Development and Validation of Liquid Biopsy ddPCR and Next Generation Sequencing Assays for Diffuse Midline Glioma, K27M Variant

PROJECT SUMMARY ABSTRACT Diffuse intrinsic pontine gliomaDIPGaffecting an estimatedchildren in the United States per yearis one of the deadliest cancers of any typeThe median survival for children with DIPG is less than one year from diagnosiswhich has not changed in three decadesThe diagnosis of DIPG is typically made using clinical symptoms and magnetic resonanceMRscansBecause of the location of the tumors in the brainstemdiagnostic biopsies are typically avoidedalthough MR guidedstereotactic needle biopsies are available in a few specialized centersMissense mutations in Histonegenes HH F A KMor HHIST H B KMare present in most DIPGs and represent an early tumorigenic eventThe World Health OrganizationWHOnow classifies DIPG and non pontine midline gliomas together as a distinct pathologic group known as diffuse midline gliomaH KmutantDMGChildren with H F A mutant tumors are more resistant to radiotherapy and relapse earlier than HIST H B C mutant tumorsDocumentation of either H Kmutation determines eligibility for clinical trial use of HKdemethylase and histone deacetylasesFurthera preliminary study published by collaborators in this proposal showed thatof children with H Kmutant tumors had detectable circulating tumor DNActDNAin plasma and mutant allele frequency in plasma correlated with tumor volume measured by MR scansdecreased with initial response to therapyand increased upon tumor progressionResourcePath is developing DMG Dxa digital droplet PCRddPCRassay for diagnosisgenotyping and monitoring of midline malignant glial neoplasms of childhood in cerebrospinal fluid and or plasma samplesi eliquid biopsyThe ddPCR assay uses advancedlocked nucleic acid probe chemistry to achieve exquisitely sensitive and specific histone HH F A KMor histone HHIST H B C KMhotspot mutations which define DMGOur long term goal is to develop DMG Dx as non invasive and precise diagnostic tests that will improve clinical management and support drug development for pediatric brainstem gliomasThis liquid biopsy will serve three unmet needsobtain diagnostic information without having to perform invasive and risky biopsies available only at special centersdetermine eligibility for clinical trials andserve as a therapeutic response biomarker providing objective information important to clinical trial of novel agents including immunotherapyIn this SBIR Phase I the aims arePerform analytic validation of DMG Dx ddPCR assays for sensitive detection of H Kmutations for diagnosis andDetermine reliability of these assays for quantitative measurement in tumor monitoring indicationsIn Phase II we will clinically validate the DMG Dx in the context of multiple clinical trialsDMG Dx will be marketed by direct outreach to the international community of pediatric oncologists and neurologists who care for individuals with diffuse midline gliomas PROJECT NARRATIVE Diffuse midline gliomaDMGaffecting an estimatedchildren in the United States per yearis one of the deadliest cancers of any typeThe median survival for children with DMG is less than one year from diagnosisResourcePath is developing ultrasensitive tests to detect DMG specific tumor mutations in blood and cerebrospinal fluid which will be useful in diagnosisprognosis and monitoring tumor response to therapy