Presentation is loading. Please wait.

Presentation is loading. Please wait.

Accurate Detection of Copy Number Changes in DNA Extracted from Formalin-Fixed, Paraffin-Embedded Melanoma Tissue Using Duplex Ratio Tests  David A. Moore,

Published byCharity Bryant Modified over 5 years ago

Similar presentations

Presentation on theme: "Accurate Detection of Copy Number Changes in DNA Extracted from Formalin-Fixed, Paraffin-Embedded Melanoma Tissue Using Duplex Ratio Tests  David A. Moore,"— Presentation transcript:

1 Accurate Detection of Copy Number Changes in DNA Extracted from Formalin-Fixed, Paraffin-Embedded Melanoma Tissue Using Duplex Ratio Tests  David A. Moore, Gerald Saldanha, Abdlrzag Ehdode, Linda Potter, Lovesh Dyall, Danielle Bury, J. Howard Pringle  The Journal of Molecular Diagnostics  Volume 15, Issue 5, Pages (September 2013) DOI: /j.jmoldx Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2 Figure 1 Comparison of diploid tonsil DNA versus melanoma cell-line DNA for the BRAF versus PTEN DRT assay. In the diploid sample, the equal quantity of DNA for the two target genes is reflected in overlapping amplification plots for each product and identical CT values for BRAF and PTEN. In the melanoma sample, the DNA-gain target (BRAF) has a lower CT than the DNA-loss target (PTEN), indicating a difference in DNA copy number between the two targets for this DRT. The difference between the two CT values is the ΔCT. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3 Figure 2 Results for five DRT assays on DNA extracted from fixed and fresh melanoma cell lines, Sk-Mel-5 and Sk-Mel-28. The accuracy of DRT in fixed tissue is demonstrated by an intraclass correlation coefficient of 0.99 for agreement between DNA from fresh and fixed cells. The results of the predicted ratio, using the Predicting Integral Copy Number In Cancer application on array CGH data from these cell lines, are also plotted. The Sk-Mel-5 cell line is known to have a homologous deletion in the CDKN2A gene and there is, therefore, no predicted ratio from the array CGH data in this case. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4 Figure 3 Scatterplots of the DRT scores for the five assays, separated by class (tonsils, nevi, and melanoma). The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Download ppt "Accurate Detection of Copy Number Changes in DNA Extracted from Formalin-Fixed, Paraffin-Embedded Melanoma Tissue Using Duplex Ratio Tests  David A. Moore,"

Similar presentations

Measurement of Relative Copy Number of CDKN2A/ARF and CDKN2B in Bladder Cancer by Real-Time Quantitative PCR and Multiplex Ligation-Dependent Probe Amplification.

Measurement of Relative Copy Number of CDKN2A/ARF and CDKN2B in Bladder Cancer by Real-Time Quantitative PCR and Multiplex Ligation-Dependent Probe Amplification.
CyclinD1/CyclinD3 Ratio by Real-Time PCR Improves Specificity for the Diagnosis of Mantle Cell Lymphoma Carol D. Jones, Katherine H. Darnell, Roger A.

CyclinD1/CyclinD3 Ratio by Real-Time PCR Improves Specificity for the Diagnosis of Mantle Cell Lymphoma Carol D. Jones, Katherine H. Darnell, Roger A.
Design and Multiseries Validation of a Web-Based Gene Expression Assay for Predicting Breast Cancer Recurrence and Patient Survival Ryan K. Van Laar The.

Design and Multiseries Validation of a Web-Based Gene Expression Assay for Predicting Breast Cancer Recurrence and Patient Survival Ryan K. Van Laar The.
Duplex Ratio Tests as Diagnostic Biomarkers in Malignant Melanoma

Duplex Ratio Tests as Diagnostic Biomarkers in Malignant Melanoma
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 1p and 19q Loss in Oligodendroglioma by Quantitative Microsatellite Analysis, a Real-Time Quantitative Polymerase Chain Reaction Assay  Janice.

Detection of 1p and 19q Loss in Oligodendroglioma by Quantitative Microsatellite Analysis, a Real-Time Quantitative Polymerase Chain Reaction Assay  Janice.
A Genome-Wide High-Resolution Array-CGH Analysis of Cutaneous Melanoma and Comparison of Array-CGH to FISH in Diagnostic Evaluation  Lu Wang, Mamta Rao,

A Genome-Wide High-Resolution Array-CGH Analysis of Cutaneous Melanoma and Comparison of Array-CGH to FISH in Diagnostic Evaluation  Lu Wang, Mamta Rao,
Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues  Martina Doleshal,

Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues  Martina Doleshal,
Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens  David H. Spencer, Jennifer K. Sehn,

Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens  David H. Spencer, Jennifer K. Sehn,
Anna Sapino, Paul Roepman, Sabine C. Linn, Mireille H. J

Anna Sapino, Paul Roepman, Sabine C. Linn, Mireille H. J
Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues  Martina Doleshal,

Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues  Martina Doleshal,
High-Resolution Genomic Profiling of Disseminated Tumor Cells in Prostate Cancer  Yu Wu, Jamie R. Schoenborn, Colm Morrissey, Jing Xia, Sandy Larson, Lisha.

High-Resolution Genomic Profiling of Disseminated Tumor Cells in Prostate Cancer  Yu Wu, Jamie R. Schoenborn, Colm Morrissey, Jing Xia, Sandy Larson, Lisha.
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.
Assessing Copy Number Alterations in Targeted, Amplicon-Based Next-Generation Sequencing Data  Catherine Grasso, Timothy Butler, Katherine Rhodes, Michael.

Assessing Copy Number Alterations in Targeted, Amplicon-Based Next-Generation Sequencing Data  Catherine Grasso, Timothy Butler, Katherine Rhodes, Michael.
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.
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,
Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe–Based Single-

Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe–Based Single-
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.
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 

Similar presentations

Ads by Google