Accurate Molecular Characterization of Formalin-Fixed, Paraffin-Embedded Tissues by microRNA Expression Profiling Anna E. Szafranska, Timothy S. Davison,

Slides:

Advertisements

Similar presentations

Development of a Novel One-Tube Isothermal Reverse Transcription Thermophilic Helicase-Dependent Amplification Platform for Rapid RNA Detection James Goldmeyer,

Advertisements

CyclinD1/CyclinD3 Ratio by Real-Time PCR Improves Specificity for the Diagnosis of Mantle Cell Lymphoma Carol D. Jones, Katherine H. Darnell, Roger A.

Accurate Molecular Characterization of Formalin-Fixed, Paraffin-Embedded Tissues by microRNA Expression Profiling Anna E. Szafranska, Timothy S. Davison,

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

Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues Martina Doleshal,

Gene expression arrays in cancer research: methods and applications

In Vitro Transcription Amplification and Labeling Methods Contribute to the Variability of Gene Expression Profiling with DNA Microarrays Changqing Ma,

Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens David H. Spencer, Jennifer K. Sehn,

M. Fu, G. Huang, Z. Zhang, J. Liu, Z. Zhang, Z. Huang, B. Yu, F. Meng

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,

Profiling and Discovery of Novel miRNAs from Formalin-Fixed, Paraffin-Embedded Melanoma and Nodal Specimens Zhihai Ma, Weng-Onn Lui, Andrew Fire, Soheil.

A Strategy to Find Suitable Reference Genes for miRNA Quantitative PCR Analysis and Its Application to Cervical Specimens Iris Babion, Barbara C. Snoek,

Genotyping of DNA Samples Isolated from Formalin-Fixed Paraffin-Embedded Tissues Using Preamplification Renee Baak-Pablo, Vincent Dezentje, Henk-Jan.

Accurate Molecular Classification of Renal Tumors Using MicroRNA Expression Eddie Fridman, Zohar Dotan, Iris Barshack, Miriam Ben David, Avital Dov, Sarit.

Bead Array–Based microRNA Expression Profiling of Peripheral Blood and the Impact of Different RNA Isolation Approaches Andrea Gaarz, Svenja Debey-Pascher,

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

Genotyping of Chimerical BCR-ABL1 RNA in Chronic Myeloid Leukemia by Integrated DNA Chip Jong-Hun Kang, Hyun-Gyung Goh, Sang-Ho Chae, Sung-Yong Kim,

A Quantitative Reverse Transcriptase-Polymerase Chain Reaction Assay to Identify Metastatic Carcinoma Tissue of Origin Dimitri Talantov, Jonathan Baden,

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.

Bongyong Lee, Joseph Mazar, Muhammad N

Hendrikus J. Dubbink, Peggy N. Atmodimedjo, Ronald van Marion, Niels M

Separate Quality-Control Measures Are Necessary for Estimation of RNA and Methylated DNA from Formalin-Fixed, Paraffin-Embedded Specimens by Quantitative.

Comparison of Snap Freezing versus Ethanol Fixation for Gene Expression Profiling of Tissue Specimens Mark A. Perlmutter, Carolyn J.M. Best, John W.

Kirby Siemering, Shehnaaz S. M. Manji, Wendy M

Christos Sotiriou, Chand Khanna, Amir A

Successful Application of Microarray Technology to Microdissected Formalin-Fixed, Paraffin-Embedded Tissue Renata A. Coudry, Sibele I. Meireles, Radka.

Characterization of microRNA transcriptome in tumor, adjacent, and normal tissues of lung squamous cell carcinoma Jun Wang, MD, PhD, Zhi Li, MD, PhD,

A Diagnostic Assay Based on MicroRNA Expression Accurately Identifies Malignant Pleural Mesothelioma Hila Benjamin, Danit Lebanony, Shai Rosenwald, Lahav.

Precision Profiling and Components of Variability Analysis for Affymetrix Microarray Assays Run in a Clinical Context Thomas M. Daly, Carmen M. Dumaual,

Immunoguided Laser Assisted Microdissection Techniques for DNA Methylation Analysis of Archival Tissue Specimens Franziska C. Eberle, Jeffrey C. Hanson,

Establishment and Study of Different Real-Time Polymerase Chain Reaction Assays for the Quantification of Cells with Deletions of Chromosome 7 Elia Mattarucchi,

Potential role of circulating microRNAs as a biomarker for unexplained recurrent spontaneous abortion Weibing Qin, M.D., Ph.D., Yunge Tang, M.D., Ning.

