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

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 conference › Poster

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 language	English
Pages	253-253
Number of pages	1
Publication status	Published - Aug 2010
Event	9th International Meeting of the International-Society-for-the-Study-of-Xenobiotics - Istanbul, Turkey Duration: 4 Sep 2010 → 8 Sep 2010 http://issx.confex.com/issx/intl9/webprogram/Paper22118.html

Conference

Conference	9th International Meeting of the International-Society-for-the-Study-of-Xenobiotics
City	Istanbul, Turkey
Period	4/09/10 → 8/09/10
Internet address	http://issx.confex.com/issx/intl9/webprogram/Paper22118.html

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Pilling, M., Mills, T., Nicholls, G., Hilgendorf, C., Andersson, T., Bjorquist, P., Aspegren, A., Sartiby, U., & P, U. (2010). Affymetrix DMET™Plus Genotyping Technology: Evaluation of Cell Lines and Healthy Volunteer Samples. 253-253. Poster session presented at 9th International Meeting of the International-Society-for-the-Study-of-Xenobiotics, Istanbul, Turkey. http://issx.confex.com/issx/intl9/webprogram/Paper22118.html

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title = "Affymetrix DMET{\texttrademark}Plus Genotyping Technology: Evaluation of Cell Lines and Healthy Volunteer Samples",

abstract = "We have conducted a pilot study to assess the robustness of SNP genotyping by the Affymetrix DMET{\texttrademark}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{\texttrademark} 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{\texttrademark} 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.",

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

year = "2010",

month = aug,

language = "English",

pages = "253--253",

note = "9th International Meeting of the International-Society-for-the-Study-of-Xenobiotics ; Conference date: 04-09-2010 Through 08-09-2010",

url = "http://issx.confex.com/issx/intl9/webprogram/Paper22118.html",

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Pilling, M, Mills, T, Nicholls, G, Hilgendorf, C, Andersson, T, Bjorquist, P, Aspegren, A, Sartiby, U & P, U 2010, 'Affymetrix DMET™Plus Genotyping Technology: Evaluation of Cell Lines and Healthy Volunteer Samples', 9th International Meeting of the International-Society-for-the-Study-of-Xenobiotics, Istanbul, Turkey, 4/09/10 - 8/09/10 pp. 253-253. <http://issx.confex.com/issx/intl9/webprogram/Paper22118.html>

TY - CONF

T1 - Affymetrix DMET™Plus Genotyping Technology: Evaluation of Cell Lines and Healthy Volunteer Samples

AU - Pilling, M.

AU - Mills, T

AU - Nicholls, G

AU - Hilgendorf, C

AU - Andersson, T

AU - Bjorquist, P

AU - Aspegren, A

AU - Sartiby, [Unknown]

AU - P, [Unknown]

PY - 2010/8

Y1 - 2010/8

N2 - 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.

AB - 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.

M3 - Poster

SP - 253

EP - 253

T2 - 9th International Meeting of the International-Society-for-the-Study-of-Xenobiotics

Y2 - 4 September 2010 through 8 September 2010

ER -

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

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