Deletion analysis of tumor samples. (A) Real-time PCR
analysis of a breast tumor sample CHTN41 is demonstrated. The abscissa
is cycle number of PCR and the ordinate is quantity of PCR products.
The control primer set in this figure is WB23 from chromosome 22.
“D” and “A” represent DNA from diploid and aneuploid
fractions, respectively. The amplification curve from aneuloid DNA with
WD31 primer set has a several cycle difference from the others,
indicating deletion of WD31 in this tumor. (B) Southern
blot analysis of DpnII representation with WD31 probe is
shown. Each lane contains 5 μg of DpnII restriction
fragments. Lanes 1 and 2 are DNA from a tumor and a matched normal
(CHTN40), respectively, showing no deletion. Lanes 3 and 4 contain DNA
from a tumor and a matched normal pair (CHTN41), showing deletion. ER48
is a control probe derived from chromosome 3. Lane 3 has a very faint
band for DBC2, whereas the control probe exhibits the
same intensity for tumor and normal samples, representing homozygous
deletion. Contamination of normal stromal cells is considered to
contribute the faint band.