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Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome
G G Mahairas1, J C Wallace, K Smith
1University of Washington High-Throughput Sequencing Center, 401 Queen Anne Avenue North, Seattle, WA 98109, USA.
Summary
The sequence-tagged connector (STC) strategy efficiently maps the human genome using bacterial artificial chromosomes (BACs). This approach enables rapid sequencing of minimum tiling paths, aiding complex genome analysis.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Large-scale genomic sequencing requires efficient methods for mapping and assembling DNA fragments.
- Bacterial artificial chromosomes (BACs) are crucial for constructing physical maps of complex genomes.
Purpose of the Study:
- To introduce and validate the sequence-tagged connector (STC) strategy for human genome mapping.
- To demonstrate the STC strategy's capability in generating minimum tiling paths for large-scale sequencing.
Main Methods:
- Arraying 450,000 BACs with randomly cleaved inserts.
- Sequencing both ends of each BAC and preparing restriction enzyme fingerprints.
- Utilizing computational analysis of STCs to identify overlapping BAC clones.
Main Results:
- Generated 314,000 STCs (135 megabases), covering 4.5% of the human genome.
- Identified numerous genes, genome-wide repeats, simple sequence repeats, and CpG islands.
- Demonstrated the STC strategy's effectiveness in creating minimum tiling paths.
Conclusions:
- The STC strategy provides a powerful tool for large-scale genomic sequencing.
- The STC resource facilitates the integration of various genomic maps (genetic, physical, gene, sequence).
- This approach is valuable for the initial analysis of the human genome and other complex genomes.
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