Quantitative Measurement of Cell-Free Plasma DNA and Applications for Detecting Tumor Genetic Variation and Promoter Methylation in a Clinical Setting

Slides:

Advertisements

Similar presentations

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

Advertisements

Detection of Exon 12 Mutations in the JAK2 Gene

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

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

Natalia Kholod, Jacques Boniver, Philippe Delvenne

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.

The Spectrum of CFTR Variants in Nonwhite Cystic Fibrosis Patients

Genome-Wide Identification and Validation of a Novel Methylation Biomarker, SDC2, for Blood-Based Detection of Colorectal Cancer TaeJeong Oh, Nayoung.

Targeted, High-Depth, Next-Generation Sequencing of Cancer Genes in Formalin- Fixed, Paraffin-Embedded and Fine-Needle Aspiration Tumor Specimens Andrew.

Detection of HIV-1 Minority Variants Containing the K103N Drug-Resistance Mutation Using a Simple Method to Amplify RNA Targets (SMART) Kenneth Morabito,

Molecular Genetics of Pediatric Soft Tissue Tumors

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

A Multiplex SNaPshot Assay as a Rapid Method for Detecting KRAS and BRAF Mutations in Advanced Colorectal Cancers Sandrine Magnin, Erika Viel, Alice.

Yanggu Shi, Sharon F. Terry, Patrick F. Terry, Lionel G

Elena Castellanos-Rizaldos, Cloud Paweletz, Chen Song, Geoffrey R

Application of Single-Molecule Amplification and Resequencing Technology for Broad Surveillance of Plasma Mutations in Patients with Advanced Lung Adenocarcinoma

Joanna Wang, Chetan Bettegowda The Journal of Molecular Diagnostics

Application of Single-Molecule Amplification and Resequencing Technology for Broad Surveillance of Plasma Mutations in Patients with Advanced Lung Adenocarcinoma

Maxim B. Freidin, Neesa Bhudia, Eric Lim, Andrew G

Noninvasive Molecular Monitoring in Multiple Myeloma Patients Using Cell-Free Tumor DNA Giulia Biancon, Silvia Gimondi, Antonio Vendramin, Cristiana.

A Clinical Grade Sequencing-Based Assay for CEBPA Mutation Testing

Development and Clinical Utility of a Blood-Based Test Service for the Rapid Identification of Actionable Mutations in Non–Small Cell Lung Carcinoma

Ken B. Waites, Li Xiao, Vanya Paralanov, Rose M. Viscardi, John I

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

Molly Yancovitz, Joanne Yoon, Maryann Mikhail, Weiming Gai, Richard L

Detection of KRAS and BRAF Mutations in Colorectal Carcinoma

Patrick R. Murray The Journal of Molecular Diagnostics

Detection of an Apparent Homozygous 3120G>A Cystic Fibrosis Mutation on a Routine Carrier Screen Denise LaMarche Heaney, Patrick Flume, Lauren Hamilton,

Shaoyu Zhou, Keyaunoosh Kassauei, David J. Cutler, Giulia C

A Rapid and Sensitive Next-Generation Sequencing Method to Detect RB1 Mutations Improves Care for Retinoblastoma Patients and Their Families Wenhui L.

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

Detection of Exon 12 Mutations in the JAK2 Gene

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

Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients Bente Risberg, Dana W.Y. Tsui, Heather Biggs,

Rapid Detection of TEM-Type Extended-Spectrum β-Lactamase (ESBL) Mutations Using Lights-On/Lights-Off Probes with Single-Stranded DNA Amplification Kenneth.

Sensitive Detection of Deletions of One or More Exons in the Neurofibromatosis Type 2 (NF2) Gene by Multiplexed Gene Dosage Polymerase Chain Reaction

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

Multiplex Amplification Coupled with COLD-PCR and High Resolution Melting Enables Identification of Low-Abundance Mutations in Cancer Samples with Low.

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

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

KRAS Mutation The Journal of Molecular Diagnostics

BRAF Mutation Testing in Solid Tumors

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

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

Comprehensive Arrayed Primer Extension Array for the Detection of 59 Sequence Variants in 15 Conditions Prevalent Among the (Ashkenazi) Jewish Population

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

Multiplex Amplification Coupled with COLD-PCR and High Resolution Melting Enables Identification of Low-Abundance Mutations in Cancer Samples with Low.

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

An Allele-Specific PCR System for Rapid Detection and Discrimination of the CYP2C19∗4A, ∗4B, and ∗17 Alleles Stuart A. Scott, Qian Tan, Usman Baber,

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.

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

A Novel Long-Range PCR Sequencing Method for Genetic Analysis of the Entire PKD1 Gene Ying-Cai Tan, Alber Michaeel, Jon Blumenfeld, Stephanie Donahue,

Genomic Technologies and the New Era of Genomic Medicine

Development of a High-Resolution Melting Curve Analysis Screening Test for SRSF2 Splicing Factor Gene Mutations in Myelodysplastic Syndromes Eduardo.

