Cellular barcoding tool for clonal analysis in the hematopoietic system

Blood. 2010 Apr 1;115(13):2610-8. doi: 10.1182/blood-2009-06-229757. Epub 2010 Jan 21.


Clonal analysis is important for many areas of hematopoietic stem cell research, including in vitro cell expansion, gene therapy, and cancer progression and treatment. A common approach to measure clonality of retrovirally transduced cells is to perform integration site analysis using Southern blotting or polymerase chain reaction-based methods. Although these methods are useful in principle, they generally provide a low-resolution, biased, and incomplete assessment of clonality. To overcome those limitations, we labeled retroviral vectors with random sequence tags or "barcodes." On integration, each vector introduces a unique, identifiable, and heritable mark into the host cell genome, allowing the clonal progeny of each cell to be tracked over time. By coupling the barcoding method to a sequencing-based detection system, we could identify major and minor clones in 2 distinct cell culture systems in vitro and in a long-term transplantation setting. In addition, we demonstrate how clonal analysis can be complemented with transgene expression and integration site analysis. This cellular barcoding tool permits a simple, sensitive assessment of clonality and holds great promise for future gene therapy protocols in humans, and any other applications when clonal tracking is important.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binomial Distribution
  • Cell Lineage*
  • Cell Separation / methods
  • Clone Cells / chemistry*
  • DNA, Recombinant / analysis*
  • Flow Cytometry / methods
  • Genetic Markers*
  • Genetic Therapy / methods
  • Genetic Vectors / analysis
  • Genetic Vectors / genetics*
  • Hematopoietic Stem Cell Transplantation
  • Hematopoietic Stem Cells / chemistry*
  • Hematopoietic Stem Cells / cytology
  • Mice
  • Mice, Inbred C57BL
  • Mice, Inbred DBA
  • Oligodeoxyribonucleotides / analysis*
  • Retroviridae / genetics*
  • Sequence Analysis, DNA / methods*
  • Transgenes
  • Virus Integration


  • DNA, Recombinant
  • Genetic Markers
  • Oligodeoxyribonucleotides