Genome aberrations in canine mammary carcinomas and their detection in cell-free plasma DNA

PLoS One. 2013 Sep 30;8(9):e75485. doi: 10.1371/journal.pone.0075485. eCollection 2013.

Abstract

Mammary tumors are the most frequent cancers in female dogs exhibiting a variety of histopathological differences. There is lack of knowledge about the genomes of these common dog tumors. Five tumors of three different histological subtypes were evaluated. Massive parallel sequencing (MPS) was performed in comparison to the respective somatic genome of each animal. Copy number and structural aberrations were validated using droplet digital PCR (ddPCR). Using mate-pair sequencing chromosomal aneuploidies were found in two tumors, frequent smaller deletions were found in one, inter-chromosomal fusions in one other, whereas one tumor was almost normal. These aberrations affect several known cancer associated genes such as cMYC, and KIT. One common deletion of the proximal end of CFA27, harboring the tumor suppressor gene PFDN5 was detected in four tumors. Using ddPCR, this deletion was validated and detected in 50% of tumors (N = 20). Breakpoint specific dPCRs were established for four tumors and tumor specific cell-free DNA (cfDNA) was detected in the plasma. In one animal tumor-specific cfDNA was found >1 year after surgery, attributable to a lung metastasis. Paired-end sequencing proved that copy-number imbalances of the tumor are reflected by the cfDNA. This report on chromosomal instability of canine mammary cancers reveals similarities to human breast cancers as well as special canine alterations. This animal model provides a framework for using MPS for screening for individual cancer biomarkers with cost effective confirmation and monitoring using ddPCR. The possibility exists that ddPCR can be expanded to screening for common cancer related variants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cell-Free System / chemistry*
  • Chromosome Aberrations / veterinary*
  • DNA / blood
  • DNA / genetics*
  • DNA Copy Number Variations / genetics
  • DNA Primers / genetics
  • Dog Diseases / genetics*
  • Dogs
  • Female
  • High-Throughput Nucleotide Sequencing / veterinary
  • Immunohistochemistry / veterinary
  • Mammary Neoplasms, Animal / genetics*
  • Molecular Sequence Data
  • Sequence Analysis, DNA / veterinary

Substances

  • DNA Primers
  • DNA

Grant support

The study was funded by Chronix Biomedical and the Institute of Veterinary Medicine of the University of Göttingen. Study design, data collection and analysis, decision to publish and preparation of the manuscript was conducted by employees of these institutions.