scholarly journals Recent developments of the cell line integrated molecular authentication database

2016 ◽  
Author(s):  
Paolo D Romano ◽  
Paola Visconti ◽  
Barbara Parodi
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Animal Cell ◽  
Cell Line Authentication ◽  
Molecular Authentication ◽  
Standard Data ◽  
Str Profile ◽  
Frequent Event ◽  
Recent Developments ◽  
Cell Banks

Cross-contamination of human and animal cell lines is a frequent event. For this reason, the results obtained with the same cell lines by different research groups are often not fully comparable, this leading to main reproducibility issues. The short tandem repeat (STR) profile has been proposed as a molecular method for cell line authentication. STR profile standard data sets for human cell lines were proposed by some of the leading cell banks worldwide which also have made the results of STR profiling of their cell lines available on-line. We have built the Cell Line Integrated Molecular Authentication Database (CLIMA) as a reference portal where authentication data are made available to the scientific community. This system, although already largely utilized by researchers from all over the world, presented some limitations and only included a limited amount of STR profiles. Here, we present its most recent developments: the inclusion of additional cell banks and profiles and the availability of a new identification tool.

scholarly journals Recent developments of the cell line integrated molecular authentication database

2016 ◽  
Author(s):  
Paolo D Romano ◽  
Paola Visconti ◽  
Barbara Parodi
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Animal Cell ◽  
Cell Line Authentication ◽  
Molecular Authentication ◽  
Standard Data ◽  
Str Profile ◽  
Frequent Event ◽  
Recent Developments ◽  
Cell Banks

Cross-contamination of human and animal cell lines is a frequent event. For this reason, the results obtained with the same cell lines by different research groups are often not fully comparable, this leading to main reproducibility issues. The short tandem repeat (STR) profile has been proposed as a molecular method for cell line authentication. STR profile standard data sets for human cell lines were proposed by some of the leading cell banks worldwide which also have made the results of STR profiling of their cell lines available on-line. We have built the Cell Line Integrated Molecular Authentication Database (CLIMA) as a reference portal where authentication data are made available to the scientific community. This system, although already largely utilized by researchers from all over the world, presented some limitations and only included a limited amount of STR profiles. Here, we present its most recent developments: the inclusion of additional cell banks and profiles and the availability of a new identification tool.

scholarly journals Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Zeljana Babic ◽  
Amanda Capes-Davis ◽  
Maryann E Martone ◽  
Amos Bairoch ◽  
I Burak Ozyurt ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Biomedical Research ◽  
Cell Line Authentication ◽  
Pubmed Central ◽  
International Cell ◽  
Unique Cell

The use of misidentified and contaminated cell lines continues to be a problem in biomedical research. Research Resource Identifiers (RRIDs) should reduce the prevalence of misidentified and contaminated cell lines in the literature by alerting researchers to cell lines that are on the list of problematic cell lines, which is maintained by the International Cell Line Authentication Committee (ICLAC) and the Cellosaurus database. To test this assertion, we text-mined the methods sections of about two million papers in PubMed Central, identifying 305,161 unique cell-line names in 150,459 articles. We estimate that 8.6% of these cell lines were on the list of problematic cell lines, whereas only 3.3% of the cell lines in the 634 papers that included RRIDs were on the problematic list. This suggests that the use of RRIDs is associated with a lower reported use of problematic cell lines.

scholarly journals Cell Banking of HEK293T cell line for clinical-grade lentiviral particles manufacturing

2020 ◽  
Author(s):  
Unai Perpiña ◽  
Cristina Herranz ◽  
Raquel Martin-Ibañez ◽  
Anna Boronat ◽  
Felipe Chiappe ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Hek293t Cell ◽  
Good Manufacturing Practice ◽  
Clinical Grade ◽  
Cell Bank ◽  
Advanced Therapy ◽  
Working Cell ◽  
Cell Banks ◽  
Hek293t Cell Line

Abstract Background: Cell banks are widely used to preserve cell properties as well as to record and control the use of cell lines in biomedical research. The generation of cell banks for the manufacturing of Advanced Therapy Medicinal Products, such as cell and gene therapy products, must comply with current Good Manufacturing Practice regulations. The quality of the cell lines used as starting materials in viral-vector manufacturing processes must be also assessed.Methods: Three batches of a Master Cell Bank and a Working Cell Bank of the HEK293T cell line were manufactured under current Good Manufacturing Practices regulations. Quality control tests were performed according to product specifications. Process validation includes the training of manufacturing personnel by performing simulation tests, and the continuous measurement of environmental parameters such as air particles and microorganisms. Cell number and viability of cryopreserved cells were periodically measured in order to define the stability of these cellular products.Results: All batches of HEK293T Master and Working Cell Banks met the acceptance criteria of their specifications showing the robustness and homogeneity of the processes. In addition, both Master and Working Cell Banks maintained the defined cell viability and concentration over a 37 month-period after cryopreservation. Conclusions: Manufacturing cell banks under Good Manufacturing Practice regulations for their use as raw materials or final cellular products is feasible. HEK293T cell banks were used to manufacture clinical-grade lentiviral particles for Chimeric Antigen Receptor T-cell based clinical trials.

The cell line data base and the new catalogue: Detailed information on 2650 human and animal cell lines

1993 ◽  
Vol 11 (S1) ◽  
pp. S130-S133 ◽  
Author(s):  
A. Manniello ◽  
O. Aresu ◽  
B. Parodi ◽  
P. Romano ◽  
B. Iannotta ◽  
...  
Keyword(s):  
Data Base ◽  
Cell Line ◽  
Cell Lines ◽  
Animal Cell

scholarly journals High-throughput Sequencing for Species Authentication and Contamination Detection of 63 Cell Lines

2021 ◽  
Author(s):  
Oliver Lung ◽  
Rebecca Candlish ◽  
Michelle Nebroski ◽  
Peter Kruckiewicz ◽  
Cody Buchanan ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Classical Swine Fever ◽  
Virus Genome ◽  
Cox1 Gene ◽  
Species Identity ◽  
Cell Line Authentication ◽  
Dna And Rna

Abstract Cell lines are widely used in research and for diagnostic tests and are often shared between laboratories. Lack of cell line authentication can result in the use of contaminated or misidentified cell lines, potentially affecting the results from research and diagnostic activities. Cell line authentication and contamination detection based on metagenomic high-throughput sequencing (HTS) was tested on DNA and RNA from 63 cell lines available at the Canadian Food Inspection Agency’s National Centre for Foreign Animal Disease. Through sequence comparison of the cytochrome c oxidase subunit 1 (COX1) gene, the species identity of 53 cell lines was confirmed, and eight cell lines were found to show a greater pairwise nucleotide identity in the COX1 sequence of a different species within the same expected genus. Two cell lines, LFBK-αvβ6 and SCP-HS, were determined to be composed of cells from a different species and genus. Mycoplasma contamination was not detected in any cell lines. However, several expected and unexpected viral sequences were detected, including part of the classical swine fever virus genome in the IB-RS-2 Clone D10 cell line. Metagenomics-based HTS is a useful laboratory QA tool for cell line authentication and contamination detection that should be conducted regularly.

Traceability Methods for Cell Line Authentication and Mycoplasma Detection

2021 ◽  
pp. 247263032110302
Author(s):  
Kate Dennert ◽  
Rajeev Kumar
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Research Community ◽  
Surveillance Strategy ◽  
Cell Line Authentication ◽  
Mycoplasma Detection ◽  
Established Cell Lines ◽  
Downstream Effects ◽  
Potential Problems ◽  
Established Cell

Many laboratories struggle with mycoplasma contamination and cell line misidentification when growing cells in culture. These well-documented issues affect the scientific research community and have detrimental downstream effects. Research published with suspect cultures can produce misleading results. There is increasing pressure to verify the integrity of experimental and established cell lines before publishing. Therefore, laboratories need to define how and when to perform these critical tests, analyze the results, and determine action plans if disparities exist. Our laboratory is committed to producing cell lines of the highest quality for use in experiments; thus, we created a surveillance strategy for these potential problems. We developed processes for both testing and tracing cell line authentication and mycoplasma detection data. Using these methods, we can protect the integrity of our patient and commercial cell lines, maintaining reliable cultures for our research.

