Progress, and Applications
of the Human Genome Project
Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Human Genome News, April-June 1996; 7(6)
Santa Fe '96
BAC clones are showing early promise as sequencing substrates, and some teams are using BAC end-sequence data to build the physical maps called - scaffold sequence maps - for further sequencing.
Cecilie Boysen (California Institute of Technology) discussed her early successes in using BAC clones to obtain the complete, contiguous, 1.1-Mb sequence of the human T-cell receptor alpha/delta locus.
BACs perform with high fidelity; the entire sequence is easily obtained using the shotgun method; contamination with Escherichia coli sequence can be kept low; and repeat areas, as well as assembly and editing steps, are handled well by Phil Green's Phred and Phrap programs (see Sequence Finishing section in "Sequencing" article).
Boysen also discussed a method to obtain insert and sequence information directly from BAC DNA. This method resulted in an almost 100% success rate, averaging 495 bp with few errors.
She briefly outlined a strategy developed by Leroy Hood (University of Washington, Seattle), Craig Venter (TIGR), and Hamilton Smith (Johns Hopkins University). In this strategy, scientists sequence the ends of BACs from a 15- to 20-fold library to generate a sequence scaffold, pick seed clones every 10 Mb or so, and sequence them completely. The sequenced clones are then compared to the database containing all the end-sequence information, and clones that overlap the least are chosen for sequencing.
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