Profiling and Discovery of Novel miRNAs from Formalin-Fixed, Paraffin-Embedded Melanoma and Nodal Specimens Zhihai Ma, Weng-Onn Lui, Andrew Fire, Soheil.

Influence of RNA Labeling on Expression Profiling of MicroRNAs

Quantitative Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays Diana Abdueva, Michele Wing, Betty Schaub, Timothy.

Interlaboratory Performance of a Microarray-Based Gene Expression Test to Determine Tissue of Origin in Poorly Differentiated and Undifferentiated Cancers

Christopher R. Cabanski, Vincent Magrini, Malachi Griffith, Obi L

Quantitative mRNA Expression Analysis from Formalin-Fixed, Paraffin-Embedded Tissues Using 5′ Nuclease Quantitative Reverse Transcription-Polymerase Chain.

Steve Byerly, Kyle Sundin, Rajiv Raja, Jim Stanchfield, Bassem A

Anna Sapino, Paul Roepman, Sabine C. Linn, Mireille H. J

QuantiGene Plex Represents a Promising Diagnostic Tool for Cell-of-Origin Subtyping of Diffuse Large B-Cell Lymphoma John S. Hall, Suzanne Usher, Richard.

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

Prognostic Gene Expression Signatures Can Be Measured in Tissues Collected in RNAlater Preservative Dondapati Chowdary, Jessica Lathrop, Joanne Skelton,

Volume 85, Issue 2, Pages (January 2014)

Jinny Liu, Elizabeth Walter, David Stenger, Dzung Thach

Microarray Analysis of Thyroid Nodule Fine-Needle Aspirates Accurately Classifies Benign and Malignant Lesions Carrie C. Lubitz, Stacy K. Ugras, J. Jacob.

Jinny Liu, Elizabeth Walter, David Stenger, Dzung Thach

Accurate and Reproducible Gene Expression Profiles from Laser Capture Microdissection, Transcript Amplification, and High Density Oligonucleotide Microarray.

RNA-Stabilized Whole Blood Samples but Not Peripheral Blood Mononuclear Cells Can Be Stored for Prolonged Time Periods Prior to Transcriptome Analysis

An Array-Based Analysis of MicroRNA Expression Comparing Matched Frozen and Formalin-Fixed Paraffin-Embedded Human Tissue Samples Xiao Zhang, Jiamin.

Molecular Monitoring of Chronic Myelogenous Leukemia

Analysis of Microarray Data Using Z Score Transformation

Microarray Gene Expression Analysis of Fixed Archival Tissue Permits Molecular Classification and Identification of Potential Therapeutic Targets in Diffuse.

Association of MicroRNA Expression with Microsatellite Instability Status in Colorectal Adenocarcinoma Jonathan S.L. Earle, Rajyalakshmi Luthra, Angela.

Reliability and Reproducibility of Gene Expression Measurements Using Amplified RNA from Laser-Microdissected Primary Breast Tissue with Oligonucleotide.

Performance and Clinical Evaluation of a Sensitive Multiplex Assay for the Rapid Detection of Common NPM1 Mutations Michael Hafez, Fei Ye, Keith Jackson,

Quality Assurance of RNA Expression Profiling in Clinical Laboratories

Gayatry Mohapatra, Rebecca A. Betensky, Ezra R

Beatrice S. Knudsen, April N. Allen, Dale F. McLerran, Robert L

Gene Expression Profiles of Cutaneous B Cell Lymphoma

Mangalathu S. Rajeevan, Suzanne D

JAZF1/JJAZ1 Gene Fusion in Endometrial Stromal Sarcomas

MiRNA Expression Profiling in Melanocytes and Melanoma Cell Lines Reveals miRNAs Associated with Formation and Progression of Malignant Melanoma Daniel.

Evaluation of High-Resolution Melting Analysis as a Diagnostic Tool to Detect the BRAF V600E Mutation in Colorectal Tumors Martin Pichler, Marija Balic,

Validation and Reproducibility of a Microarray-Based Gene Expression Test for Tumor Identification in Formalin-Fixed, Paraffin-Embedded Specimens Raji.

MicroRNA Expression in Melanocytic Nevi: The Usefulness of Formalin-Fixed, Paraffin- Embedded Material for miRNA Microarray Profiling Martin Glud, Mikkel.

