Jennifer A. Hempelmann, Sheena M. Scroggins, Colin C

Slides:

Advertisements

Similar presentations

Microsatellite Instability Detection by Next Generation Sequencing S.J. Salipante, S.M. Scroggins, H.L. Hampel, E.H. Turner, and C.C. Pritchard September.

Advertisements

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

Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement.

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

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

A Novel Method for Multiplex Genotyping in a Single Reactor Using GTPlex-PyroSeq Myungsok Oh, Benjamin Douglass Hoehn, Youngho Moon, Taejeong Oh, Youngbok.

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

Targeted Next-Generation Sequencing for Hereditary Cancer Syndromes

Single-Color Digital PCR Provides High-Performance Detection of Cancer Mutations from Circulating DNA Christina Wood-Bouwens, Billy T. Lau, Christine.

In Silico Proficiency Testing for Clinical Next-Generation Sequencing

Hybrid Model Integrating Immunohistochemistry and Expression Profiling for the Classification of Carcinomas of Unknown Primary Site Barbara A. Centeno,

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,

Next-Generation Sequencing

A Quantitative Allele-Specific PCR Test for the BRAF V600E Mutation Using a Single Heterozygous Control Plasmid for Quantitation Philippe Szankasi, N.

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

Detection of Mismatch Repair Deficiency and Microsatellite Instability in Colorectal Adenocarcinoma by Targeted Next-Generation Sequencing Jonathan A.

Yang Wang, Chanjuan Shi, Rosana Eisenberg, Cindy L. Vnencak-Jones

Molecular Genetics of Pediatric Soft Tissue Tumors

False Positives in Multiplex PCR-Based Next-Generation Sequencing Have Unique Signatures Chad M. McCall, Stacy Mosier, Michele Thiess, Marija Debeljak,

Multiplex Preamplification of Serum DNA to Facilitate Reliable Detection of Extremely Rare Cancer Mutations in Circulating DNA by Digital PCR Jennifer.

Development and Validation of a Preanalytic Procedure for Performing the cobas HPV Test in SurePath Preservative Fluid Mark D. Krevolin, David Hardy,

Detection of Microsatellite Instability in Colorectal Cancer Using an Alternative Multiplex Assay of Quasi-Monomorphic Mononucleotide Markers Vanessa.

Accurate Quantification of T Cells by Measuring Loss of Germline T-Cell Receptor Loci with Generic Single Duplex Droplet Digital PCR Assays Willem H.

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

A New Targeted CFTR Mutation Panel Based on Next-Generation Sequencing Technology Marco Lucarelli, Luigi Porcaro, Alice Biffignandi, Lucy Costantino,

Detection of KRAS and BRAF Mutations in Colorectal Carcinoma

Getting Things Backwards to Prevent Primer Dimers

Assessment of EGFR Mutation Status in Lung Adenocarcinoma by Immunohistochemistry Using Antibodies Specific to the Two Major Forms of Mutant EGFR Marie.

Patrick R. Murray The Journal of Molecular Diagnostics

Christine L. Baker, Cecily P. Vaughn, Wade S. Samowitz

A Novel and Reliable Method to Detect Microsatellite Instability in Colorectal Cancer by Next-Generation Sequencing Lizhen Zhu, Yanqin Huang, Xuefeng.

Hillary S. Sloane, James P. Landers, Kimberly A. Kelly

Use of Single Nucleotide Polymorphisms (SNP) and Real-Time Polymerase Chain Reaction for Bone Marrow Engraftment Analysis Dwight H. Oliver, Richard E.

Reliable and Sensitive Detection of Fragile X (Expanded) Alleles in Clinical Prenatal DNA Samples with a Fast Turnaround Time Sara Seneca, Willy Lissens,

Driver Gene Mutations in Stools of Colorectal Carcinoma Patients Detected by Targeted Next-Generation Sequencing Gemma Armengol, Virinder K. Sarhadi,

Development and Clinical Implementation of a Combination Deletion PCR and Multiplex Ligation-Dependent Probe Amplification Assay for Detecting Deletions.

Comprehensive Diagnostic Testing for Stereocilin

Jamal H. Carter, Samantha N. McNulty, Patrick J. Cimino, Catherine E

Molecular Aspects of Melanocytic Dysplastic Nevi

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

Target-Enriched Next-Generation Sequencing Reveals Differences between Primary and Secondary Ovarian Tumors in Formalin-Fixed, Paraffin-Embedded Tissue

A Systematic Comparison of Traditional and Multigene Panel Testing for Hereditary Breast and Ovarian Cancer Genes in More Than 1000 Patients Stephen.

Comparison of QIAsymphony Automated and QIAamp Manual DNA Extraction Systems for Measuring Epstein-Barr Virus DNA Load in Whole Blood Using Real-Time.

Reliable Transcript Quantification by Real-Time Reverse Transcriptase-Polymerase Chain Reaction in Primary Neuroblastoma Using Normalization to Averaged.

Multiplex Bead Suspension Array for Screening Neisseria gonorrhoeae Antibiotic Resistance Genetic Determinants in Noncultured Clinical Samples Sergey.

