SNP Trace Panel Proves to Be a High-Throughput, Cost-Effective SNP-Based Platform for Profiling Human Tissue and Cell Lines
Researchers at Genentech, a member of the Roche Group, and Fluidigm Corporation have used the Fluidigm SNP TraceTM panel to generate a database of SNP profiles for 907 cancer cell lines as a resource for cell line authentication. This information was published in the current issue of the journal PLOS ONE in a paper entitled “Human biosample authentication using the high-throughput, cost-effective SNP TraceTM system” (http://dx.plos.org/10.1371/journal.pone.0116218).
The SNP Trace panel generates a unique genomic profile of any human cell line or tissue sample. The authors found SNP profiling with the SNP Trace panel to be an effective and sensitive cell line authentication method comparable to short tandem repeat (STR) profiling.
Human cell lines and patient-derived tissues are essential for biomedical research. It has been estimated that between 15-35% of human cell line cultures are contaminated or misidentified in some manner which could result in the publication of false results and lead to subsequent retractions. Although cell line misidentification and contamination is a widespread and known problem, many researchers have not incorporated cell line authentication and quality control in their laboratories because current STR profiling methods are error prone and laborious.
In this paper, the authors compared the ability of the SNP Trace panel to identify and authenticate cell lines to STR profiling, the current ANSI standard for cell line authentication. The authors found SNP Trace panel performance to be equivalent to STR profiling. Pairwise comparison of SNP profiles generated by the SNP Trace panel detected identical or replicate samples, as well as distinguished unique, but closely related, samples, with a degree of confidence equivalent to STR profiling. SNP Trace also corrected the existing annotation for the cell lines by correctly assigning sex to the samples after Y chromosome exclusion.
“We demonstrated that the SNP Trace panel is a DNA profiling technology which can be used alone or in conjunction with established cell line authentication methods for labs to continually monitor cell line identity. Moreover, the analysis of SNPs can provide a fast, reliable, accurate and cost-effective method for assessing cell line or human biosample identity and intra-human cross-contamination,” said Nico Tuason, Senior Product Manager, Fluidigm. “We hope this information will help establish SNP profiling as a strong alternative or complementary option to STR profiling.”
The SNP Trace panel was tested on 907 human cell lines generating SNP profiles at least as accurate as current STR profiling. SNP profiling reduced hands-on time more than 20-fold, according to the authors, and lowered cost as much as six-fold per sample compared to STRs.
The Fluidigm SNP Trace panel is a set of 96 SNPs for DNA sample quality control and identification that:
- confirms cell line identity to find sample annotation errors;
- assesses sample quality for samples that may not perform well in a GWAS or NGS experiment;
- detects unexpected duplicates or sample contamination; and
- assigns a DNA profile to enable biological sample tracking throughout any downstream analysis.
Fluidigm (NASDAQ:FLDM) develops, manufactures, and markets life science analytical and preparatory systems for growth markets such as single-cell biology and production genomics. We sell to leading academic institutions, clinical laboratories, and pharmaceutical, biotechnology, and agricultural biotechnology companies worldwide. Our systems are based on proprietary microfluidics and multi-parameter mass cytometry technology, and are designed to significantly simplify experimental workflow, increase throughput, and reduce costs, while providing excellent data quality. Fluidigm products are provided for Research Use Only. Not for use in diagnostic procedures.
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