Mutation Patterns Predict Drug Response in Acute Myeloid Leukemia

As part of a study correlating co-occurring mutations in Acute Myeloid Leukemia (AML) with drug sensitivity, we performed single cell mutation analysis to document the subclonal composition for 8 patient samples (blood or marrow mononuclear cells) of the 99 patients studied. We utilized the Tapestri Single Cell DNA plus Protein Sequencing Kit (MissionBio) and the 45-gene myeloid panel (MissionBio) for targeted sequencing. Single cells were encapsulated, lysed, and barcoded. DNA and protein libraries were prepared. DNA analysis and sequencing was performed by the University of California Irvine High Throughput DNA Sequencing Core (NCI Shared Resource) on an Agilent Bioanalyzer and Illumina NovaSeq 6000. A total of 294 million to 893 million reads were obtained for each sample. The sequences were analyzed using Tapestri Insights 2.2 software (MissionBio) to provide the characterization of the clonal mutations and distribution. The phenotype was analyzed using Mosaic software (MissionBio). We identified the number of subclones for each patient sample, and found that most exhibited a dominant subclone representing >50% of the subclones, in 6 of the 8 patients. In addition, the variant allele frequency (VAF) by this method correlated with the VAF obtained by NextGen sequencing (MyAML). ]]>
Inclusion: Diagnosis of Acute Myeloid Leukemia]]>
Eight samples from AML patients with known multiple mutations were analyzed by single cell mutation analysis to determine the subclonal composition. The same samples had already been analyzed by high throughput drug screen for sensitivity to about 170 drugs and drug combinations. The single cell mutation data were compared to the sequence data by next gen sequencing (Invivoscribe “My AML” panel). ]]>