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Clonal Analysis of Patient-Derived Samples Using Cellular Barcodes.

Sabrina Jacobs1, Leonid V Bystrykh1, Mirjam E Belderbos2,3

  • 1Department of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands.

Methods in Molecular Biology (Clifton, N.J.)
|November 9, 2020
PubMed
Summary
This summary is machine-generated.

Cellular barcoding enables tracking of hematopoietic stem cells and leukemia dynamics. This method is optimized for reliable barcode data analysis, even with limited patient leukemia cell samples.

Keywords:
BarcodeClonal analysisCloneLeukemiaSequencing

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Area of Science:

  • Biotechnology
  • Hematology
  • Molecular Biology

Background:

  • Cellular barcoding is a technique for quantifying clonal dynamics in hematopoietic stem cells and leukemia.
  • It involves marking cells with unique DNA sequences for temporal tracking.
  • Challenges include obtaining sufficient barcoded cells and ensuring reliable data analysis, especially with limited primary leukemia cells.

Purpose of the Study:

  • To describe procedures for transfecting and transducing patient-derived leukemia cells.
  • To detail methods for retrieving barcoded data from both high and low input material.
  • To present approaches for filtering sequencing noise for accurate clonal analysis.

Main Methods:

  • Library production, transfection, and transduction of cells with synthetic DNA barcodes.
  • Barcode retrieval from both high and low cellular input material.
  • Bioinformatic filtering of barcode data to remove sequencing noise.

Main Results:

  • Successful transfection and transduction protocols for patient-derived leukemia cells.
  • Effective methods for barcode retrieval from limited cell populations.
  • Demonstrated filtering of sequencing noise for improved quantitative clonal analysis.

Conclusions:

  • The described procedures enhance cellular barcoding efficiency for leukemia research.
  • Accurate quantitative clonal analysis is achievable even with challenging sample types.
  • This work provides a framework for robust barcoding experiments in hematology.