Hornigold, James Nicholls Andrew; (1998) Physical mapping using Hinf1 cosmid fingerprinting; Its application to the human Y chromosome and to 9q34. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

The genomes of a number of organisms, including E. coli and C. elegans have been physically mapped in cloned DNAs. The method used has been based on the creation of a diagnostic 'fingerprint' for each of a large number of random clones, and the comparison of these fingerprints to detect clone overlaps. These methods have proved to be fast and effective, and are now being applied to a number of human chromosomes. For this thesis I have set out to examine a cosmid fingerprinting technique using restriction digestion with the enzyme Hinfl and a semi-automated method of construction of contiguous arrays of clones (contigs) based on these fingerprints. This work has been carried out on clones from two regions of the human genome; the Y chromosome and 9q34. The work on the Y chromosome has been done on random clones from Y specific cosmid libraries, in a manner analogous to that used to map other genomes. The clones used in mapping 9q34 have been picked out of a chromosome 9 specific library, or from a whole genome library, or in a few cases were obtained from other sources. Some of the clones were picked by methods intended to cover large portions of 9q34. Others were isolated by hybridisation to single copy probes associated with genes or markers. A third category were picked with cosmid end probes, for directed extension of existing contigs. These two pieces of work allow a number of comparisons to be drawn: between the expected and actual rates of progress in the projects; between the random and directed methods of contig assembly; between the Y chromosome and an autosome and between the maps produced using this method and other published mapping data. This gives a picture of the viability of the Hinfl fingerprinting method for the production of physical maps across large areas of genomes.

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