Routine detection of the replication error phenotype in clinical tumor specimens using fluorescence-SSCP.

Almost all tumors from patients with hereditary non-polyposis colon carcinoma and approximately 10%-15% of sporadic colon and gastric carcinomas contain widespread deletions within mono- and dinucleotide repeat sequences in their DNA. This is referred to as the replication error (RER+) phenotype and, in the case of colon carcinoma, is often associated with an improved tumor prognosis and possibly also with response to chemotherapy. The RER+ status of tumors is usually determined by examining several dinucleotide and mononucleotide repeats for size variations when compared with the matching normal DNA. Alternately, the identification of deletions within BAT-26, a quasi-monomorphic polyadenine tract within the hMSH2 gene, has been shown to establish the RER+ status of tumors with greater than 99% accuracy and without the need for normal DNA. Here, we use fluorescent PCR in combination with single strand conformation polymorphism analysis to detect deletions in BAT-26. This technique provides a sensitive, rapid, reproducible and inexpensive assay suitable for the routine identification of RER+ status in clinical tumor specimens.