Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies.
Thomas McKerrellThaidy MorenoHannes PonstinglNiccolo BolliJoão M L DiasGerman TischlerVincenza ColonnaBridget ManasseAnthony BenchDavid BloxhamBram HermanDanielle FletcherNaomi ParkMichael A QuailNicla ManesClare HodkinsonJoanna BaxterJorge SierraTheodora FoukaneliAlan J WarrenJianxiang ChiPaul CosteasRoland RadBrian HuntlyCarolyn GroveZemin NingChris Tyler-SmithIgnacio VarelaMike ScottJosep NomdedeuVille MustonenGeorge S VassiliouPublished in: Blood (2016)
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.
Keyphrases
- copy number
- acute myeloid leukemia
- genome wide
- mitochondrial dna
- dna methylation
- allogeneic hematopoietic stem cell transplantation
- flow cytometry
- high throughput
- bone marrow
- single cell
- dendritic cells
- acute lymphoblastic leukemia
- hepatitis c virus
- cell free
- gene expression
- immune response
- squamous cell carcinoma
- mass spectrometry
- tyrosine kinase
- papillary thyroid
- label free
- real time pcr
- lymph node metastasis