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

Michael N. Cornforth, Pavana Anur, Nicholas Wang, Erin Robinson, F. Andrew Ray, Joel S. Bedford, Bradford D. Loucas, Eli S. Williams, Myron Peto, Paul Spellman, Rahul Kollipara, Ralf Kittler, Joe Gray, Susan M. Bailey

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)88-97
Number of pages10
JournalRadiation Research
Volume190
Issue number1
DOIs
StatePublished - Jul 1 2018

Fingerprint

High-Throughput Nucleotide Sequencing
Genetic Translocation
sequencing
chromosomes
Computational Biology
Cytogenetics
deoxyribonucleic acid
Chromosomes
Radiation
Nucleic Acid Hybridization
Nucleic Acid Repetitive Sequences
radiation
Ionizing Radiation
Base Pairing
inversions
filters
genome
Genome
ionizing radiation
genes

ASJC Scopus subject areas

  • Biophysics
  • Radiation
  • Radiology Nuclear Medicine and imaging

Cite this

Cornforth, M. N., Anur, P., Wang, N., Robinson, E., Ray, F. A., Bedford, J. S., ... Bailey, S. M. (2018). Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells. Radiation Research, 190(1), 88-97. https://doi.org/10.1667/RR15053.1

Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells. / Cornforth, Michael N.; Anur, Pavana; Wang, Nicholas; Robinson, Erin; Ray, F. Andrew; Bedford, Joel S.; Loucas, Bradford D.; Williams, Eli S.; Peto, Myron; Spellman, Paul; Kollipara, Rahul; Kittler, Ralf; Gray, Joe; Bailey, Susan M.

In: Radiation Research, Vol. 190, No. 1, 01.07.2018, p. 88-97.

Research output: Contribution to journalArticle

Cornforth, MN, Anur, P, Wang, N, Robinson, E, Ray, FA, Bedford, JS, Loucas, BD, Williams, ES, Peto, M, Spellman, P, Kollipara, R, Kittler, R, Gray, J & Bailey, SM 2018, 'Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells', Radiation Research, vol. 190, no. 1, pp. 88-97. https://doi.org/10.1667/RR15053.1
Cornforth, Michael N. ; Anur, Pavana ; Wang, Nicholas ; Robinson, Erin ; Ray, F. Andrew ; Bedford, Joel S. ; Loucas, Bradford D. ; Williams, Eli S. ; Peto, Myron ; Spellman, Paul ; Kollipara, Rahul ; Kittler, Ralf ; Gray, Joe ; Bailey, Susan M. / Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells. In: Radiation Research. 2018 ; Vol. 190, No. 1. pp. 88-97.
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