The principle of the APOT assay is a 39 rapid amplification of cDNA ends PCR assay that achieves amplification and cloning of the region between a single short sequence in a cDNA molecule and its unknown 39- end. In general, the integrated transcripts derived from E6 and E7 oncogenes encompass viral sequences at their 59- ends and host genome sequences at their 39- ends. The expected size of products obtained from an episome-derived transcript is 1050 bp Amplimers that displayed a size different from 1050 bp may therefore be derived from an integrated HPV genome. To testify the specificity of the modified APOT assay, cDNAs from HPV16-positive Caski cell contains the integrated HPV16 genome and HPV-negative normal cervical tissues, as well as the ‘‘minus-RT’’ controls in which reverse transcriptase was omitted from the reactions were used. The amplified products of the cDNAs from HPV16-positive Caski cell were similar to the previous report, whereas no RT product was obtained from the normal cervical tissues without HPV DNA and the ‘‘minus-RT’’ control. These data indicated the modified APOT assay can specifically detect the transcripts derived from the integrated HPV genome. Furthermore, there were four different disruptions of E1 region at nt 880, 949, 1054 and 1234. The transcripts containing an E1-splice donor signal at nt 880 might belong to potential episomal pattern, whereas the transcript which truncated at nt949 might be a result of internal priming by oligo dT. Other transcripts which truncated at nt 1054 and 1234 neither contained poly A sequences, nor any polyadenylation site belong to viral or host, so these transcripts were viewed as potential integrated patterns. In addition, we also found another transcript which has E7 ORF spliced at nt 880 to the E4-splice acceptor site at nt 3358 and then spliced from the E4-splice donor signal at nt 3632 to the L1-splice acceptor site at 5639, and also terminated at poly A. In this transcript, the E4 ORF is not disrupted. Lack of a splice donor signal at nt 5815 in this transcript indicates that the HPV16 genome disrupted at nt 5815 might also take part in the virus genome integration.