Mate-Pair Sequencing as a Powerful Clinical Tool for the Characterization of Cancers with a DNA Viral Etiology

Abstract

DNA viruses are known to be associated with a variety of different cancers. Human papillomaviruses (HPV) are a family of viruses and several of its sub-types are classified as high-risk HPVs as they are found to be associated with the development of a number of different cancers. Almost all cervical cancers appear to be driven by HPV infection and HPV is also found in most cancers of the anus and at least half the cancers of the vulva, penis and vagina, and increasingly found in one sub-type of head and neck cancers namely oropharyngeal squamous cell carcinoma. Our understanding of HPVs role in cancer development comes from extensive studies done on cervical cancer and it has just been assumed that HPV plays an identical role in the development of all other cancers arising in the presence of HPV sequences, although this has not been proven. Most invasive cervical cancers have the HPV genome integrated into one or more sites within the human genome. One powerful tool to examine all the sites of HPV integration in a cancer but that also provides a comprehensive view of genomic alterations in that cancer is the use of next generation sequencing of mate-pair libraries produced from the DNA isolated. We will describe how this powerful technology can provide important information about the genomic organization within an individual cancer genome, and how this has demonstrated that HPVs role in oropharyngeal squamous cell carcinoma is distinct from that in cervical cancer. We will also describe why the sequencing of mate-pair libraries could be a powerful clinical tool for the management of patients with a DNA viral etiology and how this could quickly transform the care of these patients.

Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma

“…can potentially identify smaller deletions (<3 kb) than MPseq based on the design of the array and the library preparation for MPseq. [12][13][14]38 On the other hand, MPseq can profile the whole genome and identify other patterns of chromoanagenesis including chromoplexy. For illustration of the sensitivity of MPseq to identify rearrangements, a recent study only found 43 gene fusions in 22 specimens with RNAseq in comparison to the 1535 rearrangements and 637 gene fusions we identified in the same sample size.…”

“…[8][9][10][11] Mate-pair sequencing (MPseq) differs from standard NGS approaches by tiling the whole genome with larger fragments (2 to 5 kb) to reliably detect structural variants such as insertions, deletions, and rearrangements. 12 We previously used MPseq to determine the lineage relationships of multifocal lung cancer, to identify a chromoplectic ALK rearrangement in an inflammatory myofibroblastic tumor, to discover recurrent t(6:7)(p25.3;q32.3) translocations in ALK-negative anaplastic large cell lymphomas, and for other purposes. [13][14][15][16][17] Recently, we have also integrated MPseq with RNA sequencing (RNAseq) to identify transcribed chromosomal rearrangements in peripheral T cell lymphomas.…”

Identification of lenalidomide resistance pathways in myeloma and targeted resensitization using cereblon replacement, inhibition of STAT3 or targeting of IRF4

“…The high throughput genomic mate pair libraries from HMCLs were prepared by the Mayo Clinic Genome Core Facilities using the Illumina Mate Pair protocols and their available kit (Nextera Mate Pair Sample Preparation kit, Illumina) 10,24 , Then, two samples were run on one lane of an Illumina HiSeq2000 with 50 bp reads. The sequences were aligned to hg19 using BWA, and a BAM file containing only the clustered discordant reads with clustered mates was created.…”