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High-performance detection of somatic D-loop mutation in urothelial cell carcinoma patients by polymorphism ratio sequencing

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Abstract

Utilizing a polymorphism ratio sequencing platform, we performed a complete somatic mutation analysis of the mitochondrial D-loop region in 14 urothelial cell carcinomas. A total of 28 somatic mutations, all heteroplasmic, were detected in 8 of 14 individuals (57.1 %). Insertion/deletion changes in unstable mono- and dinucleotide repeat segments comprise the most pervasive class of mutations (9 of 28), while two recurring single-base substitution loci were identified. Seven variants, mostly insertion/deletions, represent population shifts from a heteroplasmic germline toward dominance in the tumor. In four cases, DNA from matched urine samples was similarly analyzed, with all somatic variants present in associated tumors readily detectable in the bodily fluid. Consistent with previous findings, mutant populations in urine were similar to those detected in tumor and in three of four cases were more prominent in urine.

Key messages

  • PRS accurately detects high mtDNA mutations in UCCs and their body fluids.

  • mtDNA mutations are universally heteroplasmic and often appear at low levels.

  • The PRS technology could be a viable approach to develop mitochondrial biomarkers.

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Acknowledgments

The authors gratefully acknowledge Nadia Del Bueno, Samantha Cronier, Numrin Thaitrong, Jim Scherer, Peng Liu, and Kanwar Singh for valuable consultation. The involvement of Jing Yi and Terry Speed from the UC Berkeley Statistics Department was central to the design of the automated PRS analysis software. Microfabrication was performed by Eric Chu at the UC Berkeley Microlab. This work was supported by NIH grants #HG03329, #CA77664, and #CA075115 (R.A.M.) and the University of Texas Health Science Center at Tyler, Texas (S.D.).

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Author notes

  1. David P. Duberow

    Present address: Department of Chemistry, City College of San Francisco, 50 Phelan Ave., San Francisco, CA, 94112, USA

Authors and Affiliations

  1. Department of Chemistry, University of California, 307 Lewis Hall, Berkeley, CA, 94720, USA

    David P. Duberow & Richard A. Mathies

  2. Department of Otolaryngology—Head and Neck Surgery, Head and Neck Cancer Research Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA

    Mariana Brait, Mohammad O. Hoque & David Sidransky

  3. Department of Pharmacology, University of Colorado Comprehensive Cancer Center, Aurora, CO, 80045, USA

    Dan Theodorescu

  4. Department of Surgery (Urology), University of Colorado Comprehensive Cancer Center, Aurora, CO, 80045, USA

    Dan Theodorescu

  5. Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA

    Santanu Dasgupta

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Corresponding authors

Correspondence to Santanu Dasgupta or Richard A. Mathies.

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Author contribution

R.A.M., S.D., and D.S. designed the experiments. D.P.D. and M.B. performed research. R.A.M., S.D., D.S., M.O.H., D.P.D., and D.T. analyzed the data and provided materials. R.A.M., S.D., and D.S. designed the project, supervised research. R.A.M., S.D., D.S., M.O.H., D.P.D., D.T., and M.B. wrote the paper.

Conflict of interest statement

R.A.M. has a financial interest in a company (IntegenX Inc.) working on the commercialization of microchip sequencing technologies that may benefit from the results of this research. Others have declared no competing interest.

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Duberow, D.P., Brait, M., Hoque, M.O. et al. High-performance detection of somatic D-loop mutation in urothelial cell carcinoma patients by polymorphism ratio sequencing. J Mol Med 94, 1015–1024 (2016). https://doi.org/10.1007/s00109-016-1407-2

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  • DOI: https://doi.org/10.1007/s00109-016-1407-2

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