Limitations and challenges of genetic barcode quantification

Scientific Reports

Volumn 7, Issue , 2017, Pages

  Thielecke, Lars ^a   Aranyossy, Tim ^b   Dahl, Andreas ^c   Tiwari, Rajiv ^d   Roeder, Ingo ^a   Geiger, Hartmut ^d,e   Fehse, Boris ^b   Glauche, Ingmar ^a   Cornils, Kerstin ^b  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^c DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^d UNIVERSITY OF ULM   (Germany)

^e UNIVERSITY OF CINCINNATI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE AMPLIFICATION; LIBRARY; QUANTITATIVE STUDY; RELIABILITY; REPRODUCIBILITY; CELL COUNT; DNA BARCODING; DNA SEQUENCE; HEK293 CELL LINE; HUMAN; NUCLEIC ACID AMPLIFICATION; PROCEDURES; SENSITIVITY AND SPECIFICITY;

CELL COUNT; DNA BARCODING, TAXONOMIC; HEK293 CELLS; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 85014593104     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep43249     Document Type: Article

References (40)

1. Drize, N. J. J. R. K. & Chertkov, J. L. Local clonal analysis of the hematopoietic system shows that multiple small short-living clones maintain life-long hematopoiesis in reconstituted mice. Annu. Rev. Med. 47, 11-20 (1996).
2. Jordan, C. T. & Lemischka, I. R. Clonal and systemic analysis of long-term hematopoiesis in the mouse. Genes Dev. 4, 220-232 (1990).
3. Chudakov, D. M., Matz, M. V., Lukyanov, S. & Lukyanov, K. A. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev 90, 1103-1163, doi: 10.1152/physrev.00038.2009 (2010).
4. Weber, K. et al. RGB marking facilitates multicolor clonal cell tracking. Nat Med 17, 504-509, doi: 10.1038/nm.2338 (2011).
5. Cornils, K. et al. Multiplexing clonality: combining RGB marking and genetic barcoding. Nucleic Acids Res 42, e56, doi: 10.1093/nar/ gku081 (2014).
6. Cornils, K. et al. Comparative clonal analysis of reconstitution kinetics after transplantation of hematopoietic stem cells gene marked with a lentiviral SIN or a gamma-retroviral LTR vector. Exp Hematol 41, 28-38 e23, doi: 10.1016/j.exphem.2012.09.003 (2013).
7. Brugman, M. H. et al. Evaluating a ligation-mediated PCR and pyrosequencing method for the detection of clonal contribution in polyclonal retrovirally transduced samples. Hum Gene Ther Methods 24, 68-79, doi: 10.1089/hgtb.2012.175 (2013).
8. Gabriel, R. et al. Comprehensive genomic access to vector integration in clinical gene therapy. Nat Med 15, 1431-1436, doi: 10.1038/ nm.2057 (2009).
9. Sun, J. et al. Clonal dynamics of native haematopoiesis. Nature 514, 322-327, doi: 10.1038/nature13824 (2014).
10. Busch, K. et al. Fundamental properties of unperturbed haematopoiesis from stem cells in vivo. Nature 518, 542-546, doi: 10.1038/ nature14242 (2015).
11. Schepers, K. et al. Dissecting T cell lineage relationships by cellular barcoding. J Exp Med 205, 2309-2318, doi: 10.1084/ jem.20072462 (2008).
12. Gerrits, A. D. B., Kalmykowa, O. J., Klauke, K., Verovskaya, E., Broekhuis, M. J. C., de Haan, G. & Bystrykh, L. V. Cellular barcoding tool for clonal analysis in the hematopoietic system. Blood 115, 2610-2618, doi: 10.1182/blood-2009-06-(2010).
13. Lu, R., Neff, N. F., Quake, S. R. & Weissman, I. L. Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nat Biotechnol 29, 928-933, doi: 10.1038/nbt.1977 (2011).
14. Bystrykh, L. V., Verovskaya, E., Zwart, E., Broekhuis, M. & de Haan, G. Counting stem cells: methodological constraints. Nat Methods 9, 567-574, doi: 10.1038/nmeth.2043 (2012).
15. Verovskaya, E. et al. Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding. Blood 122, 523-532, doi: 10.1182/blood-2013-01-481135 (2013).
16. Verovskaya, E. et al. Asymmetry in skeletal distribution of mouse hematopoietic stem cell clones and their equilibration by mobilizing cytokines. J Exp Med 211, 487-497, doi: 10.1084/jem.20131804 (2014).
