#DNA-PET: Because PET represent connectivity between the tags, the use of PET in genome re-sequencing has advantages over the use of single reads. This application is called  pairwise end sequencing, known colloquially as double-barrel shotgun sequencing. Anchoring one half of the pair uniquely to a single location in the genome allows mapping of the other half that is ambiguous. Ambiguous reads are those that map to more than a single location. This increased efficiency reduces the cost of sequencing as these ambiguous sequences, or reads, would normally be discarded. The connectivity of PET sequences also allows detection of structural variations: insertions, deletions, duplications, inversions, translocations. During the construction of the PET library, the fragments can be selected to all be of a certain size. After mapping, the PET sequences are thus expected to be consistently a particular distance away from each other. A discrepancy from this distance indicates a structural variation between the PET sequences. For example (Figure on the right): a deletion in the sequenced genome will have reads that map further away than expected in the reference genome as the reference genome will have a segment of DNA that is not present in the sequenced genome.
#ChIP-PET: The combined use of chromatin immunoprecipitation (ChIP) and PET is used to detect regions of DNA bound by a protein of interest. ChIP-PET has the advantage over single read sequencing by reducing ambiguity of the reads generated. The advantage over chip hybridization (ChIP-Chip) is that hybridization tiling arrays do not have the statistical sensitivity that sequence reads have. However, ChIP-PET, ChIP-Seq and ChIP-chip have all been highly successful.
#ChIA-PET: The application of PET sequencing on chromatin interaction analysis. It is a genome-wide strategy for finding de novo long-range interactions between DNA elements bound by protein factors. The first ChIA-PET was developed by Fullwood et al.. (2009) to generate a map of the interactions between chromatin bound by oestrogen receptor α (ER-α) in oestrogen-treated human breast adenocarcinoma cells. ChIA-PET is an unbiased way to analyze interactions and higher-order chromatin structures because it can detect interactions between unknown DNA elements. In contrast, 3C and 4C methods are used to detect interactions involving a specific target region in the genome. ChIA-PET is similar to finding fusion genes through RNA-PET in that the paired tags map to different regions in the genome. However, ChIA-PET involves artificial ligations between different DNA fragments located at different genomic regions, rather than naturally occurring fusion between two genomic regions as in RNA-PET.
#RNA-PET: This application is used for studying the transcriptome: transcripts, gene structures, and gene expressions. The PET library is generated using full length cDNAs, so the ditags represent the 5’ capped and the 3’ polyA tail signatures of individual transcripts. Therefore, RNA-PET is especially useful for demarcating the boundaries of transcription units. This will help identify alternative transcription start sites and polyadenylation sites of genes. RNA-PET could also be used to detect fusion genes and trans-splicing, but further experiment is needed to distinguish between them. Other methods of finding the boundaries of transcripts include the single-tag strategies CAGE, SAGE, and the most recent SuperSAGE, with the CAGE and 5’ SAGE defining the transcription start sites and the 3’ SAGE defining the polyadenylation sites. The advantages of PET sequencing over these methods are that PET identify both ends of the transcripts and, at the same time, provide more specificity when mapping back to the genome. Sequencing the cDNAs can reveal the structures of transcripts in great details, but this approach is much more expensive than RNA-PET sequencing, especially for characterizing the whole transcriptome. The major limitation of RNA-PET is the lack of information regarding the organization of the internal exons of transcripts. Therefore, RNA-PET is not suitable for detecting alternative splicing. In addition, if the cloning procedure is used construct the cDNA library before generating the PETs, cDNAs that are difficult to clone (as a result of long transcripts) would have lower coverage. Similarly, transcripts (or transcript isoforms) with low expression levels would likely be under-represented as well.