Affymetrix DMET™Plus Genotyping Technology: Evaluation of Cell Lines and Healthy Volunteer Samples

M. Pilling, T Mills, G Nicholls, C Hilgendorf, T Andersson, P Bjorquist, A Aspegren, [Unknown] Sartiby, [Unknown] P

    Research output: Contribution to conferencePoster

    Abstract

    We have conducted a pilot study to assess the robustness of SNP genotyping by the Affymetrix DMET™plus platform in the hands of Beckman Coulter Genomics , to develop data handling, statistical analysis and modelling methods and to characterise six pre-clinical cell lines & tissues and 72 samples from a healthy volunteer study. The Affymetrix DMET™ Plus Panel represents 1936 genetic variants (1931 SNPs or In-Dels and five copy number region markers) in 225 genes of importance to ADME. These include the 32 core genes of importance to the PharmADME consortium of academic & pharmaceutical researchers. One hundred and sixty-nine of these variants are located in genes that are currently classified as known valid biomarkers according to the FDA (http://www.fda.gov). The six human pre-clinical samples consisted of HepaRG, Caco2, two cryopreserved hepatocytes and two embryonic stem cell lines. A further six control samples representing blinded triplicates were included for QC purposes. Thorough QC has shown that the quality of the data generated was very high; successful genotype data (for over 98% of the SNPs on the panel) in 82 of the 84 samples tested was generated. Two samples (both cell-lines) fell below this threshold even after repeat analysis. In addition, 98% of SNPs analysed produced genotype calls for >95% of the 84 samples. Genotype concordance >99.9% was observed from two control samples triplicated and 100% genotype concordance was observed in 20 SNPs genotyped by Taqman. Hardy-Weinberg Equilibrium testing of the 72 healthy volunteer samples further suggested that there were no gross genotyping errors. Approximately 65% of the variants of the DMET™ Plus Panel are reported to have a minor allele frequency of less than 5% and this was reflected in our observation that 41.2% of the SNPs were polymorphic in the 72 Caucasian volunteer samples. Data will be presented describing the information obtained for these cell lines.
    Original languageEnglish
    Pages253-253
    Number of pages1
    Publication statusPublished - Aug 2010
    Event9th International Meeting of the International-Society-for-the-Study-of-Xenobiotics - Istanbul, Turkey
    Duration: 4 Sep 20108 Sep 2010
    http://issx.confex.com/issx/intl9/webprogram/Paper22118.html

    Conference

    Conference9th International Meeting of the International-Society-for-the-Study-of-Xenobiotics
    CityIstanbul, Turkey
    Period4/09/108/09/10
    Internet address

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