title: Illumina HiSeq 2000 paired end sequencing; Whole exome sequencing analyses of human, IDH2-mutated, acute myeloid leukemia samples from patients before or during treatment with Enasidenib.
design: Whole exome sequencing analyses of human, IDH2-mutated, acute myeloid leukemia samples from patients before or during treatment with Enasidenib.
library_construction_protocol: Bone marrow or blood samples from AML patients were collected by the Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP) of Gustave Roussy (Villejuif, France) according to Institutional Review Board-approved protocols. Informed consent was obtained from all patients, in accordance with the Declaration of Helsinki. Mononuclear cells were isolated by Ficoll density gradient, resuspended in 90% FCS/10% DMSO solution and viably frozen in liquid nitrogen. After thawing, cells were washed with DPBS (Gibco) supplemented with 2% FBS, stained with the PE-Cy7-conjugated anti-human CD45 antibody (clone HI30, BD Biosciences), the FITC-conjugated anti-human CD3 antibody (clone HIT3a, Biolegend) and the APC-conjugated anti-human CD34 (clone 581, BD Biosciences) antibody, and sorted using a BD Influx Cell Sorter (BD Biosciences). The treatment protocol is detailed in publications here: Stein, E. M. et al. Enasidenib in mutant IDH2 relapsed or refractory acute myeloid leukemia. Blood 130, 722-731, doi:10.1182/blood-2017-04-779405 (2017) and Amatangelo, M. D. et al. Enasidenib induces acute myeloid leukemia cell differentiation to promote clinical response. Blood 130, 732-741, doi:10.1182/blood-2017-04-779447 (2017).  Regarding the time point of enasidenib treatment: the "C" in C10D1 stands for "cycle". The "D" stands for "Day". One cycle is defined as a 28 days-long period of treatment. C1D1 refers to the first day of treatment. C2D15 would refer to the 15th day within the second cycle of treatment, meaning 43 days total. Characteristic[bet response to enasidenib] is defined as: "PR" stands for "partial response"; "CR" stands for "complete response"; "MLFS" stands for "morphologic leukemia-free state"; "CRp" stands for "CR with incomplete platelet recovery". Genomic DNA from FACS-sorted AML blasts or CD3-positive cells was purified using the Allprep DNA/RNA mini or micro Kits (Qiagen), according to the protocol provided by the manufacturer. Purified genomic DNA was fragmented by sonication. Exome capture was performed with the SureSelect V5 Mb All Exon kit (Agilent), according to the protocol provided by the manufacturer.