Comprehensive Genomic Profiling of Chinese Acute Myeloid Leukemia (AML) with FLT3 ITD Using Ultra Deep Sequencing

In this study, we sequenced 26 FLT3-ITD AML samples to show genomic profiling with multiple mutations types and discover the mutations associated with FLT3-ITD based on in-house bioinformatics mutation calling pipelines.Methods: DNA was extracted from blood or bone marrow of AML FLT3-ITD positive samples. Those DNA samples were subjected to comprehensive genomic profiling (CGP) assay consisting of whole exon coding region in 450 tumor actionable or cancer driver genes as well as selected introns (N=244) from 39 genes frequently involved in gene rearrangement using hybridization target capture and next generation sequencing (NGS) technologies and in house established bioinformatics pipelines. Somatic genomic alterations including SNV, short/long Indel, CNV and gene rearrangement were analyzed. Libraries were constructed with KAPA Hyper Prep kit( KAPA Biosystems), and hybridized to customized capture probes( Integrated DNA Technologies)and then sequenced on NovaSeq 6500 (Illumina). The mutation is detected with VAF of no less than 1% of point mutation, insertion and deletion, including long insertion and deletion( long indel). Long indel variants from 10bp-2kb were called with OriLindel algorithm, which is in silicon developed for structure variation calling, especially for FLT3-ITD variants calling.Results: In this study, we sequenced 26 FLT3-ITD AML samples to show genomic profiling with multiple mutations types. The average sequencing depth of 26 samples is above 700X(720-23...
Source: Blood - Category: Hematology Authors: Tags: 617. Acute Myeloid Leukemia: Biology, Cytogenetics, and Molecular Markers in Diagnosis and Prognosis Source Type: research