Abstract

A major goal of the human genome project is the generation of a two to five centimorgan linkage map of the entire genome. To this end, a first step is the establishment of an index map of highly polymorphic markers 10-15 centimorgans-apart. Currently, over 2000 markers have been identified, but only a relatively small fraction are highly informative when analyzed by conventional techniques (RFLP analysis).
The aim of this proposal is to utilize powerful new techniques to identify highly informative polymorphisms in existing markers, especially in short PCR-amplified DNA fragments termed sequence tagged sites (STSs) and in gene sequences. We will utilize two approaches to identify polymorphisms within STSs, GC-clamped denaturing gradient gel electrophoresis (DGGE)and single stranded conformational gel electrophoresis (SSCG). In addition, we will utilize two variations of denaturing gradient gel electrophoresis to identify polymorphisms which lie in close proximity to STSs, thus increasing the probability of identifying highly informative polymorphisms in a given region. Furthermore, we will use GC-clamped DGGE and SSCG to identify sequence polymorphisms within specific Alu sequences. Initially our efforts will concentrate on chromosomes 1, 4 and 21 with the plan to expand this project to include regions of other chromosomes which show a paucity of RFLPS. A particular effort will be made to make all polymorphisms identified in this study easily usable by and accessible to other laboratories. In addition, our utilization of several approaches for identifying single base polymorphisms will allow us to evaluate the utility, efficacy, reproducibility and comprehensiveness of the various approaches. This should prove useful to other investigators seeking to identify additional polymorphisms working towards the goal of a more comprehensive linkage map. In the second year of this project we will make a concerted effort to analyze about 100 STSs solicited from other laboratories, concentrating on gaps in the genome lacking highly informative polymorphisms.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG000457-02
Application #
3333635
Study Section
Genome Study Section (GNM)
Project Start
1991-09-30
Project End
1994-08-31
Budget Start
1992-09-30
Budget End
1993-08-31
Support Year
2
Fiscal Year
1992
Total Cost
Indirect Cost

  Institution

Name
University of Iowa
Department
Type
Schools of Medicine
DUNS #
041294109
City
Iowa City
State
IA
Country
United States
Zip Code
52242

  Publications

Green, Glenn E; Scott, Daryl A; McDonald, Joshua M et al. (2002) Performance of cochlear implant recipients with GJB2-related deafness. Am J Med Genet 109:167-70
Campbell, C; Cucci, R A; Prasad, S et al. (2001) Pendred syndrome, DFNB4, and PDS/SLC26A4 identification of eight novel mutations and possible genotype-phenotype correlations. Hum Mutat 17:403-11
Scott, D A; Drury, S; Sundstrom, R A et al. (2000) Refining the DFNB7-DFNB11 deafness locus using intragenic polymorphisms in a novel gene, TMEM2. Gene 246:265-74
Green, G E; Scott, D A; McDonald, J M et al. (1999) Carrier rates in the midwestern United States for GJB2 mutations causing inherited deafness. JAMA 281:2211-6
Scott, D A; Wang, R; Kreman, T M et al. (1999) The Pendred syndrome gene encodes a chloride-iodide transport protein. Nat Genet 21:440-3
Brennan, T M; Landau, D; Shalev, H et al. (1998) Linkage of infantile Bartter syndrome with sensorineural deafness to chromosome 1p. Am J Hum Genet 62:355-61
Parvari, R; Hershkovitz, E; Kanis, A et al. (1998) Homozygosity and linkage-disequilibrium mapping of the syndrome of congenital hypoparathyroidism, growth and mental retardation, and dysmorphism to a 1-cM interval on chromosome 1q42-43. Am J Hum Genet 63:163-9
Scott, D A; Kraft, M L; Carmi, R et al. (1998) Identification of mutations in the connexin 26 gene that cause autosomal recessive nonsyndromic hearing loss. Hum Mutat 11:387-94
Heaney, C; Shalev, H; Elbedour, K et al. (1998) Human autosomal recessive osteopetrosis maps to 11q13, a position predicted by comparative mapping of the murine osteosclerosis (oc) mutation. Hum Mol Genet 7:1407-10
Haider, N B; Carmi, R; Shalev, H et al. (1998) A Bedouin kindred with infantile nephronophthisis demonstrates linkage to chromosome 9 by homozygosity mapping. Am J Hum Genet 63:1404-10

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