Zooming in on Cancer Suspects

By Barbara J. Toman • August 20, 2018

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Genetic testing is like security-camera video footage of a break-in, providing essential clues to identify a culprit. In certain cancers, the "culprit" might be a rearrangement in a person's DNA, which genomic testing can capture.

But sometimes, like too-fuzzy security footage, genetic testing can't provide a positive identification. For people with cancer, the stakes are high because pinpointing the chromosomal problem may lead to a more effective treatment.

Mayo Clinic has developed a novel group of clinical tests that zoom in on a person's genome to characterize chromosomal rearrangements. The testing, available through Mayo’s global reference laboratory Mayo Medical Laboratories, was developed in conjunction with the Center for Individualized Medicine (CIM) and the Department of Laboratory Medicine and Pathology (DLMP). It relies on a technique known as "mate-pair sequencing."

"Our mate-pair sequencing testing can characterize almost any chromosomal rearrangement. We can finally answer questions about suspicious rearrangements of important genes," says Nicole Hoppman, Ph.D., a medical geneticist who helped develop the tests.

Mate-pair sequencing is performed after initial testing indicates a chromosomal abnormality. "The initial chromosome studies can tell us where a chromosomal rearrangement is located but not the specific gene content of the rearrangement," Dr. Hoppman says.

Another test, known as fluorescence in situ hybridization (FISH), can provide that gene-level information. "But FISH isn't a genome-wide test, and we often have questions about more than one region of a person's genome," Dr. Hoppman says.

Mate-pair sequencing provides genome-wide, gene-level information. The entire genome is sequenced, but analysis is restricted to regions where an abnormality was found. "Mate-pair sequencing can clarify in a single test the abnormalities seen by chromosome studies or FISH," Dr. Hoppman says.

Personalized Cancer Therapy

Mate-pair sequencing can directly impact patient care. One example at Mayo Clinic is a pediatric patient who experienced a relapse of B-cell acute lymphoblastic leukemia.

FISH studies indicated a disruption of a gene known as ETV6, which is common in many types of cancer. Genetic disruptions typically involve pairs of genes, and the effects of the disruption depend on both of the specific genes involved. ETV6 has many possible partners in cancer, and in this case, chromosome and FISH studies couldn't identify the partner.

But mate-pair sequencing did just that. The identified partnership is rare yet can be treated with a certain class of cancer therapy. "The mate-pair result led to additional treatment options for the patient," Dr. Hoppman says.

Mayo Clinic's mate-pair sequencing tests are designed to detect chromosomal rearrangements not only in leukemia but also in various types of lymphoma, certain solid-tumor cancers, and inherited abnormalities. This testing is more efficient than other genomic-sequencing strategies because it uses larger pieces of DNA as input material. Analyzing this type of data requires a sophisticated algorithm, which CIM and DLMP researchers spent years developing.

As a whole-genome test, mate-pair sequencing can keep pace with ongoing advances in individualized medicine. "If researchers make a new discovery that a gene is important, and a person has already had mate-pair sequencing, we have all the data we need," Dr. Hoppman says. "We can go back and analyze another region in the person's genome.

"Mate-pair sequencing is nimble," she adds. "It allows us to add targets and answer patients' questions faster when there's a new discovery. Better answers can lead to a better treatment."

Originally published on the Individualized Medicine blog.

Barbara J. Toman

Barbara J. Toman is a Senior Communications Specialist at Mayo Clinic Laboratories. She is also the science writer for Mayo’s Neurosciences Update newsletter, which helps referring physicians to stay informed about Mayo’s treatment and research. Barbara has worked at Mayo Clinic since 2007. She enjoys international travel and cooking.