Next-generation sequencing (NGS) is advancing at a rapid pace, and it will be interesting to see how it can be harnessed within clinical settings. The lab of Dr. Elaine Mardis, co-Director at The Genome Institute, Washington University (St. Louis, MO), studies cancer genomics by performing targeted capture with custom probe sets for specific genes of interest. For targeted capture, researchers in Dr. Mardis’s lab use xGen® Lockdown® Probes (IDT, Coralville, IA), which they find work extremely well with DNA isolated from formalin-fixed tissue.
Having been immersed in DNA sequencing and sequencing technology throughout her research career, Dr. Mardis found NGS to be a natural evolution from the early methods of fluorescent slab gel and fluorescent capillary electrophoresis that were used to sequence the human and mouse genomes (among others). Since she is a resident “expert” in the field of NGS in cancer therapy, the author quizzed her on her thoughts:
NB: Dr. Mardis, can you tell me a bit about the significance of NGS to cancer care?
EM: With advances in modern medicine meaning that people are living longer, it is inevitable that disease incidence has increased. One such disease that we are constantly battling to better understand, and to identify suitable therapeutic regimens to treat, is cancer. NGS can have a significant impact on both the treatment and monitoring of cancer patients.
The significance of NGS to cancer care is potentially huge; it gives the advantage of generating comprehensive data in a timely manner, allowing rapid decisions about treatment to take place. Doctors can therefore ensure that the most appropriate treatment is administered as early as possible. The cancer genome can then be monitored to see how it changes in response to treatment. For example, many cancer types shed cells into the circulation, meaning that blood can be sampled and evaluated via NGS to provide an indication of the impact of therapy. If treatment is unsuccessful, an increase in the level of tumor DNA in the blood will be observed, and the treatment strategy can be changed accordingly.
NB: What new NGS technologies do you think we should expect to see in the future, and what hurdles need to be overcome for them to be adopted in clinical applications?
EM: What I would like to see develop next is longer read technologies. Most of the currently available technologies used to sequence human genomes produce short reads. The availability of long read technologies would enable us to assemble human chromosomes at the first pass, rather than having to align the reads to the reference genome—a process we know has limitations. The other difficulty will be accuracy and coverage of the genome, since there is a major concern in the clinical world over the occurrence of false negatives—you can’t validate something that wasn’t detected in the first place! In terms of future scope, I expect to see widespread NGS use within the next two years, since the benefits of its application to cancer care are becoming quite clear.
NB: As an international collaboration of research groups, the Encyclopedia of DNA Elements (ENCODE) Consortium was set up to identify all functional elements in the human genome. What do you think will be the influence of ENCODE on NGS efforts and what does it mean for exome sequencing in cancer research?
EM: Personally, I am a big fan of whole genome sequencing since it provides us with the whole picture of somatic changes in the cancer genome, including non-genic regulatory sites now better defined by ENCODE. While exome sequencing has its benefits in terms of cost, it does not provide a complete picture of the complexity of cancer genomes that can only really be examined through whole genome sequencing.
ENCODE enriched our understanding of many regulatory genome features, giving us a much better ability to interpret the variants we identify outside of genes.
The author would like to thank Dr. Mardis for taking the time to talk about her work on the sequencing of cancer genomes using NGS techniques.
Nicola Brookman-Amissah is Scientific Communications Senior Writer, IDT, Coralville, IA, U.S.A.; http://www.idtdna.com/site.