LONG SPAN DNA PAIRED-END TAGS (DNA-PET) FOR UNRAVELING GENOMIC REARRANGEMENTS IN CANCER GENOMES

Abstract

All cancers are the result of changes that have occurred in the DNA sequence of the genomes of the cancer cells. Now, we are moving to the new era in which it is possible to get the complete DNA sequence of large number of cancer genomes with the help of the next generation sequencing technologies. In this study, by comparing the characteristics of the large insert libraries (10-20 kb) with short insert (1 kb) libraries, we show that large inserts are superior to short inserts in providing higher physical genome coverage and therefore achieve greater sensitivity for the identification of the different types of SVs, including copy number neutral and complex events. Applying the 10 kb DNA-PET technology to 15 cancer genomes, including both primary tumors and cancer cell lines, we show some important genomic characteristics in breast and gastric cancer genomes.