Fragment Length of Circulating Tumor DNA

PLoS Genet. 2016 Jul 18;12(7):e1006162. doi: 10.1371/journal.pgen.1006162. eCollection 2016 Jul.

Abstract

Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134-144 bp vs. 167 bp, respectively). Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132-145 bp vs. 165 bp, respectively). Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alleles
  • Animals
  • Biomarkers, Tumor / blood
  • Carcinoma, Hepatocellular / genetics
  • Carcinoma, Hepatocellular / metabolism
  • Cell Line, Tumor
  • DNA, Neoplasm / blood*
  • DNA, Neoplasm / genetics*
  • Glioblastoma / blood
  • Glioblastoma / genetics
  • Hep G2 Cells
  • Humans
  • Liver Neoplasms / genetics
  • Liver Neoplasms / metabolism
  • Lung Neoplasms / genetics
  • Lung Neoplasms / metabolism
  • Magnetic Resonance Imaging
  • Male
  • Melanoma / genetics
  • Melanoma / metabolism
  • Mutation
  • Neoplasm Transplantation
  • Proto-Oncogene Proteins B-raf / genetics
  • Rats

Substances

  • Biomarkers, Tumor
  • DNA, Neoplasm
  • BRAF protein, human
  • Proto-Oncogene Proteins B-raf