CAP TODAY Pathology/Laboratory Medicine/Laboratory Management
William Check, PhD
November 2013—When it comes to home improvement projects, we all have our own comfort level. Some of us order a load of lumber and build a new addition to our home; others limit themselves to assembling a bookcase from Ikea. And there are those who leave everything to professionals.
Dr. Kulkarni, right, and colleagues use a panel to do NGS-based diagnostic testing of cancer genes. “We focus on those genes and variants where clinical utility is unequivocal,” says Dr. Kulkarni, here at Washington University with Dr. Mardis, co-director of The Genome Institute.
For clinical laboratory directors who are planning to adopt next-generation sequencing to help with the diagnosis of cancer and guidance of therapy, there are degrees of involvement, too, from commercial multigene panels that can be run on smaller, less expensive platforms to whole exome or whole genome sequencing, which require more powerful instruments and bioinformatics expertise. Ordering out is also an option, now that reference laboratories are adding NGS testing to their menus.
Being able to access NGS at various levels that match almost any clinical laboratory’s expertise is a great boon, since this new technology offers impressive advantages. “Today we are able to do high-throughput sequencing of multiple genes in many solid tumors that we would not have been able to sequence even two years ago. And we can do it in a cost-effective manner,” says Shashikant Kulkarni, PhD, director of cytogenomics and molecular pathology, Department of Pathology and Immunology, and a clinical genomicist, Genomics and Pathology Services, Washington University School of Medicine. “We can put together different genes that are amenable to therapy and offer them on various tumor types.”
Elaine Mardis, PhD, professor of genetics and molecular microbiology and co-director of The Genome Institute, Washington University School of Medicine, makes the case for broader clinical application of NGS, including whole exome and whole genome sequencing: “With a panel of genes or whole genome sequencing we are able to look at more alterations that might be driving the patient’s cancer than with non-NGS methods, so the inquiry is significantly broader for lower price and faster turnaround time.”
Dan Jones, MD, PhD, medical director of cancer diagnostic services at Quest Diagnostics Nichols Institute, Chantilly, Va., says, “This is a rapidly evolving field. We are starting to see real utility and value and to be able to get an answer more quickly than with previous methods.”
How rapidly the field is evolving is “almost a joke,” says Toumy Guettouche, PhD, director of sequencing in the Center for Applied Genomics at Children’s Hospital of Philadelphia. “A year in the genomics field is an eternity,” he explains. “Two years ago when you went to AMP [Association for Molecular Pathology meeting], people were asking what NGS is. Even last year it was not really that common. Now almost every talk includes some form of next-gen sequencing.”
“There has been a wave of adoption of NGS,” Dr. Guettouche adds, calling it “great but also scary” in that some may not appreciate its complexity and how difficult it is to do it well.