Design and Multiseries Validation of a Web-Based Gene Expression Assay for Predicting Breast Cancer Recurrence and Patient Survival Ryan K. Van Laar

Slides:

Advertisements

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.

Advertisements

Telomerase Activity and Expression of Telomerase RNA Component and Telomerase Catalytic Subunit Gene in Cervical Cancer Kenji Nakano, Elizabeth Watney,

Design and Multiseries Validation of a Web-Based Gene Expression Assay for Predicting Breast Cancer Recurrence and Patient Survival Ryan K. Van Laar The.

Development and Clinical Validation of a Real-Time PCR Assay for PITX2 DNA Methylation to Predict Prostate-Specific Antigen Recurrence in Prostate Cancer.

PITX2 DNA Methylation as Biomarker for Individualized Risk Assessment of Prostate Cancer in Core Biopsies Barbara Uhl, Heidrun Gevensleben, Yuri Tolkach,

Molecular Analysis of the Breast Cancer Genes BRCA1 and BRCA2 Using Amplicon- Based Massive Parallel Pyrosequencing Geneviève Michils, Silke Hollants,

Ane Y. Schmidt, Thomas v. O. Hansen, Lise B

Genes with Bimodal Expression Are Robust Diagnostic Targets that Define Distinct Subtypes of Epithelial Ovarian Cancer with Different Overall Survival

Statistical Considerations for Immunohistochemistry Panel Development after Gene Expression Profiling of Human Cancers Rebecca A. Betensky, Catherine.

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

Diego M. Marzese, Dave S. B. Hoon, Kelly K. Chong, Francisco E

Morten Andersen, Morten Grauslund, Jesper Ravn, Jens B

Laboratory Guidelines for Detection, Interpretation, and Reporting of Maternal Cell Contamination in Prenatal Analyses Narasimhan Nagan, Nicole E. Faulkner,

Eligibility Criteria and Genetic Testing Results from a High-Risk Cohort for Hereditary Breast and Ovarian Cancer Syndrome in Southeastern Ontario Ricardo.

An mRNA Gene Expression–Based Signature to Identify FGFR1-Amplified Estrogen Receptor–Positive Breast Tumors Jingqin Luo, Shuzhen Liu, Samuel Leung,

Christos Sotiriou, Chand Khanna, Amir A

Quantitative Fluorescence in Situ Hybridization and its Ability to Predict Bladder Cancer Recurrence and Progression to Muscle-Invasive Bladder Cancer

Somatic Mutations of PI3K in Early and Advanced Gallbladder Cancer

High Expression of Lymphocyte-Activation Gene 3 (LAG3) in Chronic Lymphocytic Leukemia Cells Is Associated with Unmutated Immunoglobulin Variable Heavy.

A Novel Method of Amplification of FFPET-Derived RNA Enables Accurate Disease Classification with Microarrays P. Mickey Williams, Rui Li, Nathalie A.

Joanna Wang, Chetan Bettegowda The Journal of Molecular Diagnostics

Increased Sensitivity of the Roche COBAS AMPLICOR HCV Test, Version 2

Development and Clinical Validation of a Real-Time PCR Assay for PITX2 DNA Methylation to Predict Prostate-Specific Antigen Recurrence in Prostate Cancer.

Comparison of High-Resolution Melting Analysis, TaqMan Allelic Discrimination Assay, and Sanger Sequencing for Clopidogrel Efficacy Genotyping in Routine.

Utilization of Whole-Exome Next-Generation Sequencing Variant Read Frequency for Detection of Lesion-Specific, Somatic Loss of Heterozygosity in a Neurofibromatosis.

An Accurate, Clinically Feasible Multi-Gene Expression Assay for Predicting Metastasis in Uveal Melanoma Michael D. Onken, Lori A. Worley, Meghan D.

Effect of the Prebiotic Oligofructose on Relapse of Clostridium difficile-Associated Diarrhea: A Randomized, Controlled Study Stephen Lewis, Stephen.

Cornelis J. J. Huijsmans, Jeroen Poodt, Paul H. M. Savelkoul, Mirjam H

Learning More from Microarrays: Insights from Modules and Networks

Diagnostic and Prognostic Value of Metastasis Inducer S100A4 Transcripts in Plasma of Colon, Rectal, and Gastric Cancer Patients Ulrike Stein, Susen.

Molecular Classification of MYC-Driven B-Cell Lymphomas by Targeted Gene Expression Profiling of Fixed Biopsy Specimens Christopher D. Carey, Daniel.

The History and Impact of Molecular Coding Changes on Coverage and Reimbursement of Molecular Diagnostic Tests Susan J. Hsiao, Mahesh M. Mansukhani,

Patrick R. Murray The Journal of Molecular Diagnostics

Next-Generation Sequencing of the BRCA1 and BRCA2 Genes for the Genetic Diagnostics of Hereditary Breast and/or Ovarian Cancer Daniel Trujillano, Maximilian.

PITX2 DNA Methylation as Biomarker for Individualized Risk Assessment of Prostate Cancer in Core Biopsies Barbara Uhl, Heidrun Gevensleben, Yuri Tolkach,

Yuqiu Jiang, Graham Casey, Ian C

Identification of Combinatorial Genomic Abnormalities Associated with Prostate Cancer Early Recurrence Xiaoyu Qu, Claudio Jeldres, Lena Glaskova, Cynthia.

