Association of Clinical Status of Follicular Lymphoma Patients after Autologous Stem Cell Transplant and Quantitative Assessment of Lymphoma in Blood.

Slides:



Advertisements
Similar presentations
Chapter 08 Author: Kelly Elkins © 2013 Elsevier, Inc. All rights reserved.
Advertisements

Association of Clinical Status of Follicular Lymphoma Patients after Autologous Stem Cell Transplant and Quantitative Assessment of Lymphoma in Blood and.
Clinical Laboratory Analysis of Immunoglobulin Heavy Chain Variable Region Genes for Chronic Lymphocytic Leukemia Prognosis  Philippe Szankasi, David.
Quantitative Detection and Differentiation of Human Herpesvirus 6 Subtypes in Bone Marrow Transplant Patients by Using a Single Real-Time Polymerase Chain.
Direct DNA Amplification from Crude Clinical Samples Using a PCR Enhancer Cocktail and Novel Mutants of Taq  Zhian Zhang, Milko B. Kermekchiev, Wayne.
Minimal Residual Disease Detection by Droplet Digital PCR in Multiple Myeloma, Mantle Cell Lymphoma, and Follicular Lymphoma  Daniela Drandi, Lenka Kubiczkova-Besse,
Pre-Clinical Validation of a Novel, Highly Sensitive Assay to Detect PML-RARα mRNA Using Real-Time Reverse-Transcription Polymerase Chain Reaction  James.
© 2013 Elsevier, Inc. All rights reserved.
Todd S. Laughlin, Michael W. Becker, Jane L. Liesveld, Deborah A
One-Step Ligation on RNA Amplification for the Detection of Point Mutations  Lei Zhang, Jingjing Wang, Mia Coetzer, Stephanie Angione, Rami Kantor, Anubhav.
Locked Nucleic Acids Can Enhance the Analytical Performance of Quantitative Methylation-Specific Polymerase Chain Reaction  Karen S. Gustafson  The Journal.
Direct DNA Amplification from Crude Clinical Samples Using a PCR Enhancer Cocktail and Novel Mutants of Taq  Zhian Zhang, Milko B. Kermekchiev, Wayne.
Rapid Detection of the Epidermal Growth Factor Receptor Mutation in Non-Small-Cell Lung Cancer for Analysis of Acquired Resistance Using Molecular Beacons 
Multiplex Detection of Ehrlichia and Anaplasma Species Pathogens in Peripheral Blood by Real-Time Reverse Transcriptase-Polymerase Chain Reaction  Kamesh.
Optimization of a Relative Telomere Length Assay by Monochromatic Multiplex Real- Time Quantitative PCR on the LightCycler 480  Anthony Y.Y. Hsieh, Sara.
© 2013 Elsevier, Inc. All rights reserved.
Development and Evaluation of a SYBR Green–Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya.
MethySYBR, a Novel Quantitative PCR Assay for the Dual Analysis of DNA Methylation and CpG Methylation Density  Pang-Kuo Lo, Hanano Watanabe, Pi-Chun.
Adam Bagg  The Journal of Molecular Diagnostics 
Simple Detection of Telomere Fusions in Pancreatic Cancer, Intraductal Papillary Mucinous Neoplasm, and Pancreatic Cyst Fluid  Tatsuo Hata, Marco Dal.
Detection of Clonally Restricted Immunoglobulin Heavy Chain Gene Rearrangements in Normal and Lesional Skin  Minakshi Nihal, Debra Mikkola, Gary S. Wood 
Comparison of BIOMED-2 Versus Laboratory-Developed Polymerase Chain Reaction Assays for Detecting T-Cell Receptor-γ Gene Rearrangements  Keyur P. Patel,
Jonathan A. Schumacher, Stephen D. Jenson, Kojo S. J
Isothermal Multiple Displacement Amplification
Establishment and Study of Different Real-Time Polymerase Chain Reaction Assays for the Quantification of Cells with Deletions of Chromosome 7  Elia Mattarucchi,
Yanggu Shi, Sharon F. Terry, Patrick F. Terry, Lionel G
B-Cell Clonality Determination Using an Immunoglobulin κ Light Chain Polymerase Chain Reaction Method  Reetesh K. Pai, Artemis E. Chakerian, John M. Binder,
Microfluidic Chips for Detecting the t(4;14) Translocation and Monitoring Disease during Treatment Using Reverse Transcriptase-Polymerase Chain Reaction.
