Oncogenes, Fusion Genes and Tumor Suppressor Genes

Targeted next-generation sequencing detects point mutations, insertions, deletions and balanced chromosomal rearrangements as well as identifies novel leukemia-specific fusion genes in a single procedure

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DNA sequence enrichment from complex genomic samples using microarrays enables targeted next-generation sequencing (NGS). In this study, we combined 454 shotgun pyrosequencing with long oligonucleotide sequence capture arrays. We demonstrate the detection of mutations including point mutations, deletions and insertions in a cohort of 22 patients presenting with acute leukemias and myeloid neoplasms. Importantly, this one-step methodological procedure also allowed the detection of balanced chromosomal aberrations, including translocations and inversions. Moreover, the genomic representation of only one of the partner genes of a chimeric fusion on the capture platform also permitted identification of the novel fusion partner genes. Using acute myeloid leukemias harboring RUNX1 abnormalities as a model system, three novel chromosomal fusion sequences and KCNMA1 as a novel RUNX1 fusion partner gene were detected. This assay has the strong potential to become an important method for the comprehensive genetic characterization of particular leukemias and other malignancies harboring complex genomes.

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We thank H Fiegler and W Haagmans for supporting the initial phase of the study and the array design. We further thank B Kazak for excellent technical assistance and G Schramm, L Du and C Bartenhagen for help on data analysis. This work was supported in part by a grant from Roche Diagnostics GmbH (Penzberg, Germany).

Author contributions

VG and AK designed the study, carried out the experiments, interpreted the data and wrote the manuscript. H-UK and MD performed data analysis. SoS provided technical assistance. FD, SuS, WK, CH and TH provided assistance in the design of the study, characterized patient samples and critically reviewed the manuscript. All authors approved the final version submitted for publication.

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Correspondence to C Haferlach.

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Competing interests

CH, SuS, WK and TH are part owners of the MLL Munich Leukemia Laboratory GmbH. AK, VG, FD and SoS are employed by MLL Munich Leukemia Laboratory GmbH. Other authors declare no conflict of interest. A patent application has been filed under EP09-013670.6.

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Supplementary Information accompanies the paper on the Leukemia website

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  • targeted next-generation sequencing
  • balanced chromosomal rearrangements
  • fusion genes

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