Sh. Kim et al., Whole genome amplification and molecular genetic analysis of DNA from paraffin-embedded prostate adenocarcinoma tumor tissue, J UROL, 162(4), 1999, pp. 1512-1518
Purpose: Often tissues obtained from prostate adenocarcinoma tumors embedde
d in paraffin are heterogeneous in cell type and must be carefully microdis
sected to acquire tissue fragments that provide homogeneous aliquots of tum
or clones. Such tissue fragments rarely contain sufficient DNA to perform g
enomic characterization needed as an early step in localizing relevant onco
genes or tumor suppressor genes. We report that PCR using a degenerate olig
onucleotide primer (DOP-PCR) can be applied to DNA-samples from microdissec
ted paraffin-embedded prostate adenocarcinomas, and this provides sufficien
t product for fluorescent allelic imbalance measurements or comparative gen
omic hybridization (CGH).
Materials and Methods: Samples were selected to be representative of those
routinely obtained during prostatectomies,based on typical tumor stages (T2
and T3) and Gleason grades (range 3 + 3 to 4 +5). For DNA analysis without
prior DOP-PCR, only large tumors were selected to be sectioned. More than
50 specimens were analyzed. Close comparison of data obtained from analysis
of DOP-PCR with those from non-DOP DNA was obtained on a subset 8 samples.
To compare the allelic balance of DOP-PCR amplified DNA with that measured
for non-DOP DNA, we analyzed allelic ratios on DNA from 5 different tissue
samples processed by both microdissection and conventional sectioning.
Results: Systematic comparison of allelic imbalance results shows close sim
ilarity between DOP-PCR amplified product and non-DOP DNA, indicating that
PCR product is a valid representation of the tumor genome. In addition, the
difference between allelic balance and imbalance is more distinctive when
microdissection followed by DOP-PCR is performed. Performing CGH on product
s of DOP-PCR also shows distinctive regional copy number alterations in DNA
from microdissected tumor tissue.
Conclusion: Either of these procedures allows distinction between benign an
d malignant genomes, and also allows independent analysis of genomic altera
tions in different portions of tumors. They also may be applied clinically
for genomic characterization of small foci that frequently appear in prosta
tes of elderly men who are showing no obvious pathological symptoms of aden
ocarcinoma.