AML-MutationCounter, a tool to detect residual and recurrent leukemia

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Abstract AsystBio LLC proposes to market a molecular tool kit called AML-MutationCounter to count somatic mutations in genes that contribute to the development of acute myeloid leukemia (AML). We have developed a set of reagents and computer programs for application of next-generation sequencing to count AML gene mutations. The tool kit is versatile and can be used with either of the two major DNA sequencing platforms, Illumina Hi- Seq and ThermoFisher Ion Proton. Every year AML afflicts 20,000 Americans with nearly 10,000 dying from the disease. Many patients respond to primary therapy and achieve clinical remission. Remission is currently determined by a reduction of leukemic blasts in bone marrow to <5% of cells. A more sensitive and specific test for remission may guide clinicians to achieve more durable remission and improve stratification of patients for likelihood of relapse. One recent study found that forty eight percent of patients in remission retained AML gene mutations in >2.5% of marrow or blood cells and these patients’ survival was on average 25% of that seen in patients who cleared mutations to <2.5% during remission. Thus the presence or absence of residual disease at remission is highly prognostic. Patients who receive a bone marrow transplant after remission sometimes display emerging clones of host bone marrow, termed bone marrow chimerism. It is important to determine whether these emerging clones represent recurrent leukemia as early as possible to implement salvage therapies. Our advisory panel of oncologists at the University of North Carolina and NC Memorial Hospital expresses enthusiasm for a sensitive, accurate, rapid and low-cost test for residual and recurrent leukemia. Studies in this Phase I STTR grant application will involve a collaboration between AsystBio LLC and the University of North Carolina at Chapel Hill to produce a molecular tool kit for measurement of AML- associated somatic gene mutations in bone marrow specimens. Studies in Aim 1 will establish the accuracy, sensitivity and reproducibility of the kit for quantification of mutant allele frequencies using simulated data and a standard reference cell line. Studies in Aim 2 will apply the tool kit to 10 patient samples that were collected at the time of remission before a subsequent recurrence of leukemia. Samples are selected to include the NPM1 leukemia-driver gene mutation in the primary cancer. The presence of mutations in NPM1 in remission samples is a poor prognostic sign. We will show that our kit detects mutations in NPM1 and other AML- associated genes at remission in patients that were destined to relapse. This phase I project demonstrates the feasibility of AML-MutationCounter for detection of minimal residual and recurrent disease in AML. Our phase II commercialization plan will include a clinical trial to establish the utility of the test kit as well as active marketing of the test kit to academic medical centers and commercial test laboratories.