Philippe Szankasi, Mohamed Jama, David W. Bahler 
Limitations and Practical Procedure in BclII-Ig Heavy Chain Gene Rearrangement Real- Time Quantitative Polymerase Chain Reaction  Barbara Dessars, Pierre.
Single Nucleotide Polymorphism-Based System Improves the Applicability of Quantitative PCR for Chimerism Monitoring  Egle Gineikiene, Mindaugas Stoskus,
Noninvasive Molecular Monitoring in Multiple Myeloma Patients Using Cell-Free Tumor DNA  Giulia Biancon, Silvia Gimondi, Antonio Vendramin, Cristiana.
Clinical Relevance of Sensitive and Quantitative STAT3 Mutation Analysis Using Next- Generation Sequencing in T-Cell Large Granular Lymphocytic Leukemia 
Novel Molecular Method for Detection of Bovine-Specific Central Nervous System Tissues as Bovine Spongiform Encephalopathy Risk Material in Meat and Meat.
Silke Lassmann, Ulrike V
Detection of Central Nervous System Leukemia in Children with Acute Lymphoblastic Leukemia by Real-Time Polymerase Chain Reaction  Sharon R. Pine, Changhong.
Protocol for the Use of Polymerase Chain Reaction in the Detection of Intraocular Large B-Cell Lymphoma in Ocular Samples  Aires Lobo, Narciss Okhravi,
Molecular Diagnostic Approach to Non-Hodgkin's Lymphoma
Single Monochrome Real-Time RT-PCR Assay for Identification, Quantification, and Breakpoint Cluster Region Determination of t(9;22) Transcripts  Marina.
Application of Self-Quenched JH Consensus Primers for Real-Time Quantitative PCR of IGH Gene to Minimal Residual Disease Evaluation in Multiple Myeloma 
Molly Yancovitz, Joanne Yoon, Maryann Mikhail, Weiming Gai, Richard L
A Fast Real-Time Polymerase Chain Reaction Method for Sensitive and Specific Detection of the Neisseria gonorrhoeae porA Pseudogene  Stig Ove Hjelmevoll,
Specific Detection of Cytokeratin 20-Positive Cells in Blood of Colorectal and Breast Cancer Patients by a High Sensitivity Real-Time Reverse Transcriptase-Polymerase.
Rapid and Accurate Detection of Monoclonal Immunoglobulin Heavy Chain Gene Rearrangement by DNA Melting Curve Analysis in the LightCycler System  Dongsheng.
Rapid Detection of Clonal T-Cell Receptor-β Gene Rearrangements in T-Cell Lymphomas Using the LightCycler-Polymerase Chain Reaction with DNA Melting Curve.
Multiplexed Detection of Anthrax-Related Toxin Genes
Clinical Laboratory Analysis of Immunoglobulin Heavy Chain Variable Region Genes for Chronic Lymphocytic Leukemia Prognosis  Philippe Szankasi, David.
Use of Single Nucleotide Polymorphisms (SNP) and Real-Time Polymerase Chain Reaction for Bone Marrow Engraftment Analysis  Dwight H. Oliver, Richard E.
Development of a Novel One-Tube Isothermal Reverse Transcription Thermophilic Helicase-Dependent Amplification Platform for Rapid RNA Detection  James.
Janice M. Spence, Paul G. Rothberg, Nancy Wang, W. Richard Burack 
Analytical Detection of Immunoglobulin Heavy Chain Gene Rearrangements in Gastric Lymphoid Infiltrates by Peak Area Analysis of the Melting Curve in the.
Validation and Clinical Application of a Locus-Specific Polymerase Chain Reaction- and Minisequencing-Based Assay for Congenital Adrenal Hyperplasia (21-Hydroxylase.
Novel Fluorescent Ligase Detection Reaction and Flow Cytometric Analysis of SYT-SSX Fusions in Synovial Sarcoma  Robyn Gaffney, Artemis Chakerian, John.
