Abstract 5609: Next generation sequencing in acute myeloid leukemia: Correlation with cytogenetic studies highlighting different spectrums of mutations
Authors: Robert B. Daber, Jianhua Zhao, Martin Carroll, Craig Solderquest, Selina Luger, Gerald B.W. Wertheim, Adam Bagg, Jennifer J.D. Morrissette
Journal: Cancer Research (2014)

Abstract Acute myeloid leukemia (AML) represents a heterogeneous group of aggressive myeloid malignancies characterized by the accumulation of blasts in the bone marrow. The prognosis of AML is variable, likely reflecting its diversity at a genetic level. The pathogenesis of AML has not been completely defined; however it is clear that recurrent chromosomal abnormalities (e.g., translocations and numeric abnormalities) and genetic events (e.g., point mutations and indels) are necessary for disease development. Genetic changes are diverse and consist of large genomic changes such as rearrangements and ploidy anomalies, as well as submicroscopic changes, including point mutations and indels. Few studies have correlated cytogenetically detected anomalies with molecularly detected mutations in AML. Here we describe our experience using a hematological next generation sequencing (heme-NGS) panel in conjunction with conventional cytogenetic studies to interrogate diagnostic AML specimens in a routine clinical setting. Next generation sequencing was done using a custom designed amplicon panel and Illumina TruSeq Custom Amplicon (TSCA) capture. Using a customized bioinformatics pipelines we were able to detect single nucleotide variants (SNV) and small insertion/deletion (indel) to a lower limit of 5% with 100% sensitivity and specificity. 28 genes recurrently mutated in myeloid malignancies were examined including targeted regions of NPM1, FLT3, KIT, PTPN11, NRAS, IDH1, IDH2, JAK2, DNMT3a, EZH2, PTEN, CEBPA, TP53, WT1, RUNX1, TET2, ATM, BRAF, CBL, MPL, SF3B1, ASXL1, HRAS, KRAS, PHF6, GNAS, ETV6 and MYD88. Over 100 specimens were analyzed by NGS and cytogenetics , with only a single case being ‘normal’ by both tests. Comparison of mutation-positive AML demonstrated more mutations present in cytogenetically normal cases, compared with those with chromosome abnormalities detected. Conversely, in 11 cases no mutations were detected by heme-NGS, with 10/11 of these cases showing recurrent cytogenetic abnormalities. In those cases where NGS mutations were identified, comparison of cases with normal (CN-AML) and abnormal (CA-AML) cytogenetic studies demonstrated different mutation frequencies, with more mutations detected in CN-AML. Interestingly, TP53 was the most commonly mutated gene in CA-AML and least mutated in CN-AML. These results illustrate the complementary information gained from NGS sequencing performed with conventional cytogenetic studies in diagnostic AML specimens, providing a comprehensive picture of the genomic landscape in this disease. A complete description of these combined cytogenetic and molecular abnormalities seen in AML and correlation with clinical features will be presented. Citation Format: Robert B. Daber, Jianhua Zhao, Martin Carroll, Craig Solderquest, Selina Luger, Gerald B.W. Wertheim, Adam Bagg, Jennifer J.D. Morrissette. Next generation sequencing in acute myeloid leukemia: Correlation with cytogenetic studies highlighting different spectrums of mutations. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5609. doi:10.1158/1538-7445.AM2014-5609