Microsatellite analysis of melanoma lesions using (CA)13 oligonucleotides as an internal probe

The accurate assessment of microsatellite loci on specific chromosome regions for loss of heterozygosity (LOH) is important to identify potential tumor suppressor gene locations and recently correlations to clinicopathology of tumors. Analysis of microsatellite markers usually requires performing polymerase chain reaction (PCR) with labeled primers. This often leads to spurious PCR products that make interpretations of specific PCR bands difficult. Assessment of LOH by radiolabeled PCR is not always easy to interperet when there are multiple bands present, multiple markers and specimens are being assessed, and in multiplex LOH PCR. We describe an approach to accurately verify PCR-based LOH in which labeled PCR primers are not needed to detect allele expression. Specificity is determined by using a digoxigenin-labeled oligonucleotide (CA)13 as an internal specific probe for hybridization. Because the majority of di-nucleotide microsatellite markers contain the sequence of (CA)n or (GT)n repeats, this (CA)n probe is highly versatile. Forty cutaneous melanoma biopsies from advanced stage patients were assessed using the oligonucleotide probe at five chromosome regions (1q, 6q, 9p, 10q, 11q). The LOH frequency in informative cases varied from 33% to 47% in which chromosome 6q was the highest followed closely by 11q. We observed a higher frequency of LOH in the 6q (47%) and 11q (41%) compared to previously reported studies using the probe technique. This new approach was also demonstrated to be efficient in multiplex-PCR to detect LOH in melanomas. Using the probe hybridization approach it was demonstrated that in advanced cutaneous melanomas LOH are quite frequently expressed on 5 different chromosome regions.