Molecular Monitoring of Chronic Myelogenous Leukemia
Quantitative and Qualitative Analyses of the SNRPN Gene Using Real-Time PCR with Melting Curve Analysis  Chia-Cheng Hung, Shin-Yu Lin, Shuan-Pei Lin,
Characterization of Aberrant Melting Peaks in Unlabeled Probe Assays
Consensus JH Gene Probes with Conjugated 3′-Minor Groove Binder for Monitoring Minimal Residual Disease in Acute Lymphoblastic Leukemia  Michihiro Uchiyama,
Polymerase Chain Reaction Detection of Kaposi's Sarcoma-Associated Herpesvirus- Optimized Protocols and Their Application to Myeloma  Langxing Pan, Laura.
Ye Bang-Ce, Chu Xiaohe, Fan Ye, Li Songyang, Yin Bincheng, Zuo Peng 
High-Throughput Identification and Quantification of Candida Species Using High Resolution Derivative Melt Analysis of Panfungal Amplicons  Tasneem Mandviwala,
An Allele-Specific RT-PCR Assay to Detect Type A Mutation of the Nucleophosmin-1 Gene in Acute Myeloid Leukemia  Tiziana Ottone, Emanuele Ammatuna, Serena.
Amplification Refractory Mutation System, a Highly Sensitive and Simple Polymerase Chain Reaction Assay, for the Detection of JAK2 V617F Mutation in Chronic.
ChildSeq-RNA The Journal of Molecular Diagnostics
Feras M. Hantash, Arlene Rebuyon, Mei Peng, Joy B
Cecily P. Vaughn, Elaine Lyon, Wade S. Samowitz 
Rapid and Accurate Detection of Monoclonal Immunoglobulin Heavy Chain Gene Rearrangement by DNA Melting Curve Analysis in the LightCycler System  Dongsheng.
Visual Format for Detection of Mycobacterium tuberculosis and M
Characterization of a Recurrent Novel Large Duplication in the Cystic Fibrosis Transmembrane Conductance Regulator Gene  Feras M. Hantash, Joy B. Redman,
Qing-Rong Chen, Gordon Vansant, Kahuku Oades, Maria Pickering, Jun S
Quantification of bcl-2/JH Fusion Sequences and a Control Gene by Multiplex Real- Time PCR Coupled with Automated Amplicon Sizing by Capillary Electrophoresis 
Presentation transcript:

Association of Clinical Status of Follicular Lymphoma Patients after Autologous Stem Cell Transplant and Quantitative Assessment of Lymphoma in Blood and Bone Marrow as Measured by SYBR Green I Polymerase Chain Reaction  Nancy Pennell, Anthony Woods, Marciano Reis, Rena Buckstein, David Spaner, Kevin Imrie, Karen Hewitt, Angela Boudreau, Arun Seth, Neil L. Berinstein  The Journal of Molecular Diagnostics  Volume 8, Issue 1, Pages 40-50 (February 2006) DOI: 10.2353/jmoldx.2006.050050 Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Primer locations and PCR strategies. The t(14;18) translocation is illustrated to indicate the locations of the BCL2 primers. All of these BCL2 primers (MBRO, MBRE, MBRi, MBRB, MBRH, mcro, mcri) are located 3′ to the BCL2 gene exons on chromosome 18. The JH consensus primer anneals to all JH exons 1 to 6, but preferential amplification of t(14:18) amplicon occurs from the JH closest to the breakpoint. A rearranged IgH gene is illustrated to show the approach for ASO-specific amplifications. VH Framework1 and JH consensus primers are used to amplify a clonal IgH product. An ASO primer located in the N (inserted nucleotides)-D(diversity)-N region and a primer from the VH FR1 were designed based on the DNA sequence of the clonal IgH product. The Journal of Molecular Diagnostics 2006 8, 40-50DOI: (10.2353/jmoldx.2006.050050) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Qualitative nested PCR analysis of patient 009 at 42-month follow-up samples. Lane 1, baseline BM sample demonstrating size of BCL2/JH translocation product; lane 2, BM sample with PCR product identical in size; lane 3, duplicate analysis of BM with no amplification; lanes 4 and 5, blood sample amplified in one of two reactions to produce same size product as baseline; lane 6, no template DNA; lane 7, negative control DNA from Jurkat cells; lanes 8, 9, and 10, 10-fold increasing concentrations of LY8-positive control DNA with 200-bp BCL2/JH PCR product. