New sequencing methods offer the potential to dramatically advance our characterization of the genomic defects associated with cancer. However, standard next-generation sequencing libraries are not useful for detecting genomic rearrangements because of their short sequence read lengths. Paired-end libraries, also known as “jumping libraries” contain DNA molecules with two regions of genomic DNA that, when sequenced, can be used to detect genomic rearrangements such as translocations.
Rosa and her Broad colleagues constructed a jumping library from K562 cells, which contain the Philadelphia chromosome, a translocation that serves as a marker for Chronic Myeloid Leukemia. The researchers verified the library by Sanger sequencing and were able to sequence it by SOLiD sequencing. This project, which was the first mammalian SOLiD sequencing to be run at the Broad, successfully detected paired-end reads aligned to the Philadephia chromosome translocation. Further work will improve our ability to detect uncharacterized structural genomic rearrangements.
PROJECT: Detection of genomic rearrangements in K562 cells using paired-end sequencing
My summer at the Broad Institute was a wonderful experience, giving me the opportunity to engage in a challenging research project and work with highly motivated students. I appreciated the collaboration among scientists with diverse backgrounds and was impressed by how they work together to revolutionize the field of genomics.