MRD in a Mouse Model of RUNX1-mutated CN-AML
Purified genomic DNA was quantified using the Qubit Flourometer (ThermoFisher, Waltham, MA) and quality was assessed with the gDNA tapestation assay (Agilent Technologies, Santa Clara, CA).  Whole exome libraries were generated using SureSelectXT Whole Exome v5 (+UTRs) per manufacturer’s recommendations (Agilent Technologies, Santa Clara, CA).  Briefly, 4ug of good quality genomic DNA was sheared with Covaris S2 (Covaris, Woburn, MA) to a average peak size of 250bp followed by end repair, poly adenylation, Illumina adaptor ligation, and purification with AmpureXP (Beckman Coulter, Brea, CA).  Library amplification was carried out with 250ng of purified DNA with 4 cycles of PCR followed by AmpureXP purification (Beckman Coulter, Brea, CA).  Exome probe hybridization capture was performed per manufacturer’s protocols.  Exome target enriched samples were quantified using the Qubit Flourometer (ThermoFisher, Waltham, MA) and library sizing was assessed with the high sensitivity Bioanalyzer 2100  DNA assay (Agilent Technologies, Santa Clara, CA).  Whole exome libraries were normalized, pooled and 2x100 pair end sequencing was performed with the HiSeq2500 ((Illumina, San Diego, CA).