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

Liang-Chu MM, Yu M, Haverty PM, Koeman J, Ziegle J, Lee M, Bourgon R, Neve RM - PLoS ONE (2015)

Bottom Line: Cell lines are the foundation for much of the fundamental research into the mechanisms underlying normal biologic processes and disease mechanisms.Finally we assessed the sensitivity of the SNPtrace Panel to detect intra-human cross-contamination, resulting in detection of as little as 2% contaminating cell population.In conclusion, this study has generated a database of SNP fingerprints for 907 cell lines used in biomedical research and provides a reliable, fast, and economic alternative to STR profiling which can be applied to any human cell line or tissue sample.

View Article: PubMed Central - PubMed

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

ABSTRACT
Cell lines are the foundation for much of the fundamental research into the mechanisms underlying normal biologic processes and disease mechanisms. It is estimated that 15%-35% of human cell lines are misidentified or contaminated, resulting in a huge waste of resources and publication of false or misleading data. Here we evaluate a panel of 96 single-nucleotide polymorphism (SNP) assays utilizing Fluidigm microfluidics technology for authentication and sex determination of human cell lines. The SNPtrace Panel was tested on 907 human cell lines. Pairwise comparison of these data show the SNPtrace Panel discriminated among identical, related and unrelated pairs of samples with a high degree of confidence, equivalent to short tandem repeat (STR) profiling. We also compared annotated sex calls with those determined by the SNPtrace Panel, STR and Illumina SNP arrays, revealing a high number of male samples are identified as female due to loss of the Y chromosome. Finally we assessed the sensitivity of the SNPtrace Panel to detect intra-human cross-contamination, resulting in detection of as little as 2% contaminating cell population. In conclusion, this study has generated a database of SNP fingerprints for 907 cell lines used in biomedical research and provides a reliable, fast, and economic alternative to STR profiling which can be applied to any human cell line or tissue sample.

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Related in: MedlinePlus

Pairwise identity scores for cell lines using the SNPtrace Panel and STR profiling.(A) Results of pairwise analysis of all cell line samples broken out into technical and biological replicates, synonymous samples, and unrelated samples. For unrelated samples, 24- and 48- SNPs were randomly selected for pairwise comparisons and contrasted with the complete 96-SNP set. (B) Comparison of pairwise scores from the SNPtrace Panel and STR profiling. Shaded region is joint distribution of SNP and STR-based identity scores for pairwise comparisons of unrelated lines (n = 467,746); in addition, two unrelated pairs which generated unexpectedly high identity scores are called out as blue diamonds (“1” and “2”). Red and green points correspond to synonymous and replicate pairs, respectively. Table 1 describes the cell line pairs marked by 1–6 in this figure.
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pone.0116218.g001: Pairwise identity scores for cell lines using the SNPtrace Panel and STR profiling.(A) Results of pairwise analysis of all cell line samples broken out into technical and biological replicates, synonymous samples, and unrelated samples. For unrelated samples, 24- and 48- SNPs were randomly selected for pairwise comparisons and contrasted with the complete 96-SNP set. (B) Comparison of pairwise scores from the SNPtrace Panel and STR profiling. Shaded region is joint distribution of SNP and STR-based identity scores for pairwise comparisons of unrelated lines (n = 467,746); in addition, two unrelated pairs which generated unexpectedly high identity scores are called out as blue diamonds (“1” and “2”). Red and green points correspond to synonymous and replicate pairs, respectively. Table 1 describes the cell line pairs marked by 1–6 in this figure.

Mentions: Mean and standard deviation for the pairwise identity scores were computed for all synonymous pairs (excluding two outliers in Fig. 1B). The distribution of these scores was seen to be approximately Gaussian, so non-synonymous pairs were scored based on the upper tail probability of a normal distribution with the computed mean and standard deviation.


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

Liang-Chu MM, Yu M, Haverty PM, Koeman J, Ziegle J, Lee M, Bourgon R, Neve RM - PLoS ONE (2015)

Pairwise identity scores for cell lines using the SNPtrace Panel and STR profiling.(A) Results of pairwise analysis of all cell line samples broken out into technical and biological replicates, synonymous samples, and unrelated samples. For unrelated samples, 24- and 48- SNPs were randomly selected for pairwise comparisons and contrasted with the complete 96-SNP set. (B) Comparison of pairwise scores from the SNPtrace Panel and STR profiling. Shaded region is joint distribution of SNP and STR-based identity scores for pairwise comparisons of unrelated lines (n = 467,746); in addition, two unrelated pairs which generated unexpectedly high identity scores are called out as blue diamonds (“1” and “2”). Red and green points correspond to synonymous and replicate pairs, respectively. Table 1 describes the cell line pairs marked by 1–6 in this figure.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4340925&req=5

pone.0116218.g001: Pairwise identity scores for cell lines using the SNPtrace Panel and STR profiling.(A) Results of pairwise analysis of all cell line samples broken out into technical and biological replicates, synonymous samples, and unrelated samples. For unrelated samples, 24- and 48- SNPs were randomly selected for pairwise comparisons and contrasted with the complete 96-SNP set. (B) Comparison of pairwise scores from the SNPtrace Panel and STR profiling. Shaded region is joint distribution of SNP and STR-based identity scores for pairwise comparisons of unrelated lines (n = 467,746); in addition, two unrelated pairs which generated unexpectedly high identity scores are called out as blue diamonds (“1” and “2”). Red and green points correspond to synonymous and replicate pairs, respectively. Table 1 describes the cell line pairs marked by 1–6 in this figure.
Mentions: Mean and standard deviation for the pairwise identity scores were computed for all synonymous pairs (excluding two outliers in Fig. 1B). The distribution of these scores was seen to be approximately Gaussian, so non-synonymous pairs were scored based on the upper tail probability of a normal distribution with the computed mean and standard deviation.

Bottom Line: Cell lines are the foundation for much of the fundamental research into the mechanisms underlying normal biologic processes and disease mechanisms.Finally we assessed the sensitivity of the SNPtrace Panel to detect intra-human cross-contamination, resulting in detection of as little as 2% contaminating cell population.In conclusion, this study has generated a database of SNP fingerprints for 907 cell lines used in biomedical research and provides a reliable, fast, and economic alternative to STR profiling which can be applied to any human cell line or tissue sample.

View Article: PubMed Central - PubMed

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

ABSTRACT
Cell lines are the foundation for much of the fundamental research into the mechanisms underlying normal biologic processes and disease mechanisms. It is estimated that 15%-35% of human cell lines are misidentified or contaminated, resulting in a huge waste of resources and publication of false or misleading data. Here we evaluate a panel of 96 single-nucleotide polymorphism (SNP) assays utilizing Fluidigm microfluidics technology for authentication and sex determination of human cell lines. The SNPtrace Panel was tested on 907 human cell lines. Pairwise comparison of these data show the SNPtrace Panel discriminated among identical, related and unrelated pairs of samples with a high degree of confidence, equivalent to short tandem repeat (STR) profiling. We also compared annotated sex calls with those determined by the SNPtrace Panel, STR and Illumina SNP arrays, revealing a high number of male samples are identified as female due to loss of the Y chromosome. Finally we assessed the sensitivity of the SNPtrace Panel to detect intra-human cross-contamination, resulting in detection of as little as 2% contaminating cell population. In conclusion, this study has generated a database of SNP fingerprints for 907 cell lines used in biomedical research and provides a reliable, fast, and economic alternative to STR profiling which can be applied to any human cell line or tissue sample.

Show MeSH
Related in: MedlinePlus