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

Abstract

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.

Section IV: Non–small cell lung cancer and malignant melanoma

“…Although NGS panels are easily tailored to detect point mutations and insertions in genes of interest, detecting structural abnormalities such as translocations, chromosomal CN variations, deletions, and amplifications requires complex data acquisition and manipulation. Still, NGS strategies utilizing targeted capture arrays 153 and robust analytical pipelines 154,155 have yielded encouraging results. The clinical and financial ramifications of testing for additional analytes or therapy eligibility by a methodology other than an FDA-approved companion diagnostic (eg, FISH testing for crizotinib eligibility or cobas testing for BRAF mutations) are unclear at this time.…”

Positional cloning and next-generation sequencing identified a TGM6 mutation in a large Chinese pedigree with acute myeloid leukaemia

“…The combination of linkage analysis with recently developed NGS technology have greatly accelerated the discovery of novel susceptible genes in rare Mendelian disorders. 19 Using this combined strategy, we identified a previously unreported candidate region linked to 20p13 in our family, with a maximum multipoint HLOD score of 3.56 (P ¼ 0.00005). Subsequent targeted NGS of the linkage interval revealed a missense mutation in TGM6 (L517W) that cosegregated with the phenotype in this family, and was absent in 530 healthy controls and the dbSNP138 and 1000 Genome Project databases.…”

Next-Generation Gene Sequencing and Its Applications in Oncohematology

“…Одно из ран-них исследований подобного рода было проведено V. Grossmann и соавт. [6] с применением пиросеквени-рования. В работе использовали материал от 22 па-циентов с острыми лейкозами и миелоидными ново-образованиями.…”