ABSTRACT
This chapter describes the concept of the multiplex sequencing of paired-end ditags (MS-PET) approach and its applications in transcriptome analysis, mapping the deoxyribonucleic acids (DNA)-protein interactions, and identifying genomic structural variations. It discusses the potential of applying PET analysis on re-sequencing the human genomes and its implications in personalized genome medicine. The principal concept of the PET methodology is to extract the paired end signatures from each of the target DNA fragments, and map the paired tag sequences to the reference genome for accurate demarcation of the boundaries of the tested DNA fragments on the genome landscape. The advancement of DNA microarray fabrication that covers the entire genome is an attractive approach to study transcriptome. In order to profile transcription factor binding in an unbiased and genome-wide fashion, paired end ditag sequencing was developed to characterize the chromatin immunoprecipitation (ChIP) enriched DNA fragments as ChIP-PET method.
