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Limitations and challenges of genetic barcode quantification

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Limitations and challenges of genetic barcode quantification. / Thielecke, Lars; Aranyossy, Tim; Dahl, Andreas; Tiwari, Rajiv; Roeder, Ingo; Geiger, Hartmut; Fehse, Boris; Glauche, Ingmar; Cornils, Kerstin.

in: SCI REP-UK, Jahrgang 7, 03.03.2017, S. 43249.

Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung

Harvard

Thielecke, L, Aranyossy, T, Dahl, A, Tiwari, R, Roeder, I, Geiger, H, Fehse, B, Glauche, I & Cornils, K 2017, 'Limitations and challenges of genetic barcode quantification', SCI REP-UK, Jg. 7, S. 43249. https://doi.org/10.1038/srep43249

APA

Thielecke, L., Aranyossy, T., Dahl, A., Tiwari, R., Roeder, I., Geiger, H., Fehse, B., Glauche, I., & Cornils, K. (2017). Limitations and challenges of genetic barcode quantification. SCI REP-UK, 7, 43249. https://doi.org/10.1038/srep43249

Vancouver

Thielecke L, Aranyossy T, Dahl A, Tiwari R, Roeder I, Geiger H et al. Limitations and challenges of genetic barcode quantification. SCI REP-UK. 2017 Mär 3;7:43249. https://doi.org/10.1038/srep43249

Bibtex

@article{25b0114082c24d6aab39b17a2a590b45,
title = "Limitations and challenges of genetic barcode quantification",
abstract = "Genetic barcodes are increasingly used to track individual cells and to quantitatively assess their clonal contributions over time. Although barcode quantification relies entirely on counting sequencing reads, detailed studies about the method's accuracy are still limited. We report on a systematic investigation of the relation between barcode abundance and resulting read counts after amplification and sequencing using cell-mixtures that contain barcodes with known frequencies ({"}miniBulks{"}). We evaluated the influence of protocol modifications to identify potential sources of error and elucidate possible limitations of the quantification approach. Based on these findings we designed an advanced barcode construct (BC32) to improved barcode calling and quantification, and to ensure a sensitive detection of even highly diluted barcodes. Our results emphasize the importance of using curated barcode libraries to obtain interpretable quantitative data and underline the need for rigorous analyses of any utilized barcode library in terms of reliability and reproducibility.",
keywords = "Journal Article",
author = "Lars Thielecke and Tim Aranyossy and Andreas Dahl and Rajiv Tiwari and Ingo Roeder and Hartmut Geiger and Boris Fehse and Ingmar Glauche and Kerstin Cornils",
year = "2017",
month = mar,
day = "3",
doi = "10.1038/srep43249",
language = "English",
volume = "7",
pages = "43249",
journal = "SCI REP-UK",
issn = "2045-2322",
publisher = "NATURE PUBLISHING GROUP",

}

RIS

TY - JOUR

T1 - Limitations and challenges of genetic barcode quantification

AU - Thielecke, Lars

AU - Aranyossy, Tim

AU - Dahl, Andreas

AU - Tiwari, Rajiv

AU - Roeder, Ingo

AU - Geiger, Hartmut

AU - Fehse, Boris

AU - Glauche, Ingmar

AU - Cornils, Kerstin

PY - 2017/3/3

Y1 - 2017/3/3

N2 - Genetic barcodes are increasingly used to track individual cells and to quantitatively assess their clonal contributions over time. Although barcode quantification relies entirely on counting sequencing reads, detailed studies about the method's accuracy are still limited. We report on a systematic investigation of the relation between barcode abundance and resulting read counts after amplification and sequencing using cell-mixtures that contain barcodes with known frequencies ("miniBulks"). We evaluated the influence of protocol modifications to identify potential sources of error and elucidate possible limitations of the quantification approach. Based on these findings we designed an advanced barcode construct (BC32) to improved barcode calling and quantification, and to ensure a sensitive detection of even highly diluted barcodes. Our results emphasize the importance of using curated barcode libraries to obtain interpretable quantitative data and underline the need for rigorous analyses of any utilized barcode library in terms of reliability and reproducibility.

AB - Genetic barcodes are increasingly used to track individual cells and to quantitatively assess their clonal contributions over time. Although barcode quantification relies entirely on counting sequencing reads, detailed studies about the method's accuracy are still limited. We report on a systematic investigation of the relation between barcode abundance and resulting read counts after amplification and sequencing using cell-mixtures that contain barcodes with known frequencies ("miniBulks"). We evaluated the influence of protocol modifications to identify potential sources of error and elucidate possible limitations of the quantification approach. Based on these findings we designed an advanced barcode construct (BC32) to improved barcode calling and quantification, and to ensure a sensitive detection of even highly diluted barcodes. Our results emphasize the importance of using curated barcode libraries to obtain interpretable quantitative data and underline the need for rigorous analyses of any utilized barcode library in terms of reliability and reproducibility.

KW - Journal Article

U2 - 10.1038/srep43249

DO - 10.1038/srep43249

M3 - SCORING: Journal article

C2 - 28256524

VL - 7

SP - 43249

JO - SCI REP-UK

JF - SCI REP-UK

SN - 2045-2322

ER -