scholarly journals Digital Karyotyping for Rapid Authentication of Cell Lines

2019 ◽  
Author(s):  
Ahmed Ibrahim Samir Khalil ◽  
Anupam Chattopadhyay ◽  
Amartya Sanyal
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
De Novo ◽  
Simulated Data ◽  
Read Depth ◽  
Cancer Cell Lines ◽  
Scientific Data ◽  
Cell Line Authentication ◽  
A Cell

Abstract Background The widespread concern about genetic drift and cross-contamination of cell lines calls for a pressing need for their authentication. The current genetic techniques for authentication are time-consuming and require specific documentary standard and laboratory protocols. Given the fact that whole-genome sequencing (WGS) data are readily available, read depth (RD)-based computational analyses has allowed the estimation of genetic profiles of cell lines. Results We propose WGS-derived aneuploidy profiling as a prototype of digital karyotyping for authentication of cancer cell lines. Here, we describe a Python-based software AStra for de novo estimation of the genome-wide aneuploidy profile, the copy number of every genomic loci, from raw WGS reads. We demonstrated that aneuploidy profile offers a unique signature that can distinguish the clonal variants (strains) of a cell line. We evaluated our approach using simulated data and variety of cancer cell lines. We further showed that cell lines exhibit distinct aneuploidy patterns which corroborate well with the experimental observations. Conclusions AStra is a simple, user-friendly, and free tool that provides the elementary information about the chromosomal aneuploidy for cell line authentication. AStra provides an analytical and visualization platform for rapid and easy comparison between different cell lines/strains. We recommend AStra for rapid first-pass quality assessment of scientific data that employ cancer cell lines. AStra is an open source software and is available at https://github.com/AISKhalil/AStra.

scholarly journals Advances in paraganglioma–pheochromocytoma cell lines and xenografts

2020 ◽  
Vol 27 (12) ◽  
pp. R433-R450
Author(s):  
Jean-Pierre Bayley ◽  
Peter Devilee
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Animal Cell ◽  
Basic Research ◽  
Cell Models ◽  
Strong Recommendation ◽  
Organoid Culture ◽  
Disease Mechanisms ◽  
Pheochromocytoma Cell ◽  
Cell Line Derivation

This review describes human and rodent-derived cell lines and xenografts developed over the last five decades that are suitable or potentially suitable models for paraganglioma–pheochromocytoma research. We outline the strengths and weaknesses of various models and emphasize the recurring theme that, despite the major challenges involved, more effort is required in the search for valid human and animal cell models of paraganglioma–pheochromocytoma, particularly those relevant to cancers carrying a mutation in one of the succinate dehydrogenase genes. Despite many setbacks, the recent development of a potentially important new model, the RS0 cell line, gives reason for optimism regarding the future of models in the paraganglioma–pheochromocytoma field. We also note that classic approaches to cell line derivation such as SV40-mediated immortalization and newer approaches such as organoid culture or iPSCs have been insufficiently explored. As many existing cell lines have been poorly characterized, we provide recommendations for reporting of paraganglioma and pheochromocytoma cell lines, including the strong recommendation that cell lines are made widely available via the ATCC or a similar cell repository. Basic research in paraganglioma–pheochromocytoma is currently transitioning from the analysis of genetics to the analysis of disease mechanisms and the clinically exploitable vulnerabilities of tumors. A successful transition will require many more disease-relevant human and animal models to ensure continuing progress.

scholarly journals Interlab Cell Line Collection: Bioresource of Established Human and Animal Cell Lines

2015 ◽  
Vol 2 ◽  
Author(s):  
Barbara Parodi ◽  
Ottavia Aresu ◽  
Paola Visconti ◽  
Maria Assunta Manniello ◽  
Paolo Strada
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Animal Cell
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