COMPARISON OF THE POLYMERASE CHAIN-REACTION AND SOUTHERN BLOT ANALYSIS IN DETECTING AND TYPING HUMAN PAPILLOMA-VIRUS DEOXYRIBONUCLEIC-ACID IN TUMORS OF THE LOWER FEMALE GENITAL-TRACT

To conduct studies on the clinical and pathologic significance of huma n papilloma virus (HPV) in genital malignancies, accurate detection an d typing of the virus in clinical material are essential. Currently, S outhern blotting and the polymerase chain reaction (PCR) are two of th e most commonly used methods to identify HPV. This study was undertake n to compare these techniques in the detection and typing of HPV in 24 2 invasive malignancies of the lower female genital tract. BamHI and P stI restriction digests of tumor DNA were hybridized to P-32-labeled p robes for HPV types 6, 16, and 18 at Tm - 20 degrees C after Southern transfer. Blots were then washed at Tm - 20 degrees C and Tm - 9 degre es C. The DNA was also amplified by PCR using both highly conserved co nsensus L1 primers that detect 25 different HPV genotypes and primers specific for HPV 6 E6, 16 E7, and 18 E6. All PCR products were hybridi zed to type-specific radiolabeled probes. In 202 of the 242 (83%) samp les, HPV was detected, including 189 of 218 (87%) cervical cancers, 11 of the 20 (55%) vulvar cancers, and two of four tumors from the vagin a, urethra, or anus. In 67% of the specimens, there was agreement betw een the Southern blot technique and both methods of PCR (consensus and type-specific primers), including 121 of the 202 HPV-positive specime ns and 40 HPV-negative specimens. Of the 141 tumors with HPV detected by Southern blot analysis, the same HPV type was detected by PCR in 12 1 (86%). The discrepant typing for HPV in the tumors positive by South ern blot included four tumors negative by PCR, 10 tumors with a mixtur e of HPV types by PCR, five tumors positive by PCR with the consensus primers but negative with the corresponding type-specific primers; and , in one case, the Southern blot was read as HPV 16, whereas PCR showe d the tumor to contain HPV 18. Of the 101 cases negative for HPV by So uthern blot, HPV was detected in 61 (60%) cases by PCR. Forty-two case s were positive with both sets of primers, 15 cases were positive only with the consensus primers, and four cases were positive only with ty pe-specific primers. Comparison of PCR detection of HPV by consensus a nd type-specific primers showed that 191 cases were positive with the consensus primers, 170 with the type-specific primers, and 163 positiv e using both sets of primers. In conclusion, PCR was more sensitive fo r detection of HPV in tumor tissue than Southern blot analysis, and co nsensus primers detected more HPV types than type-specific primers. Th ere was good agreement between typing HPV by Southern blot and PCR whe n the Southern blot was positive. We concluded that PCR using both con sensus and type-specific primers is optimal for detection of HPV in ge nital tumors.