Recurring mutations found by sequencing an acute myeloid leukemia genome

Abstract

Background: The full complement of DNA mutations that are responsible for the pathogenesis of acute myeloid leukemia (AML) is not yet known.

Methods: We used massively parallel DNA sequencing to obtain a very high level of coverage (approximately 98%) of a primary, cytogenetically normal, de novo genome for AML with minimal maturation (AML-M1) and a matched normal skin genome.

Results: We identified 12 acquired (somatic) mutations within the coding sequences of genes and 52 somatic point mutations in conserved or regulatory portions of the genome. All mutations appeared to be heterozygous and present in nearly all cells in the tumor sample. Four of the 64 mutations occurred in at least 1 additional AML sample in 188 samples that were tested. Mutations in NRAS and NPM1 had been identified previously in patients with AML, but two other mutations had not been identified. One of these mutations, in the IDH1 gene, was present in 15 of 187 additional AML genomes tested and was strongly associated with normal cytogenetic status; it was present in 13 of 80 cytogenetically normal samples (16%). The other was a nongenic mutation in a genomic region with regulatory potential and conservation in higher mammals; we detected it in one additional AML tumor. The AML genome that we sequenced contains approximately 750 point mutations, of which only a small fraction are likely to be relevant to pathogenesis.

Conclusions: By comparing the sequences of tumor and skin genomes of a patient with AML-M1, we have identified recurring mutations that may be relevant for pathogenesis.

Figure 1. Flow Chart for Identification of Somatic Point Mutations in the Acute Myeloid Leukemia Genome

Maq denotes Mapping and Assembly with Quality, SNP single-nucleotide polymorphism, and SNV single-nucleotide variant.

Figure 2. Allele Frequency in Tumor DNA, Tumor Complementary DNA, and Skin DNA

Panel A shows the percentage of variant alleles that were detected in tumor DNA, tumor complementary DNA (cDNA), and skin DNA for the 10 validated nonsynonymous tier 1 somatic mutations in the index patient. For comparison, variant allele frequencies are shown for six known single-nucleotide polymorphisms (SNPs). The patient was homozygous for the reference sequence for the first two variants, heterozygous for the next two variants, and homozygous for a rare SNP for the last two variants. Panel B shows variant allele frequencies for all validated tier 1 and tier 2 mutations and the six control SNPs for tumor DNA and skin DNA.