title: High-performance detection of somatic D-loop mutation in urothelial cell carcinoma patients by polymorphism ratio sequencing.
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.
  
  
  
  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.
authors.affiliation: Department of Chemistry, University of California, 307 Lewis Hall, Berkeley, CA, 94720, USA.|Department of Chemistry, City College of San Francisco, 50 Phelan Ave., San Francisco, CA, 94112, USA.
authors.forename: David P
authors.initials: DP
authors.lastname: Duberow
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery, Head and Neck Cancer Research Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
authors.forename: Mariana
authors.initials: M
authors.lastname: Brait
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery, Head and Neck Cancer Research Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
authors.forename: Mohammad O
authors.initials: MO
authors.lastname: Hoque
authors.affiliation: Department of Pharmacology, University of Colorado Comprehensive Cancer Center, Aurora, CO, 80045, USA.|Department of Surgery (Urology), University of Colorado Comprehensive Cancer Center, Aurora, CO, 80045, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Theodorescu
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery, Head and Neck Cancer Research Division, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
authors.forename: David
authors.initials: D
authors.lastname: Sidransky
authors.affiliation: Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA. santanu.dasgupta@uthct.edu.
authors.forename: Santanu
authors.initials: S
authors.lastname: Dasgupta
authors.affiliation: Department of Chemistry, University of California, 307 Lewis Hall, Berkeley, CA, 94720, USA. ramathies@berkeley.edu.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Mathies
mesh_terms: D000483:Alleles; D002277:Carcinoma / Q000235:genetics* / Q000473:pathology; D004252:DNA Mutational Analysis / Q000379:methods; D004272:DNA, Mitochondrial; D056726:Genetic Association Studies / Q000379:methods; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D009154:Mutation; D011110:Polymorphism, Genetic; D014571:Urologic Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D004272:DNA, Mitochondrial
keywords: D-loop; Polymorphism ratio sequencing; Somatic mutation; Urothelial cell carcinoma; mtDNA