DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Abstract

Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little in the past two decades, because most of the genetic events that initiate the disease remain undiscovered. Whole-genome sequencing is now possible at a reasonable cost and timeframe to use this approach for the unbiased discovery of tumour-specific somatic mutations that alter the protein-coding genes. Here we present the results obtained from sequencing a typical acute myeloid leukaemia genome, and its matched normal counterpart obtained from the same patient's skin. We discovered ten genes with acquired mutations; two were previously described mutations that are thought to contribute to tumour progression, and eight were new mutations present in virtually all tumour cells at presentation and relapse, the function of which is not yet known. Our study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.

Figure 1. Overlap of SNPs detected in 933124 and other genomes

(A) Venn diagram of overlap between SNPs detected in the 933124 tumor genome and the genomes of Watson and Venter. (B) Venn Diagram of overlap among 933124 tumor genome, skin genome, and dbSNP (ver. 127). Single nucleotide variants were defined with a MAQ SNP quality ≥ 15.

Figure 2. Filters used to identify somatic point mutations in the tumor genome

See text for details.

Figure 3. Summary of Roche/454 FLX readcount data obtained for 10 somatic mutations and 2 validated SNPs in the primary tumor, relapse tumor, and skin specimens

The readcount data for the variant alleles in the primary tumor sample and relapse tumor sample are statistically different than that of the skin sample for all mutations (p<0.000001 for all mutations, Fisher’s exact test, denoted by a single asterisk in all cases). Note that the normal skin sample was contaminated with leukemic cells containing the somatic mutations. The patient’s WBC count was 105,000 (85% blasts) when the skin punch biopsy was obtained.