Highly Sensitive Droplet Digital PCR Method for Detection of EGFR-Activating Mutations in Plasma Cell–Free DNA from Patients with Advanced Non–Small Cell.

A Highly Sensitive Genetic Protocol to Detect NF1 Mutations

EPCAM Germ Line Deletions as Causes of Lynch Syndrome in Spanish Patients Carla Guarinos, Adela Castillejo, Víctor-Manuel Barberá, Lucía Pérez-Carbonell,

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

A Multi-Exonic BRCA1 Deletion Identified in Multiple Families through Single Nucleotide Polymorphism Haplotype Pair Analysis and Gene Amplification with.

Larissa V. Furtado, Helmut C. Weigelin, Kojo S. J

Larissa V. Furtado, Helmut C. Weigelin, Kojo S. J

Design and Evaluation of a Real-Time PCR Assay for Quantification of JAK2 V617F and Wild-Type JAK2 Transcript Levels in the Clinical Laboratory Jason.

Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement.

Genomic Technologies and the New Era of Genomic Medicine

Low Incidence of Minor BRAF V600 Mutation-Positive Subclones in Primary and Metastatic Melanoma Determined by Sensitive and Quantitative Real-Time PCR

Dale Muzzey, Shera Kash, Jillian I. Johnson, Laura M

Danielle C. Smith, Alina Esterhuizen, Jacquie Greenberg

A Platform for Rapid Detection of Multiple Oncogenic Mutations With Relevance to Targeted Therapy in Non–Small-Cell Lung Cancer Zengliu Su, Dora Dias-Santagata,

Evidence That the Penetrance of Mutations at the RP11 Locus Causing Dominant Retinitis Pigmentosa Is Influenced by a Gene Linked to the Homologous RP11.

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

Xiangfeng Cui, Helen Feiner, Honghua Li

Nathan D. Montgomery, Sara R. Selitsky, Nirali M. Patel, D

Improved Detection of the KIT D816V Mutation in Patients with Systemic Mastocytosis Using a Quantitative and Highly Sensitive Real-Time qPCR Assay Thomas.

Clinical Experience with the Cervista HPV HR Assay

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

Optimized Allele-Specific Real-Time PCR Assays for the Detection of Common Mutations in KRAS and BRAF Alois H. Lang, Heinz Drexel, Simone Geller-Rhomberg,

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

Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis Paolo A. Ascierto, Carlo Bifulco, Giuseppe.

Presentation transcript:

MSIplus for Integrated Colorectal Cancer Molecular Testing by Next-Generation Sequencing Jennifer A. Hempelmann, Sheena M. Scroggins, Colin C. Pritchard, Stephen J. Salipante The Journal of Molecular Diagnostics Volume 17, Issue 6, Pages 705-714 (November 2015) DOI: 10.1016/j.jmoldx.2015.05.008 Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Study design and summary of results. Diagnostic testing algorithm and results are depicted. The number of specimens at each stage is indicated numerically at corresponding nodes. Fifteen specimens were tested for both microsatellite instability (MSI) status and mutational hotspots; thus, inclusion in these categories is not mutually exclusive. IHC, immunohistochemistry. The Journal of Molecular Diagnostics 2015 17, 705-714DOI: (10.1016/j.jmoldx.2015.05.008) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Correlation of allele fraction by MSIplus and targeted gene-capture next-generation sequencing. Allele fractions are estimated by either the MSIplus assay or the UW-OncoPlex targeted gene-capture sequencing panel. The subset of 55 specimens for which data from both assays were available is shown. Dashed gray line indicates a theoretical perfect correlation between the two estimations. The Journal of Molecular Diagnostics 2015 17, 705-714DOI: (10.1016/j.jmoldx.2015.05.008) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Inferring microsatellite instability (MSI) status by MSIplus. Data are stratified according to testing results by MSI-PCR. The mSINGS score (the fraction of interrogated microsatellite loci that are unstable) is plotted for each specimen. The dashed lines at mSINGS scores of 0.27 and 0.54 indicate the cutoffs for delineating MSI-positive and MSI-negative specimens by MSIplus: mSINGS scores falling below these values were interpreted as negative, scores above those values were interpreted as positive, and scores falling between the values could not be reliably interpreted. Arrowheads indicate specimens misclassified by MSI-PCR; asterisk indicates specimen misclassified by MSIplus, as resolved by alternative clinical testing results (immunohistochemical and/or genetic testing). For specimens that were typed multiple times, one representative mSINGS score is displayed. The Journal of Molecular Diagnostics 2015 17, 705-714DOI: (10.1016/j.jmoldx.2015.05.008) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Correlation of locus instability measured by microsatellite instability (MSI)-PCR and MSIplus. The mSINGS score (the fraction of interrogated microsatellite loci that are unstable) is plotted against the fraction of unstable loci determined by MSI-PCR. Overall mSINGS score for the MSIplus assay is shown separately from mSINGS score calculated for the five loci in common with MSI-PCR. Dashed gray line indicates a theoretical perfect correlation between the two measures of instability. The Journal of Molecular Diagnostics 2015 17, 705-714DOI: (10.1016/j.jmoldx.2015.05.008) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions