A silver lining in cell line authentication: Short tandem repeat analysis of 1373 cases in China from 2010 to 2019

Gu, Meijia; Yang, Meimei; He, Jing; Xia, Sixuan; Zhang, Zhe; Wang, Yudong; Zheng, Chengchao; Shen, Chao

doi:10.1002/ijc.33789

Cited by 9 publications

(20 citation statements)

References 37 publications

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“…Fourteen percent (15/107) of cell lines were wrongly identified (Table 1), and almost one third (6/21, 29%) of miR-145 papers that described cell lines included at least one wrongly identified cell line. All wrongly identified cell lines were claimed human cancer cell lines, where most have been found to be contaminated by HeLa and/or other cancer cell lines (38–41) (Table S3).…”

Section: Resultsmentioning

confidence: 99%

“…To understand how the 8 NV cell line identifiers have been described in the literature, we assessed 420 articles that referred to at least one of these NV identifiers (Data file S1). In 185/420 (44%) papers, NV identifier(s) appeared to represent misspellings of similarly named cell lines, which were typically contaminated cancer cell lines (38–41). For example, in the 79 papers that referred to both GSE-1 and GES-1, GSE-1 appeared to consistently represent a misspelling of GES-1 (Data file S1).…”

Section: Resultsmentioning

confidence: 99%

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Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications

Oste,

Pathmendra,

Richardson

et al. 2024

Preprint

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Reproducible laboratory research relies on correctly identified reagents. We have previously described human gene research papers with wrongly identified nucleotide sequence reagent(s), including papers studying miR-145. Manually verifying reagent identities in more recent miR-145 papers found 20/36 (56%) and 6/36 (17%) miR-145 papers with misidentified nucleotide sequence reagent(s) and human cell line(s), respectively. We also found 5 cell line identifiers in two miR-145 papers with wrongly identified nucleotide sequences and cell lines, and 18 identifiers published elsewhere that did not correspond to indexed cell lines. These cell line identifiers were described as non-verifiable, as their identities appeared uncertain. Studying 420 papers that mentioned 8 different non-verifiable cell line identifier(s) found 235 papers (56%) that appeared to refer to BGC-803, BSG-803, BSG-823, GSE-1, HGC-7901, HGC-803 and/or MGC-823 as independent cell lines. We could not find publications describing how these cell lines were established, and they were not indexed in claimed externally accessible cell line repositories. While some papers stated that STR profiles had been generated for BGC-803, GSE-1 and/or MGC-823 cells, no STR profiles were identified. In summary, non-verifiable human cell lines represent new challenges to research reproducibility and require further investigation to clarify their identities.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications

Oste,

Pathmendra,

Richardson

et al. 2024

Preprint

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“…Two additional reports published in 2017 confirmed the high prevalence of misidentified cell lines in China (20.5 and 46%, respectively) (Bian et al , 2017 ; Huang et al , 2017 ). In a recent study of the CCTCC, the authors claim that the situation in China has started to improve, with a misidentified cell line rate of 24.1% in 2019 (Gu et al , 2022 ). However, the observed improvement is mostly due to the increasing number of cell line samples received from company labs, while the misidentified cell line rate among samples received from Chinese hospitals remained high (∼45%) (Gu et al , 2022 ).…”

Section: The Prevalence Of Misidentified Cell Linesmentioning

confidence: 99%

Cell line authentication: a necessity for reproducible biomedical research

Souren¹,

Fusenig²,

Heck³

et al. 2022

The EMBO Journal

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Immortalized or continuous cell lines are invaluable tools in basic and preclinical research. However, the widespread use of misidentified cell lines is a serious threat to scientific reproducibility. Based on the experiences of mandatory cell line authentication at the International Journal of Cancer (IJC), we provide an overview of the issues pertinent to misidentified cell lines and discuss available solutions. We also summarize the lessons learned, revealing that at least 5% of the human cell lines used in manuscripts considered for peer review are misidentified. About 4% of the considered manuscripts are rejected for severe cell line problems, and most are subsequently published in other journals. In order to diminish such malpractice and its consequences for the scientific record, we postulate that strict multi‐layered quality control is essential. Besides journals and publishers, we encourage scientists, research institutions, and funders to take action on the matter and revise their respective policies. Hence, we provide concrete recommendations on introducing regular authentication schemes and staff training, and discuss future steps for enhancing good cell culture practices.

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“…This property enables one to identify a specific individual based on genotyping the STR variations. This application is the basis of widely used forensic applications, , population and disease studies, − as well as cell line profiling. − Their presence is also related to secondary DNA motifs like hairpins or G quadruplex complexes and serious pathologies such as cancer, , among others. − …”

Section: Introductionmentioning

confidence: 99%

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

Hernández Bustos,

Martiny,

Bom Pedersen

et al. 2023

Anal. Chem.

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We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.

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A silver lining in cell line authentication: Short tandem repeat analysis of 1373 cases in China from 2010 to 2019

Cited by 9 publications

References 37 publications

Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications

Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications

Cell line authentication: a necessity for reproducible biomedical research

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

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