Targeted TMB assessment
November 2018
by Ilene Schneider  |  Email the author

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PORTLAND, Ore.—MolecularMD, a diagnostics company that enables the development and commercialization of precision medicines in oncology, has validated Thermo Fisher Scientific’s Oncomine Tumor Mutation Load (TML) Assay for clinical research trials to facilitate immunotherapy drug development programs for the pharmaceutical industry. Tumor mutation burden (TMB) analysis, often described as the latest approach in immuno-oncology, is becoming an independent predictor for patient stratification and response to immunotherapies, such as checkpoint inhibitors.
 
The Oncomine Tumor Mutation Load Assay is available to MolecularMD’s clients involved in translational research and clinical trials. The company is doing additional studies to determine the clinical utility of TMB analysis for predicting patient response to checkpoint inhibitors.
 
According to Dr. Cindy Spittle, vice president of development and scientific affairs at MolecularMD, “The methods used so far to assess tumor mutation burden in clinical studies have included whole-exome sequencing and several laboratory-developed, targeted next-generation sequencing panels, but in order to fully determine the value of TMB as a predictive biomarker, a standardized panel, workflow and data analysis pipeline for TMB assessment is needed.”
 
She added, “The Oncomine Tumor Mutation Load Assay is unique in that it is the first commercially available assay that is designed for assessing TMB in formalin-fixed paraffin-embedded (FFPE) samples that can be validated by a clinical laboratory for use as a laboratory-developed test. Since the reagents and software are provided for the end to end workflow, labs that adopt the method will be able to provide standardized TMB analysis. The TML Assay is also unique in that the AmpliSeq-based chemistry is superior to probe-based capture when using FFPE-derived DNA. The amount of tumor tissue that is available for clinical lab testing is typically very limited, so the low DNA input requirement of 20 ng is ideal.”
 
According to Spittle, the quality of DNA extracted from FFPE tissue can be poor. Because MolecularMD supports global clinical trials and receives tissue samples from all over the world, the quality of those samples can be “quite variable.”
 
As she explained, “We must be able to provide robust methods that will allow the highest rate of successful testing and accuracy possible. Therefore, we have incorporated stringent data QC and review processes into all of our NGS and PCR assay workflows. For TMB analysis, deamination errors that are generated during the PCR steps can artificially inflate the TMB count. Our lab has developed an alternative workflow that allows for accurate analysis of poorer quality samples. Deamination errors are not reproducible, so by running the samples in duplicate and modifying the data analysis pipeline we are able to filter out the false positive results. This will allow more patient samples to be successfully tested for TMB and potentially identify more patients who could benefit from checkpoint inhibitor therapies.”
 
Major considerations for MolecularMD’s selection of an assay for clinical research studies and diagnostic applications were sample quantity and quality requirements. Thus, MolecularMD can leverage the RecoverAll Total Nucleic Acid Isolation Kit for DNA/RNA dual extraction to maximize the amount of data that can be obtained from a minimal amount of tissue. Using a targeted panel approach reduces the amount of input material, minimizing the amount of tumor tissue needed for TMB testing as compared to other methods, according to Spittle.
 
Early in its evolution, MolecularMD developed an alternative workflow and quality control method for deamination errors in certain cases. Determining that samples of the poorest quality—which sometimes contain these errors—can overestimate TMB, MolecularMD came up with a modified approach that leverages duplicate sample runs and proprietary bioinformatics to filter out and reduce false positive variant calls.
 
“By building on the successes and lessons learned in the early days of targeted therapy in CML, MolecularMD has become a leader in providing biomarker assays and diagnostics to support oncology drug development,” Spittle remarked. “As targeted drug development evolved into solid tumors, the biomarker landscape also evolved beyond single mutation analysis. The biomarker assay landscape has continued to evolve with immunotherapy. By focusing on oncology, we have been able to anticipate and monitor these changes and rapidly expand our technology platforms. By focusing on pharma and biotech, we also implemented a comprehensive QMS that could meet the demands of drug and diagnostic assay co-development. In keeping with the evolving regulatory guidance our conversations with our pharma and biotech partners have also evolved to include regulatory planning, even at very early stages of the drug program.”
 
She concluded, “MolecularMD will continue to build upon its foundational capabilities and will scale to meet the needs of our clients. We will continue to address their unmet needs as they arise.”
Code: E111821

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