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Issue No. 83
QUARTERLY NEWSLETTER
October 2005
Genetic Mapping of Structural Chromosomal Anomalies
People are more aware of DNA, genes and human genome since the completion of the human genome project.
Patients frequently ask how the completion of human genome project will affect their families. How will the
knowledge and database of this project affect the clinical practice of medical genetics? One application that is
emerging in cytogenetics is the use of DNA probes that can specifically locate the presence or absence of single
genes throughout the genome. This technique is very useful for the fine characterization of exactly which genes
are lost, rearranged, or found in extra copies as a result of structural rearrangements such as translocations,
deletions, inversions, ring chromosomes, and extra marker chromosomes. Previously, our ability to identify the
genes affected by such novel structural rearrangements was frustratingly limited; because virtually all such
abnormalities have unique breakpoints that rarely arise independently more than once, it was impractical for a
service laboratory to try to clone the abnormal regions and analyze large segments of DNA by sequencing and
other methods to find the affected genes. Now, by using "BAC" probes, it is possible to develop a molecular
map customized to a particular patient. While not typically a service technique offered broadly in many
laboratories, BAC probe investigations are increasingly applied to selected cases
To generate the reagents for these investigations, DNA sequences spanning the human genome have been
cloned and inserted into different vectors. One type of vector, the bacterial artificial chromosome (BAC), is
particularly useful because the BACs can divide indefinitely in culture, and can be used to package relatively
long lengths of DNA sequence. We can then amplify the BAC with the inserted clone of human DNA in culture.
The exact positions of the DNA clones ("inserts") are known in the genome and therefore can be precisely
mapped to specific chromosomal regions.
After the BAC clones are labelled so that the inserts have a fluorescent dye attached, these clones can be used
to determine if a person has or does not have that particular insert in his/her genome by using a technique
called fluorescence in situ hybridization (FISH). The fluorescent probes are applied to harvested cells by a
cytogenetic technique, the cloned DNA inserts hybridize to their corresponding sequences in the specimen, and
the fluorescence label is visible in the microscope. The absence, presence, and location of coloured dots
identify very specifically whether the gene in question is present, how many copies are present, and where they
are located in the karyotype.
FISH with BAC probes can be used to characterize many complex chromosomal rearrangements. In one
example from my previous work, we identified a deletion of a gene that appears to be responsible for the cat-like
cry voiced by babies with cri-du-chat syndrome. This patient had a rare chromosomal rearrangement on
chromosome 5p, called inverted duplication 5p, which was only published once in the literature. The successful
localization of a candidate gene for a specific developmental anomaly, prompted by investigation of a single
patient, demonstrates how this technique can be customized to novel structural rearrangements and provide
clinically useful information.
These types of investigations also have another benefit beyond enhanced diagnostic information for selected
patients. While the human genome project provided a consensus DNA sequence for the entire genome, the
actual number and protein structure and functions for thousands of genes that have been cloned, sequenced,
and mapped are completely unknown. These investigations provide useful information linking abnormalities of
mapped genes to specific clinical outcomes; this type of correlation of genotype and phenotype is an important
component in the overall goal of analyzing how the human genome works, delineating "normal" and "abnormal"
variations in DNA sequence and protein functions, and developing improved treatment options.
Dr. Jia-Chi (Jack) Wang, MD, MSc., Ph.D., FCCMG
Head, Cytogenetics
Hamilton Regional Laboratory Medicine Program
MUMC Site