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Human biosample authentication using the high-throughput, cost-effective SNPtrace(TM) system.

May M Y Liang-Chu1, Mamie Yu1, Peter M Haverty2

  • 1Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States of America.

Plos One
|February 26, 2015
PubMed
Summary
This summary is machine-generated.

Misidentified cell lines waste resources. This study introduces a reliable SNP assay for authenticating human cell lines, determining sex, and detecting contamination, offering a fast and economical alternative to STR profiling.

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Area of Science:

  • Biotechnology
  • Genomics
  • Cell Biology

Background:

  • Cell line misidentification and contamination are significant issues in biomedical research, leading to wasted resources and unreliable data.
  • Accurate authentication of cell lines is crucial for the validity of fundamental research into biological processes and disease mechanisms.

Purpose of the Study:

  • To evaluate a novel panel of 96 single-nucleotide polymorphism (SNP) assays for human cell line authentication and sex determination.
  • To assess the panel's sensitivity in detecting intra-human cross-contamination and compare its performance with existing methods like short tandem repeat (STR) profiling.

Main Methods:

  • Utilized Fluidigm microfluidics technology for a panel of 96 SNP assays (SNPtrace Panel).
  • Tested the SNPtrace Panel on 907 human cell lines, performing pairwise comparisons.
  • Compared sex determination results with annotated sex, STR profiling, and Illumina SNP arrays.
  • Assessed the panel's sensitivity for detecting low-level cross-contamination.

Main Results:

  • The SNPtrace Panel reliably discriminated between identical, related, and unrelated cell line samples with high confidence, comparable to STR profiling.
  • Identified a significant number of male samples incorrectly classified as female due to Y chromosome loss.
  • Demonstrated high sensitivity in detecting intra-human cross-contamination, identifying as little as 2% contaminating cell populations.

Conclusions:

  • Generated a comprehensive database of SNP fingerprints for 907 human cell lines.
  • The SNPtrace Panel offers a reliable, fast, and cost-effective alternative to STR profiling for human cell line and tissue sample authentication.
  • This method aids in improving the integrity of biomedical research by ensuring cell line accuracy.