Intratumoral Heterogeneity of MicroRNA Expression in Breast Cancer

Validation of Denaturing High Performance Liquid Chromatography as a Rapid Detection Method for the Identification of Human INK4A Gene Mutations Irene.

Danielle C. Smith, Alina Esterhuizen, Jacquie Greenberg

A Pyrosequencing-Based Assay for the Rapid Detection of the 22q11

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,

Novel Method for PIK3CA Mutation Analysis

Rapid Polymerase Chain Reaction-Based Detection of Epidermal Growth Factor Receptor Gene Mutations in Lung Adenocarcinomas Qiulu Pan, William Pao, Marc.

Improved Detection of KIT Exon 11 Duplications in Formalin-Fixed, Paraffin-Embedded Gastrointestinal Stromal Tumors Jerzy Lasota, Bartosz Wasag, Sonja.

Development and Clinical Utility of a Blood-Based Test Service for the Rapid Identification of Actionable Mutations in Non–Small Cell Lung Carcinoma

Relationship between CFTR and CTRC Variants and the Clinical Phenotype in Late- Onset Cystic Fibrosis Disease with Chronic Pancreatitis Anna C. Tomaiuolo,

Two Novel Methods for Rapid Detection and Quantification of DNMT3A R882 Mutations in Acute Myeloid Leukemia Melissa Mancini, Syed Khizer Hasan, Tiziana.

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

Characterization of a Recurrent Novel Large Duplication in the Cystic Fibrosis Transmembrane Conductance Regulator Gene Feras M. Hantash, Joy B. Redman,

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

Development of a Novel Next-Generation Sequencing Assay for Carrier Screening in Old Order Amish and Mennonite Populations of Pennsylvania Erin L. Crowgey,

Presentation transcript:

Quantitative Measurement of Cell-Free Plasma DNA and Applications for Detecting Tumor Genetic Variation and Promoter Methylation in a Clinical Setting Sunil K. Kadam, Mark Farmen, John T. Brandt The Journal of Molecular Diagnostics Volume 14, Issue 4, Pages 346-356 (July 2012) DOI: 10.1016/j.jmoldx.2012.03.001 Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Effect of sample collection tube type (EDTA or Streck), DNA extraction method (Nucleospin extraction column, A; and Qiagen DNA extraction kit, B), and storage time on cfDNA measurement. The box plots illustrate the 25th and 75th percentiles, the line within each box is the median value, and the whiskers extend to the outermost data points that fall within the computed distances. The Journal of Molecular Diagnostics 2012 14, 346-356DOI: (10.1016/j.jmoldx.2012.03.001) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Effect of centrifugation on cellular depletion and plasma cfDNA extraction for off-site quantification from batched clinical samples. Group A contains samples in which plasma was separated with two centrifugation steps of 1600 × g at the collection site, shipped frozen, and spun at 16,000 × g just before supernatant DNA quantification. Group B contains duplicate samples in which plasma was separated by one centrifugation step at 1600 × g followed by a 16,000 × g spin at the collection site, shipped frozen, and thawed before DNA quantification. The Journal of Molecular Diagnostics 2012 14, 346-356DOI: (10.1016/j.jmoldx.2012.03.001) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 A: SpectruMedix electropherograms showing the Surveyor Nuclease digestion products. B: Bidirectional sequence analysis of a known mutation (c.658TAT, p.Y220C) spiked into normal plasma at 100- and 50-ng quantities. The Journal of Molecular Diagnostics 2012 14, 346-356DOI: (10.1016/j.jmoldx.2012.03.001) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 A: SpectruMedix electropherograms showing the Surveyor Nuclease digestion products at mutant (c.658TAT>TGT, p.Y220C) to WT (c658TAT) ratios of 45%, 22.5%, and 11.2%. B: Bidirectional sequence analysis of a known mutation (p.Y220C) spiked into normal plasma at mutant to WT ratios of 45% and 22.5% and the forward primer for 11.2%. The Journal of Molecular Diagnostics 2012 14, 346-356DOI: (10.1016/j.jmoldx.2012.03.001) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 5 Immunohistochemical detection of p53 protein and molecular characterization of TP53 gene variants in tissue and cfDNA extracted from corresponding samples. A and B: The presence of nuclear p53 in tumor biopsy sections. C and D: DNA sequence trace in the region of exon 5 and exon 8, respectively, from tumor tissue. E and F: cfDNA sequence trace in the region of exon 5 and exon 8, respectively, from corresponding plasma. G and H: DNA sequence trace in the region of exon 5 and exon 8, respectively, from WT reference. The Journal of Molecular Diagnostics 2012 14, 346-356DOI: (10.1016/j.jmoldx.2012.03.001) Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions