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Genome sequencing at Johns Hopkins marks a first for patient-specific cancer care

Erin Podolak

Complete genome sequencing of patients with cancer has led to the development of a blood test that helps physicians determine an appropriate plan of care.

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Researchers at the Johns Hopkins Kimmel Cancer Center have sequenced the complete genomes of cancer patients to create individualized blood tests, which the patients’ physicians then used to tailor their treatments. According to Johns Hopkins, the genome-based patient-specific tests are the first instance of clinically viable patient-specific medicine. The test looks for rearrangements of sections of the genome—which can indicate the presence of tumors—to monitor the growth of tumors, determine appropriate levels of therapy, and show instances of recurrence.

“We believe this is the first application of newer generations of whole-genome sequencing that could be clinically useful for cancer patients,” Victor Velculescu, associate professor of oncology and co-director of the Cancer Biology Program at Johns Hopkins, said in a press release. “Using this approach, we can develop biomarkers for potentially any cancer patient.”

A new blood test can be used to screen for cancer. Source: National Cancer Institute.

Previously, sequencing genomes to look for cancer biomarkers focused on identifying single nucleotide mutations. This was problematic because there are billions of single nucleotides in the human genome, and identifying the correct mutations that would lead to cancer was time consuming and complex. In their new approach, the researchers searched for rearrangements of larger sections of DNA, in a technique called personalized analysis of rearranged ends (PARE).

The rearrangement of sections of DNA is a widely known trait in cancer cells, which makes it a good biomarker. “These alterations, like the reordering of chapters of a book, are easier to identify and detect in the blood than single-letter changes,” said Bert Vogelstein, professor of oncology and co-director of the Ludwig Institute at Johns Hopkins University.

The researchers extracted DNA from cancerous and normal tissues of four colorectal and two breast cancer patients. The samples were sequenced using the Sanger method to serve as a reference. Applied Biosystems’ SOLiD system, which uses a sequencing-by-ligation approach, was used to create libraries of mate-paired tags which were then amplified by emulsion PCR. An average of 198.1 million 25-bp reads was obtained from each sample.

To identify rearrangements in the tumor tissue, the researchers used a copy-number analysis to identify which regions of the genome contained either more or fewer copies of DNA than were anticipated, and which regions contained chromosomes that were fused together. Further analysis, by comparing the samples with their normal tissue counterpart, revealed specific sections of the genome that displayed incorrect ordering, orientation, and spacing. A range of 4–15 rearrangements was found in each of the six samples, serving as unique PARE-based biomarkers for each patient.

After identifying the genetic rearrangements in the tumor samples, the researchers looked for the same mutations in DNA shed from the tumors into the patients’ blood. Blood samples were taken from two of the colorectal cancer patients and sequenced in a similar method as the tumors. The blood sample analysis identified the same biomarkers as the tumor sample analysis.

According to the researchers, PARE-based biomarkers can inform physicians if a patient has cancer and how best to treat it. The test can also be applied to evaluate if cancer cells are present at surgical margins or lymph node tissue removed during surgery. This would lead to earlier diagnosis of the disease. “Eventually, we believe this type of approach could be used to detect recurrent cancers before they are found by conventional imaging methods, like CT scans,” Luis Diaz, assistant professor of oncology at Johns Hopkins, said in a press release.

Current trends in genome sequencing technology indicate that researchers are getting closer to the landmark $1000 genome. Velculescu said that achieving this milestone would make their blood test even more useful in a clinical setting. Sequencing for this research cost approximately $5,000 per patient. But since conventional cancer detection methods like a CT scan still cost approximately $1,500, a $1000 technique would be a viable alternative.

The team from Johns Hopkins will continue testing samples obtained from cancer patients to refine the technique, and has filed for patents in order to refine the technology into a commercially available genome-based blood test for cancer.

The research was funded by the National Institutes of Health, the Lustgarten Foundation, the National Colorectal Cancer Research Alliance, and a fellowship with UNCF-Merck. The paper, “Development of personalized tumor biomarkers using massively parallel sequencing,” was published Feb. 24, in Science Translational Medicine.