A group at the Fred Hutchinson Cancer Research Center has developed a high throughput sequencing platform to detect minimal residual disease in patients with T cell acute lymphoblastic leukemia that could be more accurate and cost effective than current approaches. The team has spun out Adaptive Biotechnologies Corp. to develop the technology.

Previous T-ALL studies have shown that minimal residual disease (MRD), or cancer cells that remain in circulation following treatment, can be a good indicator of patient outcomes and risk of relapse. Current strategies to detect MRD-flow cytometry and quantitative PCR-each measure the amount of cancer cells remaining in the blood or bone marrow after treatment, but both have limitations, according to Adaptive cofounder and Fred Hutchinson associate member Harlan Robins.

"There are four primary difficulties with using flow cytometry for measuring MRD. First, it has been difficult to standardize across different labs because there is not one established protocol. Second, the antibodies used to tag the cancerous cells are expensive. Third, every cancer type requires a different test because the protein markers vary for each disease. Finally, the sensitivity is low, which means that cancerous cells are sometimes not recognized," he said.

Allele-specific quantitative PCR involves isolating and amplifying the cancer clone in each patient and is slow-taking more than a month to design, create and test an assay for each patient, he added.

His team opted for a third approach to detect MRD-relying on the often unique gene rearrangements that occur in T cell receptors (TCRs) as a result of the disease. Robins and colleagues reasoned that genotyping TCR loci could help diagnose T cell malignancies and that the genetic information obtained from high throughput sequencing of the regions could help determine whether cancer cells persist after treatment.

In 43 T-ALL samples taken at the time of diagnosis and before treatment, complete sequencing of the T cell receptor b-chain (TCRB) region detected specific gene rearrangements in 31 of the samples.

Using matched blood samples from the same patients 29 days after treatment, the team screened each sample for the patient-specific TCRB sequences to determine whether cancer cells were still present. The screening method identified 22 cases of MRD, including 10 that were not detected by conventional flow cytometry. In nine cases, neither method detected MRD.

Robins noted that the assays used in this paper limited the researchers to studying 200,000 cells. "We could certainly have sequenced more blood or bone marrow cells and found the rare clones in some of the patients with no reported MRD," he said. But "below the level of 1 cancerous cell in 100,000, no data exist on correlation with clinical outcome. So, if we tested for one cancer cell in a million, we would not have information on prognosis."

He added that other versions of the company's assay are capable of sequencing more than 10,000,000 cells.

Results were published in Science Translational Medicine.1

"The next steps to move this strategy towards the clinic are to broaden the research to a larger patient population, follow the patients for a longer period of time to demonstrate a correlation between the detection of MRD and survival and expedite the run time on sequencing machines from weeks to days," said Robins.

He added that Adaptive already is running studies on cells from many more patients with a variety of T and B cell cancers. The company is involved with at least 4 trials that will enroll a total of 500-1,000 patients each.

The company hopes to have its lab CLIA certified by year end and to have its MRD assay, dubbed immunoSEQ, available for clinical use within a year.

Measuring MRD is the first of several potential clinical uses of high throughput immune sequencing in oncology. ImmunoSEQ, which sequences T and B cell receptor chains, also is being used to segment patients according to likelihood of response to cancer immunotherapeutics, said Robins.

"Beyond oncology, immunoSEQ is also being studied to identify and develop immunologic biomarkers in various autoimmune diseases such as multiple sclerosis, Crohn's disease and lupus," he added. "Adaptive is also developing a second assay platform, called quanTILfy, to measure the quantity and activity of immune cells in solid tumors."

Adaptive's quanTILfy is a platform to sequence and quantify tumor-infiltrating lymphocytes (TILs).

Adaptive has filed patent applications and licensed patents from Fred Hutchinson covering the TCR sequencing platform. The IP is not available for licensing.

Martz, L. SciBX 5(24); doi:10.1038/scibx.2012.620
Published online June 14, 2012


1.   Wu, D. et al. Sci. Transl. Med.; published online May 16, 2012; doi:10.1126/scitranslmed.3003656
Contact: Harlan Robins, Fred Hutchinson Cancer Research Center, Seattle, Wash.
e-mail: hrobins@fhcrc.org
Contact: Brent L. Wood, University of Washington, Seattle, Wash.
e-mail: woodbl@u.washington.edu


Adaptive Biotechnologies Corp., Seattle, Wash.

Fred Hutchinson Cancer Research Center, Seattle, Wash.