Detection of Dual IDH1 and IDH2 Mutations by Targeted Next-Generation Sequencing in Acute Myeloid Leukemia and Myelodysplastic Syndromes

Abstract

Studies in myeloid neoplasms have described recurrent IDH1 and IDH2 mutations as primarily mutually exclusive. Over a 6-month period of clinical testing with a targeted next-generation sequencing assay, we evaluated 92 patients with acute myeloid leukemia, myelodysplastic syndrome, and chronic myelomonocytic leukemia and identified a subset of 21 patients (23%) who harbored mutations in either IDH1 or IDH2. Of the 21 patients with IDH mutations, 4 (19%) were found to have single nucleotide variants in both IDH1 and IDH2. An additional patient included in the study was found to have two different IDH2 mutations. The mutations were typically present at different variant allelic frequencies, with one predominating over the other, consistent with the presence of multiple subclones in a single patient. In one case, the variant allelic frequencies in both IDH1 and IDH2 were equally low in the setting of a high percentage of blasts, suggesting that the IDH mutations were unlikely to be present in the founding clone. Given these data, we conclude that dual IDH1/2 mutations likely were previously underestimated, a finding that may carry important treatment implications. (J Mol Diagn 2015, 17: 661e668; http://dx.doi.org/10.1016/j.jmoldx.2015 In recent years, whole-genome sequencing of acute myeloid leukemias (AMLs) led to the identification of frequent heterozygous mutations in isocitrate dehydrogenase 1 gene (IDH1).1,2 Subsequent exome sequencing and targeted resequencing studies in AML also identified frequent IDH2 mutations. 3,4 Overall, approximately 15% to 30% of AML have mutations in IDH1 or IDH2, almost exclusively at codon Arg132 for IDH1 and at codons Arg140 and Arg172 for IDH2.1,3e6 Patients with cytogenetically normal AML are enriched for these mutations. The mutations confer neomorphic enzyme activity through the NADPH-dependent reduction of the normal end-product a-ketoglutarate to the putative oncometabolite 2-hydroxyglutarate. The accumulation of high levels of 2-hydroxyglutarate in the IDH1/2-mutant tumor provides an important mechanism of cellular transformation through the targeting of epigenetic regulators. 7IDH mutations were also identified in preleukemic clonal malignancies, including myelodysplastic syndromes (MDSs) and myeloproliferative neoplasms (approximately 5% of MDS/myeloproliferative neoplasm and approximately 20% of AML arising from MDS or myeloproliferative neoplasm).

Isocitrate dehydrogenase mutations in myeloid malignancies

“… 1 , 8 , 10 , 32 , 33 IDH1 and IDH2 mutations only rarely co-occur in the same patient. 34 , 35 In myeloid malignancies, IDH1 mutations most often involve a cysteine (R132C) or histidine (R132H) substitution for arginine at R132. IDH2 -R140 mutations are more common than IDH2 -R172 mutations, representing ~80% of IDH2 mutations in AML.…”

Evolving Treatment Strategies for Elderly Leukemia Patients with IDH Mutations

“…The reported frequency of mIDH in AML varies, ranging from 7–14% for IDH1 and 8–19% for IDH2 , and mutations of either isozyme have been reported in up to 33% of collective cases [ 33 , 34 , 35 , 36 ]. Co-occurring mutations in both isozymes have been reported to be rare, but more recent investigation in a sample of patients with AML, MDS, or chronic myelomonocytic leukemia indicates that simultaneous IDH1/2 mutations may occur in up to 19% of mIDH patients [ 37 , 38 , 39 ]. However, one or both genes were detected at low allele frequencies in patients harboring dual mutations and required ultra-deep orthogonal sequencing for confirmation.…”

IDH1 Mutation Is an Independent Inferior Prognostic Indicator for Patients with Myelodysplastic Syndromes

“…Our study showed that all of the identified mutations were mutually exclusive. Notably, a recent study identified dual mutations in the IDH1 and IDH2 genes in MDS via targeted next-generation sequencing [31]. …”