Mayo Clinic Uses Next-Generation Sequencing Method to Understand HPV in Cancer
The human papillomavirus, commonly known as HPV, plays a significant role in the development of cervical cancer. However, the virus has recently been found in individuals that develop other types of cancer, including head and neck as well as the whole spectrum of anogenital cancers. Due to its recent development in these other types of cancers, its role in progression, aggressiveness, and prognosis remains largely unknown.
According to a recent article posted on GenomeWeb, researchers from the Mayo Clinic have begun using a next-generation sequencing (NGS) method, called mate-pair sequencing, or MP-seq, that could cost-effectively shed light on the role of HPV in these cancer types and lead to better prognostics and decision making for patient management.
David Smith, Ph.D. professor of laboratory medicine and pathology at Mayo Clinic and co-author of a recent review published in the journal Viruses, told GenomeWeb, "If you can look at a cancer and determine where the virus is integrated, you may begin to be able to tell if that cancer is going to be aggressive or not, and make a decision on how to treat that patient."
Mayo Clinic researchers are focused specifically on oropharyngeal cancers, because of its recent increase. At Mayo, the frequency of oropharyngeal cancer patients that are HPV positive has increased to 80 percent from less than 20 percent over the past several decades.
To study the cancer in closer detail, Dr. Smith and his group are employing MP-seq, a low-pass sequencing strategy being developed by Mayo's biomarker discovery program. MP-seq involves circularizing fragments of DNA around 5 kb long and adding a biotin at the junction. The circularized DNA is fragmented and sequenced at low coverage, and the biotin-labeled ends can be used to provide information about the entire 5-kb fragment. The strategy provides genome-wide information.
According to Dr. Smith, "most of what is known about HPV and cancer is based on studies of cervical cancer. But better technology is changing researchers' understanding of HPV's role in both cervical cancer and also finding out that it may have a very different role in other cancers. For instance, researchers previously assumed that HPV integration occurred at random spots in the genome; however, genomic hotspots have been found in cervical cancer. In addition, the HPV integration site likely matters in terms of the cancer's progression."
While whole-genome sequencing could also be used to identify this information, MP-seq is less expensive, less complicated to interpret, and produces less data.
"It's a simpler way to characterize the genome," Dr. Smith said. "You don't get base-pair resolution, but you do get a lot of information about what's happening to the genome, including actionable things that you can potentially make clinical decisions on at a really decent price point."
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