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Director: James R. Lupski, M.D.,
Ph.D.
Email: jlupski@bcm.tmc.edu
Phone: 713-798-6530 |
Co-Director: Lisa White, Ph.D.
Email: lisaw@bcm.tmc.edu
Phone: 713-798-7607 |
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The overall objective of the newly proposed genome-based
array core is to provide MRDDRC researchers with access to genome-based
microarrays for use in high-resolution genomic analyses of the human
genome and comparative genome hybridization (CGH). Core services will
include assistance with development of microarrays for specific research
purposes, as well as production of standardized arrays that allow diagnostic
and research inquiries. This core will provide Center investigators
with access to unprecedented resolution for the identification and characterization
of constitutional chromosomal rearrangements.
The clinical problem: An unknown, but substantial fraction
of Mental Retardation (MR) and Developmental Disabilities (DD) results
from genetic etiologies that remain unrecognized. These often take the
form of chromosome abnormalities, typically occurring de novo
in the patient. Some of these lesions can be recognized by typical chromosome
banding methods, but the majority remain undetected1. Estimates
of undetected chromosome anomalies range from 6-18% of the MR population2,3.
For many known and recurring deletions, specific probes can be individually
applied to a patient’s chromosomes in fluorescence in situ
hybridization (FISH) studies to detect or rule out involvement
of specific regions4. Recent advances have also demonstrated
that telomeric deletions can often be found in patients with MR through
the use of multiplexed telomere FISH probe studies5. These
advances have led to improved detection of chromosomal anomalies in
patients with MR/DD, but have limitations, especially in the number
of loci that can be investigated in a cost-effective manner.
Figure 1. Bac Array
CGH resolution compared with other methods. |
A solution: Advances in FISH methodologies
and in the description of the human genome have converged to provide a
solution to this difficult clinical problem. Comparative genome hybridization
(CGH) has been widely applied to the problem of defining chromosomal abnormalities
in tumors6. The technique applies sample and control DNAs labeled
with different fluorescent dyes to metaphase chromosomes and measures
the ratio of the two colors to detect differential abundance of sequences
in the patient sample. The resolution of CGH is limited by detection of
metaphase chromosome segments, and is estimated to have a lower limit
of ~5 million base pairs (Mb). A modification
of this method that can provide much higher resolution uses the same principal
of comparing differentially labeled samples, but now applied to cloned
fragments of the human genome arrayed on glass slides (genomic microarrays:
Figures 1-2). A number of groups, including several at BCM, have begun
to develop genome-based microarrays using large insert bacterial artificial
chromosome clones (BACs) as the genomic substrate7-9. This
method offers the potential of performing hundreds of simultaneous FISH
experiments, limited only by the number of clones on the microarray. Advances
locally have now validated this technology, demonstrating that it has
high utility for characterizing patient collections and for detecting
previously unknown deletions and duplications8,9. The method
has advanced to the stage where a core facility to provide genome-based
arrays is feasible.
Figure 2. Comparison of conventional
Comparative Genome Hybridization with BAC Array based hybridization.
References
1 Flint, J., Wilkie, A.O.M., Buckle, V.J.,
Winter, R.M., Holland, A.J., McDermid, H.E. (1995). The detection of
subtelomeric chromosomal rearrangements in idiopathic mental retardation.
Nat. Genet. 9:132-140.
2 Knight, S.J.L., Horsely, S.W., Regan, R., Lawrie, N.M.,
Maher, E.J., Cardy, D.L.N., et al. (1997). Development and clinical
application of an innovative fluorescence in situ hybridization
technique which detects submicroscopic rearrangements involving telomeres.
Eur. J. Hum. Genet. 5:1-81.
3 Knight, S.J.L., Regan, R., Nicod, A., Horsley, S.W., Kearney,
L., Homfray, T., et al. (1999). Subtle chromosomal rearrangements in
children with unexplained mental retardation. Lancet 354:1676-1681.
4 Riegel, M., Castellan, C., Balmer, D., Brecevic, L., Schinzel,
A. (1999). Terminal deletion, del(1)(p36.3), detected through screening
for terminal deletions in patients with unclassified malformation syndromes.
Am. J. Med. Genet. 82:249-253.
5 National Institutes of Health and Institute of Molecular
Medicine Collaboration. (1996). A complete set of human telomeric probes
and their clinical application. Nat. Genet. 14:86-89.
6 Kallioniemi OP, Kallioniemi A, Sudar D, Rutovitz D, Gray
JW, Waldman F, Pinkel D. (1993). Comparative genomic hybridization:
a rapid new method for detecting and mapping DNA amplification in tumors.
Semin. Cancer Biol. 1993 4:41-46.
7 Albertson DG, Pinkel D. (2003). Genomic microarrays in
human genetic disease and cancer. Hum. Mol. Genet. 12:145-152.
8 Yu W., Ballif BC, Kashork CD, Heilstedt HA, Howard LA,
Cai W, White LD, Liu W, Beaudet AL, Bejjani BA, Shaw CA, and Shaffer
LG. (2003). Development of a comparative genomic hybridization microarray
and demonstration of its utility with 25 well-characterized 1p36 deletions.
Hum. Mol. Genet. 12:2145-2152.
9 Shaw CJ, Shaw CA, Yu W, Stankiewicz P, White LD, Beaudet
AL, and Lupski, JR. (2004) Comparative genomic hybridization using a
proximal 17p BAC/PAC array detects rearrangements responsible for four
genomic disorders. J. Med. Genet. (in press).
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