482
UWE R. MULLER et aI.
Applications
Rapid and cost efficient testing for gene copy number changes in pathological tissues is likely to result in a considerable increase in our understanding ofgenetic disease. The ideal test would allow whole genome scanning at gene level resolution or better with a single chip and a minimum of
sample. The sensitivity of array based CGH is already sufficient for detection of low-level amplifications and aneuploidies if the tumor tissue is not
too diluted with normal cells and if most of the cells carry the mutation. In
very homogeneous tissues, such as cell lines, certain leukemias, or tissues
from patients with hereditary disease the detection of single copy deletions
or additions has already been shown to be feasible with arrays of large
genomic clones (Pinkel et al. 1998; Bao et al. 1999; Lese et al. 1999). Further
improvements in sensitivity and robustness of this technology will soon
make high resolution genome-wide scanning possible for cytogenetic applications with the use of cDNA arrays that cover the whole genome.
An important consideration is the amount of sample material required
for this analysis, since tumor specimens are getting smaller as diagnoses
are being made earlier. Especially for clinical applicability, this technology
should work with samples obtained by biopsy. Until a robust and reliable
total genome PCR amplification method becomes available, that does not
distort the sequence ratios, this technique has to rely on non-amplified
sample material. To that end we have achieved satisfactory results with
as little as 3 f.lg of tumor DNA in overnight hybridizations without the
aid of signal amplification or hybridization systems that are designed
to overcome the barriers of diffusion. Preliminary results in our labs suggest that significantly greater sensitivity is possible. More demanding applications, such as analysis of individual clones in tumor tissue or the analysis of single fetal cells obtained from maternal blood, will clearly demand
a reliable amplification technology for the sample DNA. Promising reports
by other laboratories (Beltinger et al. 1997; Wells et al. 1999) suggest that
such applications may not be very far off.
Acknowledgements. The cancer arrays used in our work were generated by the dedicated
work of many of our colleagues in the pilot line and development teams at Corning Incorporated.
UWE R. MULLER et aI.
Applications
Rapid and cost efficient testing for gene copy number changes in pathological tissues is likely to result in a considerable increase in our understanding ofgenetic disease. The ideal test would allow whole genome scanning at gene level resolution or better with a single chip and a minimum of
sample. The sensitivity of array based CGH is already sufficient for detection of low-level amplifications and aneuploidies if the tumor tissue is not
too diluted with normal cells and if most of the cells carry the mutation. In
very homogeneous tissues, such as cell lines, certain leukemias, or tissues
from patients with hereditary disease the detection of single copy deletions
or additions has already been shown to be feasible with arrays of large
genomic clones (Pinkel et al. 1998; Bao et al. 1999; Lese et al. 1999). Further
improvements in sensitivity and robustness of this technology will soon
make high resolution genome-wide scanning possible for cytogenetic applications with the use of cDNA arrays that cover the whole genome.
An important consideration is the amount of sample material required
for this analysis, since tumor specimens are getting smaller as diagnoses
are being made earlier. Especially for clinical applicability, this technology
should work with samples obtained by biopsy. Until a robust and reliable
total genome PCR amplification method becomes available, that does not
distort the sequence ratios, this technique has to rely on non-amplified
sample material. To that end we have achieved satisfactory results with
as little as 3 f.lg of tumor DNA in overnight hybridizations without the
aid of signal amplification or hybridization systems that are designed
to overcome the barriers of diffusion. Preliminary results in our labs suggest that significantly greater sensitivity is possible. More demanding applications, such as analysis of individual clones in tumor tissue or the analysis of single fetal cells obtained from maternal blood, will clearly demand
a reliable amplification technology for the sample DNA. Promising reports
by other laboratories (Beltinger et al. 1997; Wells et al. 1999) suggest that
such applications may not be very far off.
Acknowledgements. The cancer arrays used in our work were generated by the dedicated
work of many of our colleagues in the pilot line and development teams at Corning Incorporated.