17. Naik, S. H., Schumacher, T. N. & Perie, L. Cellular barcoding: a technical appraisal. Exp Hematol 42, 598-608, doi: 10.1016/j. exphem.2014.05.003 (2014).
18. Nguyen, L. V. et al. Clonal analysis via barcoding reveals diverse growth and differentiation of transplanted mouse and human mammary stem cells. Cell Stem Cell 14, 253-263, doi: 10.1016/j.stem.2013.12.011 (2014).
19. Nguyen, L. V. et al. Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells. Nature 528, 267-271, doi: 10.1038/nature15742 (2015).
20. Bhang, H. E. et al. Studying clonal dynamics in response to cancer therapy using high-complexity barcoding. Nat Med 21, 440-448, doi: 10.1038/nm.3841 (2015).
21. Bystrykh, L. V. & Belderbos, M. E. Clonal Analysis of Cells with Cellular Barcoding: When Numbers and Sizes Matter. Methods Mol Biol, doi: 10.1007/7651-2016-343 (2016).
22. Beltman, J. B. et al. Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. BMC Bioinformatics 17, 151, doi: 10.1186/s12859-016-0999-4 (2016).
23. Deakin, C. T. et al. Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence. Nucleic Acids Res 42, e129, doi: 10.1093/nar/gku607 (2014).
24. Weber, K., Bartsch, U., Stocking, C. & Fehse, B. A multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors for functional gene analysis. Mol Ther 16, 698-706, doi: 10.1038/mt.2008.6 (2008).
25. Fehse, B., Kustikova, O. S., Bubenheim, M. & Baum, C. Pois(s)on-it's a question of dose. Gene Ther 11, 879-881, doi: 10.1038/ sj.gt.3302270 (2004).
26. Kustikova, O. S., Baum, C. & Fehse, B. Retroviral integration site analysis in hematopoietic stem cells. Methods Mol Biol 430, 255-267, doi: 10.1007/978-1-59745-182-6-18 (2008).
27. Schmidt, M. et al. High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR). Nat Methods 4, 1051-1057, doi: 10.1038/nmeth1103 (2007).
28. Huston, M. W. et al. Comprehensive investigation of parameter choice in viral integration site analysis and its effects on the gene annotations produced. Human gene therapy 23, 1209-1219, doi: 10.1089/hum.2011.037 (2012).
29. Pezza, J. A., Rebecca, K. & Sun, L. Fidelity: What is it, and what does it mean for your PCR? New England Biolabs, Inc.
30. Peikon, I. D., Gizatullina, D. I. & Zador, A. M. In vivo generation of DNA sequence diversity for cellular barcoding. Nucleic Acids Res 42, e127, doi: 10.1093/nar/gku604 (2014).
31. Brugman, M. H. W. A., van Eggermond, M., Wolvers-Tettero, I., Langerak, A. W., de Haas, E. F., Bystrykh, L. V., van Rood, J. J., de Haan, G., Fibbe, W. E. & Staa, F. J. Development of a diverse human T-cell repertoire despite stringent restriction of hematopoietic clonality in the thymus. PNAS 112, E6020-E6027 (2015).
32. Gerlach, C. et al. Heterogeneous differentiation patterns of individual CD8+ T cells. Science 340, 635-639, doi: 10.1126/ science.1235487 (2013).
33. Keohavong, P. T. W. Fidelity of DNA polymerases in DNA amplification. PNAS 86, 9253-9257 (1989).
34. Miner, B. E., Stoger, R. J., Burden, A. F., Laird, C. D. & Hansen, R. S. Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR. Nucleic Acids Res 32, e135, doi: 10.1093/nar/gnh132 (2004).
35. McKenna, A. et al. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907, doi: 10.1126/science.aaf7907 (2016).
36. Kivioja, T. et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 9, 72-74, doi: 10.1038/ nmeth.1778 (2011).
37. Kou, R. et al. Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations. PLoS One 11, e0146638, doi: 10.1371/journal.pone.0146638 (2016).
38. Kircher, M., Heyn, P. & Kelso, J. Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 12, 382, doi: 10.1186/1471-2164-12-382 (2011).
39. Mitra, A., Skrzypczak, M., Ginalski, K. & Rowicka, M. Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform. PLoS One 10, e0120520, doi: 10.1371/journal.pone.0120520 (2015).
40. Illumina. Low-Diversity Sequencing on the Illumina HiSeq® Platform. (2014).