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Cell Line Authentication with Deep Sequencing

Ensure the reproducibility of your research with our deep sequencing-based QC service

Are your cell lines and biological models REALLY what you think they are? According to multiple studies, 1/5 to 1/3 of popular cell lines have been contaminated by intraspecies/interspecies cells, mycoplasma and/or viruses. The International Cell Line Authentication Committee (ICLAC) has documented a growing list of more than 530 misidentified cell lines (updated in June 2021) having no known authentic stock.

Ensure confidence in your models and reproducibility of high quality data by using our deep sequencing-based cell line authentication service. The panel encompasses over 600 SNPs and chromosome segments to accurately characterize mouse and human samples including cell lines, organoids, xenograft models, and patient tissues. We have also generated unique DNA fingerprints for the most commonly used oncology research models, covering over 1,200 human cancer and 30 mouse cell lines.

Conventional PCR-based STR assays target only 9 to 24 STR sites, depending on the vendors. The accuracy of the PCR-based STR assay can be low in cases of close genetic relationships such as the authentication of murine cell lines derived from specific strains of inbred animals that lack unique genetic markers and different tumor cell lineages from the same human donor. Further, biosamples with mutations in mismatch repair (MMR) genes are known to exhibit microsatellite instability and a hypermutator phenotype. Consequently, this can lead to genetic drift and/or outgrowth of contaminating cells and STR misclassification.

Cell Line Authentication with Deep Sequencing

Outperforms Conventional PCR-based STR/SNP Assays
  • Increased Accuracy
  • Increased Sensitivity
  • Higher Throughput
  • Extensive Information
  • Lower Cost Per Sample
  • Rapid Turnaround

With deep sequencing-based QC panel, you will achieve three-level sample authentication.

Client Testimonial

"We have used STR assays for cell line authentication in the past, but found that this technique lacks the sensitivity and ability to detect mouse cell contamination. Unlike other services, the cell line authentication service from Crown Bioscience provides a high-level of sensitivity and accuracy, and the ability to detect interspecies, and other, contamination so we can continue our ground-breaking research."

Professor Hongchun Liu,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences

Cell Line (CLA) Authentication
Assay Comparison
CLA with Deep Sequencing CLA with PCR-based STR Assay
Technology Barcode deep sequencing

Multiplex PCR
& capillary electrophoresis

Readout Type Digital
(clean, near-zero quantification error)
(noisy, high quantification error)
Human Cell Authentication Yes Yes
Mouse Cell Authentication Yes Limited
MMR Deficient Cell lines identification Yes No
Contamination-Detecting Sensitivity High (1%) Low to medium (5-20%)
Accuracy High Low to medium
Throughput High Low
Contaminant Identification Yes No
Qualification of Contamination Ratio Yes No
Suitable for Large Biobanks Yes No
Interspecies Contamination Detection Yes Limited
Intraspecies Contamination Detection Yes Limited
Detecting Contamination w/o Reference Yes No
Estimating Mix Ratios for 3+ Cell Lines Yes (1% sensitivity) No

List of authenticatable human and mouse cell lines
NAR Genomics and Bioinformatics, Volume 2, Issue 3, September 2020, lqaa060 

Sample Requirements and Submission

Sample Type Amount Shipping Conditions
DNA Powder 100-500μg Room tempature (RT)
Liquid Wet ice
Cell Pellet At least 1 million cells

Dry ice

Fresh Tumor Tissue Snap Frozen At least 200mg or 1 million cells Dry ice
Formalin Fixed RT for delivery within 72hr
FFPE Tissue Unstained tissue sections (and H&E stained adjacent sections) RT

Download detailed sample preparation and collection guide

Frequently Asked Questions


What types of cells and models are better characterized with SNP compared to STR?

SNP is especially useful for cells:

  • With deficiencies in mismatch repair/microsatellite instability
  • Derived from closely related inbred strains
  • With chromosomal copy number aberrations

What is the turnaround time?

7-11 business days

How is gender determined?

Human gender is inferred via 3 SNPs on the Y chromosome. Please note that the Y chromosome is lost in some cancer genomes, therefore a predicted result of ‘female’ may not always be accurate.

Which human races can be determined?

Our panel can classify three reference populations, Han Chinese (CHB), Nigeria Yoruba (YRI), and Utah residents with Northern and Western European ancestry (CEU). The race can be predicted when >70% of total SNPs support one population.

What is considered a ‘match’?

Greater than 90% similarity ratio is considered a match.

What does the summary report look like?

Download example report here.

Discuss Your Cell Line Authentication Project

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