Kyong-Ah Yoon, Sohee Park, Sang Hee Lee, Jin Hee Kim, Jin Soo Lee

Katja Lundgren, Nicholas P

The Human Androgen Receptor X-Chromosome Inactivation Assay for Clonality Diagnostics of Natural Killer Cell Proliferations Michaël Boudewijns, Jacques.

Development of an NPM1/MLF1 D-FISH Probe Set for the Detection of t(3;5)(q25;q35) Identified in Patients with Acute Myeloid Leukemia Umut Aypar, Ryan.

Accurate Classification of Germinal Center B-Cell–Like/Activated B-Cell–Like Diffuse Large B-Cell Lymphoma Using a Simple and Rapid Reverse Transcriptase–Multiplex.

Molecular Analysis of the Breast Cancer Genes BRCA1 and BRCA2 Using Amplicon- Based Massive Parallel Pyrosequencing Geneviève Michils, Silke Hollants,

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

Benjamin P. Song, Surbhi Jain, Selena Y. Lin, Quan Chen, Timothy M

Development of a Diagnostic Microarray Assay to Assess the Risk of Recurrence of Prostate Cancer Based on PITX2 DNA Methylation Philipp Schatz, Dimo.

The Molecular Pathology of Primary Immunodeficiencies

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

Serum DNA Motifs Predict Disease and Clinical Status in Multiple Sclerosis Julia Beck, Howard B. Urnovitz, Marina Saresella, Domenico Caputo, Mario Clerici,

Amplification Patterns of Three Genomic Regions Predict Distant Recurrence in Breast Carcinoma Lisa M. Davis, Cole Harris, Lei Tang, Patti Doherty, Peter.

Sanger Confirmation Is Required to Achieve Optimal Sensitivity and Specificity in Next- Generation Sequencing Panel Testing Wenbo Mu, Hsiao-Mei Lu, Jefferey.

Diego M. Marzese, Dave S. B. Hoon, Kelly K. Chong, Francisco E

Multiplexed High Resolution Melting Assay for Versatile Sample Tracking in a Diagnostic and Research Setting Céline Helsmoortel, R. Frank Kooy, Geert.

Molecular Classification of Non–Muscle-Invasive Bladder Cancer (pTa Low-Grade, pT1 Low-Grade, and pT1 High-Grade Subgroups) Using Methylation of Tumor-Suppressor.

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

Sarah-Jane Schramm, Anna E. Campain, Ricenterd A

miR-210 Is a Prognostic Marker in Clear Cell Renal Cell Carcinoma

Multiplexed Methylation Profiles of Tumor Suppressor Genes in Bladder Cancer Maria José Cabello, Laura Grau, Noreli Franco, Esteban Orenes, Miguel Alvarez,

Expression Of Human Chorionic Gonadotropin β-Subunit Type I Genes Predicts Adverse Outcome In Renal Cell Carcinoma Kristina Hotakainen, Susanna Lintula,

Next-Generation Sequencing for Infectious Disease Diagnosis and Management Martina I. Lefterova, Carlos J. Suarez, Niaz Banaei, Benjamin A. Pinsky The.

Matthew D. Wilkerson, Jason M. Schallheim, D. Neil Hayes, Patrick J

Quality Assurance of RNA Expression Profiling in Clinical Laboratories

Examination of Gene Fusion Status in Archival Samples of Alveolar Rhabdomyosarcoma Entered on the Intergroup Rhabdomyosarcoma Study-III Trial Frederic.

Statistical Treatment of Fluorescence in Situ Hybridization Validation Data to Generate Normal Reference Ranges Using Excel Functions Allison L. Ciolino,

Karen Snow-Bailey, Ph.D., 1961–2006

Custom Design of a GeXP Multiplexed Assay Used to Assess Expression Profiles of Inflammatory Gene Targets in Normal Colon, Polyp, and Tumor Tissue Janice.

Efficient Identification of miRNAs for Classification of Tumor Origin

Immunohistochemistry versus Microsatellite Instability Testing for Screening Colorectal Cancer Patients at Risk for Hereditary Nonpolyposis Colorectal.

The History and Impact of Molecular Coding Changes on Coverage and Reimbursement of Molecular Diagnostic Tests Susan J. Hsiao, Mahesh M. Mansukhani,

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

Presentation transcript:

Design and Multiseries Validation of a Web-Based Gene Expression Assay for Predicting Breast Cancer Recurrence and Patient Survival Ryan K. Van Laar The Journal of Molecular Diagnostics Volume 13, Issue 3, Pages 297-304 (May 2011) DOI: 10.1016/j.jmoldx.2010.12.003 Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Visualization of the 200-gene signature in the training series of patients with breast cancer. Patients are represented horizontally, and genes are represented vertically. Rows are ordered by increasing prognostic index (range, –2 to 2), and those individuals experiencing disease relapse within 10 years are indicated with a black bar adjacent to the gene-expression matrix. Patients without disease recurrence but less than a 3-year follow-up are excluded. Gene expression: red, up-regulated; green, down-regulated; and black, no change or absent. The Journal of Molecular Diagnostics 2011 13, 297-304DOI: (10.1016/j.jmoldx.2010.12.003) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Kaplan-Meier analysis of risk-group–stratified training and validation series. P values are from log-rank testing of the high- versus the low-risk group. Validation series 5 was analyzed using a 99-gene subset classifier, generated using 99 of 200 genes available on the NKI custom microarray used (see Supplemental Figure S1 at http://jmd.amjpathol.org). The Journal of Molecular Diagnostics 2011 13, 297-304DOI: (10.1016/j.jmoldx.2010.12.003) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions