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Cited by 19Identification and Quantification in FoodEnvironmental DNA in Biodiversity StudiesGenomics and Phylogenetic Studies

Authentication, characterization and contamination detection of cell lines, xenografts and organoids by barcode deep NGS sequencing

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Chen, Xiaobo, Qian, Wubin, Song, Zhenzhen, Li, Qi-Xiang, Guo, Sheng·2020·NAR Genomics and Bioinformatics
DOI 10.1093/nargab/lqaa060PMC PMC7671372
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Abstract

Misidentification and contamination of biobank samples (e.g. cell lines) have plagued biomedical research. Short tandem repeat (STR) and single-nucleotide polymorphism assays are widely used to authenticate biosamples and detect contamination, but with insufficient sensitivity at 5–10% and 3–5%, respectively. Here, we describe a deep NGS-based method with significantly higher sensitivity (≤1%). It can be used to authenticate human and mouse cell lines, xenografts and organoids. It can also reliably identify and quantify contamination of human cell line samples, contaminated with only small amount of other cell samples; detect and quantify species-specific components in human–mouse mixed samples (e.g. xenografts) with 0.1% sensitivity; detect mycoplasma contamination; and infer population structure and gender of human samples. By adopting DNA barcoding technology, we are able to profile 100–200 samples in a single run at per-sample cost comparable to conventional STR assays, providing a truly high-throughput and low-cost assay for building and maintaining high-quality biobanks.

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  • Technologies such as STR profiling, karyotyping, and barcoding do not meet the needs of fledgling procurement networks because they do not exhibit robustness, uniqueness, and unclonability.

    “Technologies such as STR profiling, karyotyping, and barcoding do not meet the needs of fledgling procurement networks because they do not exhibit the three requisite attributes for source attestation: robustness, uniqueness, and unclonability [134].”

    From The history, landscape, and outlook of human cell line authentication and security (2024) · cites this paper as [134]

    The Introduction (page unavailable) says STR assays have limitations for authenticating large batches of biosamples, supporting only a narrower concern about STR profiling. It does not assess fledgling procurement networks or say that STR profiling, karyotyping, and barcoding lack robustness, uniqueness, and unclonability. The Discussion (page unavailable) instead presents DNA barcoding as a useful part of the paper’s robust, high-throughput authentication method. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Next-Generation Sequencing authentication experiments have shown extremely high accuracy, even in lines derived from the same parent.

    “Authentication experiments with Next-Generation Sequencing (”

    From The history, landscape, and outlook of human cell line authentication and security (2024) · cites this paper as [134]

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Cited by

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Authors
Chen, X., Qian, W., Song, Z., Li, Q.-X., & Guo, S.
Affiliations
  • Crown Bioscience (China) (CN)
  • Crown Bioscience, Inc., 16550 W Bernardo Dr, Building 5, San Diego, CA 92127, USA
Corresponding author
Guo, Sheng
ORCID
Venue
NAR Genomics and Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2020-08-18
Volume
2
Issue
3
Pages
lqaa060-lqaa060
ISSN
2631-9268 (ISSN-L)
DOI
10.1093/nargab/lqaa060
PMC
PMC7671372
OpenAlex
W3064583715
Cited by
19
References
14
Citations by year
2025: 2 · 2024: 2 · 2023: 11 · 2022: 3 · 2021: 1
FWCI
1.22
Type
journal article
Language
en
Open access
Licence
Locations
  • NAR Genomics and Bioinformatics (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
Crown Bioscience, Inc.
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Identification and Quantification in Food
  • Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
cell line authentication, contamination detection, DNA barcoding, xenografts, organoids, mycoplasma detection, population structure inference, sex determination

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