Pui-Yan Kwok, Qiang Deng, Hamideh Zakeri, Scott L. Taylor, and Deborah A. Nickerson,
Division of Dermatology, Washington University School of Medicine, St.Louis, MO 63110.
Numerous groups are engaged in the physical mapping of the human genome by constructing STS-content maps. STS mapping has been the dominant method by which large, well validated clone-based maps have been constructed. More than 30,000 STSs, with the average spacing of 100 kb, will be available when STS-content maps of the human genome are completed. It is interesting to note that although thousands of well characterized and physically mapped STSs are available already, no attempts to screen these STSs for DNA variations have been reported to date. Given the fact that these STSs represent hundreds of kilobase-pairs (kb) of unique human DNA sequence, and the estimate that DNA sequence variations such as single base-pair substitutions are found approximately every 1 to 2 kb, hundreds of new diallelic markers can be developed from these mapped STSs with minimal additional effort.
By screening 154 of the STSs published by the Whitehead Institute/MIT Genome Center, we have identified 45 new DNA sequence polymorphisms among the 37.2 kb of unique DNA sequence contained in these STSs, or one polymorphism every 827 bp. Forty of these variations are substitution polymorphisms (1 every 930 bp scanned) while the remaining five sequence variations are unique insertion/deletion polymorphisms (1 in 7.5 kb scanned). Using a sequence-based approach to estimate allele frequencies for these variations, 27 of the substitution polymorphisms (one in every 1.4 kb of sequence scanned) were found to have heterozygosities exceeding 32%.
Use of STS markers on the genetic map were crucial to the construction of the first generation physical maps. However, our study demonstrates that with limited investment, the genetic map can be further enhanced by developing markers from STSs on the physical map. For example, the goal of current physical mapping efforts is aimed at developing STSs ordered along a chromosome at 100 kb intervals. Assuming that 1 out of every 4 STSs are >250 bp in size, or 1 such STS every 400 kb (4 X 100 kb spacing), and that a polymorphism is identified in every 5 STSs >250 bp in size, suggesting that 1 in every 20 STSs on the physical map would be polymorphic. Thus, minimal scanning efforts on longer STSs would yield one new genetic marker every 2 Mb on the rapidly emerging physical maps of human chromosomes and would produce more than 1,500 new diallelic markers suitable for high throughput genotyping of human populations for linkage disequilibrium or allelic association studies.
* Supported by a grant from the U.S. Department of Energy under contract DE-FG0694FR-619090
 Department of Molecular Biotechnology, University of Washington School of Medicine, Seattle, WA 98195
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