Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics Maksym.

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

Nine Novel Germline Gene Variants in the RET Proto-Oncogene Identified in Twelve Unrelated Cases Syed A. Ahmed, Karen Snow-Bailey, W. Edward Highsmith,

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

Overall (regardless of smoking Hx) Prior or current smoking Hx

Lawrence J. Jennings, Maria E

Keyur P. Patel, Bedia A. Barkoh, Zhao Chen, Deqin Ma, Neelima Reddy, L

Molecular Diagnostic Profiling of Lung Cancer Specimens with a Semiconductor-Based Massive Parallel Sequencing Approach Volker Endris, Roland Penzel,

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

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.

Assessing Copy Number Alterations in Targeted, Amplicon-Based Next-Generation Sequencing Data Catherine Grasso, Timothy Butler, Katherine Rhodes, Michael.

In Silico Proficiency Testing for Clinical Next-Generation Sequencing

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.

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

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.

Robustness of Amplicon Deep Sequencing Underlines Its Utility in Clinical Applications Vera Grossmann, Andreas Roller, Hans-Ulrich Klein, Sandra Weissmann,

Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic.

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

Improving Mutation Screening in Patients with Colorectal Cancer Predisposition Using Next-Generation Sequencing Jean-Marc Rey, Vincent Ducros, Pascal.

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

Molecular Analysis of Circulating Cell-Free DNA from Lung Cancer Patients in Routine Laboratory Practice Stephan Bartels, Sascha Persing, Britta Hasemeier,

Clinical Validation of a Next-Generation Sequencing Genomic Oncology Panel via Cross-Platform Benchmarking against Established Amplicon Sequencing Assays

A Melting Curve Analysis–Based PCR Assay for One-Step Genotyping of β- Thalassemia Mutations Fu Xiong, Qiuying Huang, Xiaoyun Chen, Yuqiu Zhou, Xinhua.

Joanna Wang, Chetan Bettegowda The Journal of Molecular Diagnostics

A Method for Next-Generation Sequencing of Paired Diagnostic and Remission Samples to Detect Mitochondrial DNA Mutations Associated with Leukemia Ilaria.

Single Nucleotide Polymorphism-Based System Improves the Applicability of Quantitative PCR for Chimerism Monitoring Egle Gineikiene, Mindaugas Stoskus,

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

Clinical Relevance of Sensitive and Quantitative STAT3 Mutation Analysis Using Next- Generation Sequencing in T-Cell Large Granular Lymphocytic Leukemia

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

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

Evaluation of the Cepheid GeneXpert BCR-ABL Assay

Donavan T. Cheng, Talia N. Mitchell, Ahmet Zehir, Ronak H

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

Study of Preanalytic and Analytic Variables for Clinical Next-Generation Sequencing of Circulating Cell-Free Nucleic Acid Meenakshi Mehrotra, Rajesh.

Patrick R. Murray The Journal of Molecular Diagnostics

黃其晟1 塗昭江1 張景年1 黃清水2 1天主教輔仁大學附設醫院乳房外科 2國泰綜合醫院外科部

Detection of Germline Mutation in Hereditary Breast and/or Ovarian Cancers by Next- Generation Sequencing on a Four-Gene Panel Ava Kwong, Vivian Y. Shin,

High-Throughput and Sensitive Quantification of Circulating Tumor DNA by Microfluidic- Based Multiplex PCR and Next-Generation Sequencing Yinghui Guan,

Markus Rechsteiner, Adriana von Teichman, Jan H

Validation and Implementation of a Custom Next-Generation Sequencing Clinical Assay for Hematologic Malignancies Michael J. Kluk, R. Coleman Lindsley,

Comprehensive Diagnostic Testing for Stereocilin

Study of Preanalytic and Analytic Variables for Clinical Next-Generation Sequencing of Circulating Cell-Free Nucleic Acid Meenakshi Mehrotra, Rajesh.

Rapid Next-Generation Sequencing Method for Prediction of Prostate Cancer Risks Viacheslav Y. Fofanov, Kinnari Upadhyay, Alexander Pearlman, Johnny Loke,

Keyur P. Patel, Bedia A. Barkoh, Zhao Chen, Deqin Ma, Neelima Reddy, L

Utility of NIST Whole-Genome Reference Materials for the Technical Validation of a Multigene Next-Generation Sequencing Test Bennett O.V. Shum, Ilya.

