An extension of microarray technology may also be used to analyse tissue sections.
This process, termedtissue microarrays(TMA), uses tissue cores or biopsies from
conventional paraffin-embedded tissues. Thousands of tissue cores are sliced and placed
on a solid support such as glass where they may all be subjected to the same immuno-
histochemical staining process or analysis with gene probes usingin situhybridisation.
As with DNA microarrays many samples may be analysed simultaneously, less tissue is
required and greater standardisation is possible.6.9 Analysing whole genomes
Perhaps the most ambitious project in biosciences is the initiative to map and completely
sequence a number of genomes from various organisms. The mapping and sequencing of
a number of organisms indicated in Table 6.6. has been completed and many more are
due for completion. A number have been completed already such as the bacteriumE. coli.
The demands of such large-scale mapping and sequencing have provided the impetus for
the development and refinement of even the most standard of molecular biology tech-
niques such as DNA sequencing. It has also led to new methods of identifying the
important coding sequences that represent proteins and enzymes. The use of bioinfor-
matics to collate, annotate and publish the information on the World Wide Web has also
been an enormous undertaking. The availability of an informative map of the human
genome that may be analysed and studied in detail chromosome by chromosome, such as
theMap Viewer(NCBI), is just one of the rapid developments in the field of genome
analysis and bioinformatics. Such is the power and ease of use of resources such as these
that it is now inconceivable to work without these resources.6.9.1 Physical genome mapping
In terms of genome mapping a physical map is the primary goal.Genetic linkagemaps
have also been produced by determining the recombination frequency between two
particular loci. YAC-based vectors essential for large-scale cloning contain DNA inserts
that are on average 300 000 bp in length, which is longer by a factor of ten than the longest
inserts in the clones used in early mapping studies. The development of vectors with large
insert capacity has enable the production ofcontigs. These are continuous overlapping
cloned fragments that have been positioned relative to one another. Using these maps any
cloned fragment may be identified and aligned to an area in one of the contig maps. In order
to position cloned DNA fragments resulting from the construction of a library in a YAC or
cosmid it is necessary to detect overlaps between the cloned DNA fragments. Overlaps are
created because of the use of partialdigestion conditions with a particular restriction
endonuclease when constructing the libraries. This ensures that when each DNA fragment
is cloned into a vector it has overlapping ends which theoretically may be identified and
the clones positioned or ordered so that a physical map may be produced (Fig. 6.47).
In order to position the overlapping ends it is preferable to undertake DNA sequen-
cing; however, due to the impracticality of this approach a fingerprint of each clone is254 Recombinant DNA and genetic analysis