Presentation is loading. Please wait.

Presentation is loading. Please wait.

Technical Reproducibility of Single-Nucleotide and Size-Based DNA Biomarker Assessment Using DNA Extracted from Formalin-Fixed, Paraffin-Embedded Tissues 

Published byCory Cameron Modified over 6 years ago

Similar presentations

Presentation on theme: "Technical Reproducibility of Single-Nucleotide and Size-Based DNA Biomarker Assessment Using DNA Extracted from Formalin-Fixed, Paraffin-Embedded Tissues "— Presentation transcript:

1 Technical Reproducibility of Single-Nucleotide and Size-Based DNA Biomarker Assessment Using DNA Extracted from Formalin-Fixed, Paraffin-Embedded Tissues  Shenli Zhang, Iain B. Tan, Nur S. Sapari, Heike I. Grabsch, Alicia Okines, Elizabeth C. Smyth, Toru Aoyama, Lindsay C. Hewitt, Imran Inam, Dan Bottomley, Matthew Nankivell, Sally P. Stenning, David Cunningham, Andrew Wotherspoon, Akira Tsuburaya, Takaki Yoshikawa, Richie Soong, Patrick Tan  The Journal of Molecular Diagnostics  Volume 17, Issue 3, Pages (May 2015) DOI: /j.jmoldx Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2 Figure 1 GSTT1 and TYMS 5′ untranslated region (UTR) genotyping on formalin-fixed, paraffin-embedded (FFPE) samples. A: GSTT1 genotyping on 50 FFPE samples. Samples 1 to 30 are from the MAGIC cohort and 31 to 50 from the JUST cohort. Complete absence of the GSTT1 product (top panel) in the presence of an ACTB amplicon (bottom panel) was interpreted as a homozygous deletion (GSTT1 *0/0 null genotype). The presence of a GSTT1 product was interpreted as GSTT1 positive. Samples labeled with stars exhibit discrepant results between two independent runs. Sample 21 (arrow) failed in the second run and was excluded from the analysis. The concordance rate between the two runs was 69.4% for FFPE DNA. B: TYMS 5′-UTR genotyping on 50 FFPE samples. Sequence repeats in the TYMS 5′-UTR enhancer region can be classified into 2R/2R, 2R/3R, and 3R/3R genotypes. Samples labeled with stars exhibited discrepant results between the two independent runs. Sample 21 (arrow) failed in both runs, and sample 37 failed in the first run. The concordance rate between the two runs was 95.8% for FFPE DNA. gDNA, genomic DNA; M, 100-bp DNA ladder; NC, negative control. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3 Figure 2 GSTT1 and TYMS 5′ untranslated region (UTR) genotyping on fresh-frozen gastric cell lines and normal tissues. A: GSTT1 (top panel) and TYMS 5′-UTR (bottom panel) genotyping on gastric cell lines. B: GSTT1 (top panel) and TYMS 5′-UTR (bottom panel) genotyping on normal tissues. There is no discrepancy found between the two independent runs on both fresh-frozen gastric cell lines and normal tissues. gDNA, genomic DNA; M, 100-bp DNA ladder; NC, negative control. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Download ppt "Technical Reproducibility of Single-Nucleotide and Size-Based DNA Biomarker Assessment Using DNA Extracted from Formalin-Fixed, Paraffin-Embedded Tissues "

Similar presentations

High-Quality Genotyping Data from Formalin-Fixed, Paraffin-Embedded Tissue on the Drug Metabolizing Enzymes and Transporters Plus Array  Hanneke I. Vos,

High-Quality Genotyping Data from Formalin-Fixed, Paraffin-Embedded Tissue on the Drug Metabolizing Enzymes and Transporters Plus Array  Hanneke I. Vos,
Detection of Exon 12 Mutations in the JAK2 Gene

Detection of Exon 12 Mutations in the JAK2 Gene
Anna Sapino, Paul Roepman, Sabine C. Linn, Mireille H. J

Anna Sapino, Paul Roepman, Sabine C. Linn, Mireille H. J
Simultaneous Detection of Clinically Relevant Mutations and Amplifications for Routine Cancer Pathology  Marlous Hoogstraat, John W.J. Hinrichs, Nicolle.

Simultaneous Detection of Clinically Relevant Mutations and Amplifications for Routine Cancer Pathology  Marlous Hoogstraat, John W.J. Hinrichs, Nicolle.
Carol Beadling, Tanaya L. Neff, Michael C

Carol Beadling, Tanaya L. Neff, Michael C
A Targeted High-Throughput Next-Generation Sequencing Panel for Clinical Screening of Mutations, Gene Amplifications, and Fusions in Solid Tumors  Rajyalakshmi.

