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Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies

Thomas McKerrell, Thaidy Moreno, Hannes Ponstingl, Niccolo Bolli, João M. L. Dias, German Tischler, Vincenza Colonna, Bridget Manasse, Anthony Bench, David Bloxham, Bram Herman, Danielle Fletcher, Naomi Park, Michael A. Quail, Nicla Manes, Clare Hodkinson, Joanna Baxter, Jorge Sierra, Theodora Foukaneli, Alan J. Warren, Jianxiang Chi, Paul Costeas, Roland Rad, Brian Huntly, Carolyn Grove, Zemin Ning, Chris Tyler-Smith, Ignacio Varela, Mike Scott, Josep Nomdedeu, Ville Mustonen and George S. Vassiliou

Key Points

  • We develop and validate Karyogene, a comprehensive one-stop diagnostic platform for the genomic analysis of myeloid malignancies.

  • Karyogene simultaneously detects substitutions, insertions/deletions, translocations, copy number and zygosity changes in a single assay.

Publisher's Note: There is an Inside Blood Commentary on this article in this issue.

Abstract

The diagnosis of hematologic malignancies relies on multidisciplinary workflows involving morphology, flow cytometry, cytogenetic, and molecular genetic analyses. Advances in cancer genomics have identified numerous recurrent mutations with clear prognostic and/or therapeutic significance to different cancers. In myeloid malignancies, there is a clinical imperative to test for such mutations in mainstream diagnosis; however, progress toward this has been slow and piecemeal. Here we describe Karyogene, an integrated targeted resequencing/analytical platform that detects nucleotide substitutions, insertions/deletions, chromosomal translocations, copy number abnormalities, and zygosity changes in a single assay. We validate the approach against 62 acute myeloid leukemia, 50 myelodysplastic syndrome, and 40 blood DNA samples from individuals without evidence of clonal blood disorders. We demonstrate robust detection of sequence changes in 49 genes, including difficult-to-detect mutations such as FLT3 internal-tandem and mixed-lineage leukemia (MLL) partial-tandem duplications, and clinically significant chromosomal rearrangements including MLL translocations to known and unknown partners, identifying the novel fusion gene MLL-DIAPH2 in the process. Additionally, we identify most significant chromosomal gains and losses, and several copy neutral loss-of-heterozygosity mutations at a genome-wide level, including previously unreported changes such as homozygosity for DNMT3A R882 mutations. Karyogene represents a dependable genomic diagnosis platform for translational research and for the clinical management of myeloid malignancies, which can be readily adapted for use in other cancers.

  • Submitted November 22, 2015.
  • Accepted April 21, 2016.
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