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Introduction to the Workshop
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Abstracts

Mapping

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The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Marker development for the EPM1 region of human chromosome 21, q22.3.

J.A. Warrington[1], K. O'Connor[1], S. Hebert[1], M. Harris[1], R. Goold[1], A.E. Lehesjoki[2], A. de la Chapelle[2], N. Stone[1], R. Myers[1] and D.R. Cox[1].
[1]Stanford University, Stanford, CA., [2]University of Helsinki, Finland.

New STSs have been developed for a 0.9 Mb region of chromosome 21 that is not represented in existing YAC libraries using an efficient method that is generally applicable to any region of the genome. The region, 21q22.3 is of particular interest because the gene for progressive myoclonic epilepsy of the Unverricht-Lundborg type (EPM1) maps to this region. Until recently there were only three probes for the 1.3 Mb surrounding the EPM1 gene (D21S141, LJ112, LB2T). This very limited number of probes is problematic for obtaining clone coverage and for confirming map position of newly developed markers in the EPM1 region. To develop new markers, a somatic cell hybrid containing chromosome 21 as its only human complement (GMO8854) was digested with NOT 1 and hybridized with D21S141. The fragment hybridizing with D21S141 was excised, amplified by Alu PCR and the amplification products were cloned and sequenced. Of the fifteen clones sequenced, four were duplicates and one consisted entirely of repeat sequence. STSs were developed for the remaining ten unique clones. To determine the map position of the new STSs, quantitative PCR was used in conjunction with whole genome radiation hybrid mapping. Quantitative PCR confirmed that the STSs mapped to appropriate sized PFGE fragments and whole genome RH mapping showed that the markers were linked and gave order and distance information. Three of the new STSs are in the EPM1 region, providing additional starting points for obtaining clone coverage and gene isolation. This combination of techniques for developing markers and confirming map position is an effective approach for obtaining probes and has general applicability for regions of the genome not represented in YAC or cosmid libraries.

Not funded by DOE.