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

• Published in: Leukemia Vol. 25; no. 4; pp. 671 - 680
• Main Authors: GROSSMANN, V, KOHLMANN, A, KLEIN, H.-U, SCHINDELA, S, SCHNITTGER, S, DICKER, F, DUGAS, M, KERN, W, HAFERLACH, T, HAFERLACH, C
• Format: Journal Article
• Language: English
• Published: Avenel, NJ Nature Publishing Group 01.04.2011
• Subjects: Abnormalities; Base Sequence; Biological and medical sciences; Bone Marrow; Cells, Cultured; Chromosome Aberrations; Chromosome rearrangements; Chromosome translocations; Diagnosis; DNA microarrays; DNA sequencing; Female; Fusion protein; Gene Fusion; Gene mutations; Genes; Genetic aspects; Genomes; Genomics; Health aspects; Hematologic and hematopoietic diseases; Humans; Inversions; Leukemia; Leukemia - genetics; Leukemias. Malignant lymphomas. Malignant reticulosis. Myelofibrosis; Male; Medical genetics; Medical sciences; Molecular Sequence Data; Mutagenesis, Insertional; Mutation; Neoplasms; Next-generation sequencing; Nucleotide sequence; Nucleotide sequencing; Oligonucleotides; Oncogene Proteins, Fusion - genetics; Point Mutation - genetics; Runx1 protein; Sequence Analysis, DNA; Sequence Deletion; Sequence Homology, Nucleic Acid; Germany; Chromosomal aberration; fusion genes; Targeting; Hematology; balanced chromosomal rearrangements; Leukemia; Malignant hemopathy; targeted next-generation sequencing; Insertion mutation; Point mutation; Deletion; Abnormal chromosome; Sequencing; Hybrid gene; Cancer; Chromosome translocation
• ISSN: 0887-6924; 1476-5551
• DOI: 10.1038/leu.2010.309

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.