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

BRAF Mutation Testing in Solid Tumors

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

Technical Validation of a Next-Generation Sequencing Assay for Detecting Clinically Relevant Levels of Breast Cancer–Related Single-Nucleotide Variants.

Ashleigh C. McEvoy, Benjamin A. Wood, Nima M. Ardakani, Michelle R

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

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

Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next- Generation Sequencing Bioinformatics and Variant Interpretation Kurtis.

External Quality Assessment for Detection of Fetal Trisomy 21, 18, and 13 by Massively Parallel Sequencing in Clinical Laboratories Rui Zhang, Hongyun.

Application of COLD-PCR for Improved Detection of NF2 Mosaic Mutations

Genomic Technologies and the New Era of Genomic Medicine

Lawrence J. Jennings, Maria E

Molecular Diagnosis of Mosaic Overgrowth Syndromes Using a Custom-Designed Next- Generation Sequencing Panel Fengqi Chang, Liu Liu, Erica Fang, Guangcheng.

Processed Pseudogene Confounding Deletion/Duplication Assays for SMAD4

Validation for Clinical Use of, and Initial Clinical Experience with, a Novel Approach to Population-Based Carrier Screening using High-Throughput, Next-Generation.

Clinical Validation of a Next-Generation Sequencing Screen for Mutational Hotspots in 46 Cancer-Related Genes Rajesh R. Singh, Keyur P. Patel, Mark J.

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

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

Tong Zhang, Sylvie Grenier, Bevoline Nwachukwu, Cuihong Wei, Jeffrey H

Monique A. Johnson, Marvin J. Yoshitomi, C. Sue Richards

Multilaboratory Assessment of a New Reference Material for Quality Assurance of Cell- Free Tumor DNA Measurements Hua-Jun He, Erica V. Stein, Yves Konigshofer,

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

Lawrence J. Jennings, Maria E

Presentation transcript:

Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics Maksym Misyura, Tong Zhang, Mahadeo A. Sukhai, Mariam Thomas, Swati Garg, Suzanne Kamel-Reid, Tracy L. Stockley The Journal of Molecular Diagnostics Volume 18, Issue 6, Pages 842-850 (November 2016) DOI: 10.1016/j.jmoldx.2016.06.004 Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Variant allele frequency detection between the Ion Proton-Cancer Hotspot Panel (CHP) and the MiSeq-Amplicon Cancer Panel (ACP) was compared according to Bland-Altman (A) and linear regression (B) analyses of concordant calls. The values for degree of agreement (black dashed lines), bias (black dotted line), and systematic error (gray line) are shown, including the P values for the presence of bias and systematic error. The Journal of Molecular Diagnostics 2016 18, 842-850DOI: (10.1016/j.jmoldx.2016.06.004) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 A total of 749 and 346 variants detected by the MiSeq-Amplicon Cancer Panel (A and B) and the Ion Proton-Cancer Hotspot Panel (C and D) were distributed across a range of genes and variant allele frequencies. Variants listed as other were detected in one of the following genes: RET, AKT1, CDH1, ERBB4, GNA11, IDH2, KIT, MLH1, NOTCH1, RB1, ABL1, FGFR2, HRAS, IDH1, MPL, SMARCB1, SMO, GNAQ, STK11, CSF1R, FLT3, KDR, PDGFRA, FGFR1, HNF1A, PTPN11, and SMAD4. The Journal of Molecular Diagnostics 2016 18, 842-850DOI: (10.1016/j.jmoldx.2016.06.004) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Integration of the MiSeq-Amplicon Cancer Panel (ACP) and the Ion Proton-Cancer Hotspot Panel (CHP) sequencing platforms into a single workflow. Four hundred forty-two samples were sequenced by the MiSeq-ACP. Two hundred three cases were sequenced by the Ion Proton-CHP because of low quantity and/or quality, including 24 samples that yielded inconclusive results by the MiSeq-ACP because of borderline quality and/or quantity. DNA quantity: >40 ng/μL∗, 10–40 ng/μL†, <10 ng/μL‡. DNA quality: ΔCt >3.2§ and ΔCt <3.2¶. n = 179 (low quantity and/or quality). The Journal of Molecular Diagnostics 2016 18, 842-850DOI: (10.1016/j.jmoldx.2016.06.004) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions