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Radiat Res. 2018 Jul;190(1):88-97. doi: 10.1667/RR15053.1. Epub 2018 May 11.

Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells.

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a   Department of Radiation Oncology, University of Texas Medical Branch, Galveston, Texas 77555.
c   KromaTiD Inc., Fort Collins, Colorado 80523.
b   Departments of Molecular and Medical Genetics, Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97201.
d   Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523.
e   Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia 22908.
f   McDermott Center, University of Texas Southwestern Medical Center, Dallas, Texas 75235.


Chromosome rearrangements are large-scale structural variants that are recognized drivers of oncogenic events in cancers of all types. Cytogenetics allows for their rapid, genome-wide detection, but does not provide gene-level resolution. Massively parallel sequencing (MPS) promises DNA sequence-level characterization of the specific breakpoints involved, but is strongly influenced by bioinformatics filters that affect detection efficiency. We sought to characterize the breakpoint junctions of chromosomal translocations and inversions in the clonal derivatives of human cells exposed to ionizing radiation. Here, we describe the first successful use of DNA paired-end analysis to locate and sequence across the breakpoint junctions of a radiation-induced reciprocal translocation. The analyses employed, with varying degrees of success, several well-known bioinformatics algorithms, a task made difficult by the involvement of repetitive DNA sequences. As for underlying mechanisms, the results of Sanger sequencing suggested that the translocation in question was likely formed via microhomology-mediated non-homologous end joining (mmNHEJ). To our knowledge, this represents the first use of MPS to characterize the breakpoint junctions of a radiation-induced chromosomal translocation in human cells. Curiously, these same approaches were unsuccessful when applied to the analysis of inversions previously identified by directional genomic hybridization (dGH). We conclude that molecular cytogenetics continues to provide critical guidance for structural variant discovery, validation and in "tuning" analysis filters to enable robust breakpoint identification at the base pair level.

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