our experience with the construction of long range restriction maps using pulsed field gel electrophoresis, together with more recent experience isolating YAC clones, has led us to an important conclusion. While neither PFG maps or YAC contigs alone are sufficient to generate a comprehensive physical map necessary for completion of the first phase of the Genome Initiative, the combination of the two approaches is extremely powerful and can rapidly lead to completion. These studies will also provide the materials for the rapid isolation of disease gents encoded on this chromosome, and will facilitate our understanding of the relationship between structure and function of the human genome.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG000358-05
Application #
3333511
Study Section
Genome Study Section (GNM)
Project Start
1989-07-01
Project End
1994-08-31
Budget Start
1992-09-30
Budget End
1993-08-31
Support Year
5
Fiscal Year
1992
Total Cost
Indirect Cost
Name
University of Colorado Denver
Department
Type
Schools of Medicine
DUNS #
065391526
City
Aurora
State
CO
Country
United States
Zip Code
80045
Korch, C; Drabkin, H (1999) Improved DNA sequencing accuracy and detection of heterozygous alleles using manganese citrate and different fluorescent dye terminators. Genome Res 9:588-95
Korch, C; Drabkin, H (1999) Manganese citrate improves base-calling accuracy in DNA sequencing reactions using rhodamine-based fluorescent dye-terminators. Nucleic Acids Res 27:1405-7
David, G; Abbas, N; Stevanin, G et al. (1997) Cloning of the SCA7 gene reveals a highly unstable CAG repeat expansion. Nat Genet 17:65-70
Piemontese, M R; Memeo, E; Carella, M et al. (1997) A YAC contig spanning the blepharophimosis-ptosis-epicanthus inversus syndrome and propionic acidemia loci. Eur J Hum Genet 5:171-4
Boldog, F; Gemmill, R M; West, J et al. (1997) Chromosome 3p14 homozygous deletions and sequence analysis of FRA3B. Hum Mol Genet 6:193-203
David, G; Giunti, P; Abbas, N et al. (1996) The gene for autosomal dominant cerebellar ataxia type II is located in a 5-cM region in 3p12-p13: genetic and physical mapping of the SCA7 locus. Am J Hum Genet 59:1328-36
Song, W J; Van Keuren, M L; Drabkin, H A et al. (1996) Assignment of the human slow twitch skeletal muscle/cardiac troponin C gene (TNNC1) to human chromosome 3p21.3-->3p14.3 using somatic cell hybrids. Cytogenet Cell Genet 75:36-7
Cotter, P D; Drabkin, H A; Varkony, T et al. (1995) Assignment of the human housekeeping delta-aminolevulinate synthase gene (ALAS1) to chromosome band 3p21.1 by PCR analysis of somatic cell hybrids. Cytogenet Cell Genet 69:207-8
van den Berg, A; van der Veen, A Y; Hulsbeek, M M et al. (1995) Defining the position of the breakpoint of the constitutional t(3;6) occurring in a family with renal cell carcinoma. Genes Chromosomes Cancer 12:224-8
Roche, J; Whisenant, E; Boldog, F et al. (1994) Dinucleotide repeats flanking the renal carcinoma breakpoint at 3p14.2. Hum Mol Genet 3:215

Showing the most recent 10 out of 18 publications