A Targeted High-Throughput Next-Generation Sequencing Panel for Clinical Screening of Mutations, Gene Amplifications, and Fusions in Solid Tumors  Rajyalakshmi.
Genotyping of DNA Samples Isolated from Formalin-Fixed Paraffin-Embedded Tissues Using Preamplification  Renee Baak-Pablo, Vincent Dezentje, Henk-Jan.

Genotyping of DNA Samples Isolated from Formalin-Fixed Paraffin-Embedded Tissues Using Preamplification  Renee Baak-Pablo, Vincent Dezentje, Henk-Jan.
Sensitive Detection of KRAS Mutations in Archived Formalin-Fixed Paraffin-Embedded Tissue Using Mutant-Enriched PCR and Reverse-Hybridization  Christoph.

Sensitive Detection of KRAS Mutations in Archived Formalin-Fixed Paraffin-Embedded Tissue Using Mutant-Enriched PCR and Reverse-Hybridization  Christoph.
RT-PCR Analysis of RNA Extracted from Bouin-Fixed and Paraffin-Embedded Lymphoid Tissues  Annunziata Gloghini, Barbara Canal, Ulf Klein, Luigino Dal Maso,

RT-PCR Analysis of RNA Extracted from Bouin-Fixed and Paraffin-Embedded Lymphoid Tissues  Annunziata Gloghini, Barbara Canal, Ulf Klein, Luigino Dal Maso,
Application of Selected Reaction Monitoring for Multiplex Quantification of Clinically Validated Biomarkers in Formalin-Fixed, Paraffin-Embedded Tumor.

Application of Selected Reaction Monitoring for Multiplex Quantification of Clinically Validated Biomarkers in Formalin-Fixed, Paraffin-Embedded Tumor.
Molecular Diagnosis of Clear Cell Sarcoma

Molecular Diagnosis of Clear Cell Sarcoma
A Method to Evaluate the Quality of Clinical Gene-Panel Sequencing Data for Single- Nucleotide Variant Detection  Chung Lee, Joon S. Bae, Gyu H. Ryu, Nayoung.

A Method to Evaluate the Quality of Clinical Gene-Panel Sequencing Data for Single- Nucleotide Variant Detection  Chung Lee, Joon S. Bae, Gyu H. Ryu, Nayoung.
Analytical Validation of a Next-Generation Sequencing Assay to Monitor Immune Responses in Solid Tumors  Jeffrey M. Conroy, Sarabjot Pabla, Sean T. Glenn,

Analytical Validation of a Next-Generation Sequencing Assay to Monitor Immune Responses in Solid Tumors  Jeffrey M. Conroy, Sarabjot Pabla, Sean T. Glenn,
Laboratory Guidelines for Detection, Interpretation, and Reporting of Maternal Cell Contamination in Prenatal Analyses  Narasimhan Nagan, Nicole E. Faulkner,

Laboratory Guidelines for Detection, Interpretation, and Reporting of Maternal Cell Contamination in Prenatal Analyses  Narasimhan Nagan, Nicole E. Faulkner,
Whole Genome Amplification for Array Comparative Genomic Hybridization Using DNA Extracted from Formalin-Fixed, Paraffin-Embedded Histological Sections 

Whole Genome Amplification for Array Comparative Genomic Hybridization Using DNA Extracted from Formalin-Fixed, Paraffin-Embedded Histological Sections 
Performance of Common Analysis Methods for Detecting Low-Frequency Single Nucleotide Variants in Targeted Next-Generation Sequence Data  David H. Spencer,

Performance of Common Analysis Methods for Detecting Low-Frequency Single Nucleotide Variants in Targeted Next-Generation Sequence Data  David H. Spencer,
Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing  Ming Wang, Leire.

Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing  Ming Wang, Leire.
Suppression of Wild-Type Amplification by Selectivity Enhancing Agents in PCR Assays that Utilize SuperSelective Primers for the Detection of Rare Somatic.

Suppression of Wild-Type Amplification by Selectivity Enhancing Agents in PCR Assays that Utilize SuperSelective Primers for the Detection of Rare Somatic.
Multiplex Preamplification of Serum DNA to Facilitate Reliable Detection of Extremely Rare Cancer Mutations in Circulating DNA by Digital PCR  Jennifer.

Multiplex Preamplification of Serum DNA to Facilitate Reliable Detection of Extremely Rare Cancer Mutations in Circulating DNA by Digital PCR  Jennifer.
A Multiplex SNaPshot Assay as a Rapid Method for Detecting KRAS and BRAF Mutations in Advanced Colorectal Cancers  Sandrine Magnin, Erika Viel, Alice.

A Multiplex SNaPshot Assay as a Rapid Method for Detecting KRAS and BRAF Mutations in Advanced Colorectal Cancers  Sandrine Magnin, Erika Viel, Alice.

Similar presentations

Ads by Google