Melanoma study with SNV Aggregate (.MAF), Targeted-Capture + 1 more data on dbGaP (9 participants)

phs003447 — MAESTRO-Pool Enables Highly Parallel and Specific Mutation-Enrichment    Sequencing for Minimal Residual Disease Detection in Cohort Studies

<p>MAESTRO-Pool builds upon the technology MAESTRO (Minor Allele Enriched Sequencing Through Recognition Oligonucleotides) by pooling tumor-specific MAESTRO probes from multiple patients and applying these to all samples from all patients. In this study, MAESTRO-Pool was applied to a cohort of 9 melanoma patients where 98 plasma samples were screened for 22,333 mutations. Additionally, a new dynamic minimal residual disease (MRD) caller was used to estimate the likelihood of MRD detection based on the number mutations and cell-free DNA molecules interrogated which allowed each bespoke MRD test to be properly calibrated against false detection. These developments led to sensitive detection in patient-matched samples down to 0.78 parts per million (ppm) while limiting false detection in negative controls to 1/784 (tumor fraction=2.7 ppm). MAESTRO-Pool and the dynamic MRD caller enable a unique blend of sensitivity, specificity, and efficiency, which will improve the ability to detect MRD.</p><p>The data contained in this repository consists of:</p><ol><li>Tumor and normal whole genome sequencing data used to call patient-specific tumor mutations and design the MRD Tracker and MAESTRO-Pool fingerprints</li><li>MAESTRO-Pool data (enriched duplex sequencing via hybrid capture) of tumor gDNA, normal gDNA and cfDNA </li><li>MRD Tracker data (duplex sequencing via hybrid capture) of tumor gDNA, normal gDNA and cfDNA </li></ol>