Paired-end Tagsとは 意味・読み方・使い方

Paired-end tags, also known as PET, refer to the short sequences at the 5’ and 3’ ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA. These short sequences are called tags or signatures because, in theory, they should contain enough sequence information to be uniquely mapped to the genome and thus represent the whole DNA fragment of interest. It was shown conceptually that 13 bp is sufficient to map tags uniquely. However, longer sequences are more practical for mapping reads uniquely. The endonucleases (discussed below) used in PET produce longer tags (18/20 bp and 25/27 bp) but sequences of 50-100 base pairs would be optimal for both mapping and cost efficiency. After extracting the PETs from many DNA fragments, they are linked (concatenated) together for efficient sequencing. On average, 20-30 tags could be sequenced with the Sanger method, which has a longer read length. Since the tag sequences are short, individual PETs are well suited for next-generation sequencing that has short read lengths and higher throughput. The main advantages of PET sequencing are its reduced cost by sequencing only short fragments, detection of structural variants in the genome, and increased specificity when aligning back to the genome compared to single tags, which involves only one end of the DNA fragment.