Detection of BRCA1 and BRCA2 Ashkenazi Jewish Founder Mutations in Formalin- Fixed Paraffin-Embedded Tissues Using Conventional PCR and Heteroduplex/Amplicon.

In Vitro Transcription Amplification and Labeling Methods Contribute to the Variability of Gene Expression Profiling with DNA Microarrays Changqing Ma,

MammaPrint and BluePrint Molecular Diagnostics Using Targeted RNA Next-Generation Sequencing Technology Lorenza Mittempergher, Leonie J.M.J. Delahaye,

Presentation transcript:

Accurate Molecular Characterization of Formalin-Fixed, Paraffin-Embedded Tissues by microRNA Expression Profiling Anna E. Szafranska, Timothy S. Davison, Jaclyn Shingara, Martina Doleshal, Judith A. Riggenbach, Carl D. Morrison, Scott Jewell, Emmanuel Labourier The Journal of Molecular Diagnostics Volume 10, Issue 5, Pages 415-423 (September 2008) DOI: 10.2353/jmoldx.2008.080018 Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 miRNA expression profiling in four mouse tissues. A: Unsupervised hierarchical clustering of miRNA expression in paired frozen and fixed mouse brain, stomach (Stom), small intestine (SmInt), and kidney (Kidn) using a two-color array platform. Expression levels are color-coded from green to red relative to the common reference hybridization sample used for each array, with red indicating enrichment in a given sample. Gray squares represent flagged miRNAs probes with low array signal below threshold (no data). B and C: Correlation of miRNA expression levels for paired fixed versus frozen mouse kidney, brain, small intestine, and stomach. Correlations were calculated using mean normalized expression levels in fixed and frozen samples (n = 4 donors per tissue). The Journal of Molecular Diagnostics 2008 10, 415-423DOI: (10.2353/jmoldx.2008.080018) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Correlation between fixed and frozen miRNA expression profiles in myometrium according to tissue age. A–C: Mean miRNA expression in 1-, 7-, and 11-year-old FFPE myometrium samples relative to frozen samples. The correlation value in brackets was calculated following removal of miR-494 and miR-513. D: Mean expression level of miR-494 and miR-513 in indicated fixed samples, relative to expression levels in frozen samples. The Journal of Molecular Diagnostics 2008 10, 415-423DOI: (10.2353/jmoldx.2008.080018) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Variation of microarray platform performance according to FFPE tissue block age. A: Mean percentage of miRNAs detected above threshold for frozen (Myo_(1yr), n = 2), fixed 1-year-old (Myo_(1yr), n = 2), fixed 7-year-old (Myo_(7yr), n = 3), and fixed 11-year-old (Myo_(11yr), n = 4) myometrium tissues. The minimum threshold was defined as the 5% symmetric trimmed mean plus two standard deviations of the foreground minus background median intensities across all empty spots on individual arrays. B: Average foreground signals (excluding control spots) and background signals (including all spots) for microarrays described in A. C: Mean percentage of miRNAs detected above threshold in fixed myometrium samples according to expression levels in frozen samples. The Journal of Molecular Diagnostics 2008 10, 415-423DOI: (10.2353/jmoldx.2008.080018) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Differential miRNA expression for paired fixed versus frozen myometrium (n = 6 samples) and B-cell lymphoma (n = 6 samples). A: Principal component analysis of miRNA expression in fixed and paired frozen myometrium and B-cell lymphoma. B: Correlation between mean differential miRNA expression level (Δh) in fixed myometrium and B-cell lymphoma as compared to corresponding frozen tissue set. The indicated correlation coefficient includes probes that were detected in any of the eight analyzed samples. The Journal of Molecular Diagnostics 2008 10, 415-423DOI: (10.2353/jmoldx.2008.080018) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 5 Comparison between microarray and qRT-PCR platforms. A: Example of miRNAs differentially expressed in three independent liver NAT and spleen technical replicates as determined by microarray and qRT-PCR. For each RNA sample, duplicate reverse transcription reactions followed by duplicate PCR from each reverse transcription reaction was performed. B: Correlation between the microarray and qRT-PCR platforms for the mean differential expression of 14 miRNAs in liver NAT and spleen replicates. The Journal of Molecular Diagnostics 2008 10, 415-423DOI: (10.2353/jmoldx.2008.080018) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions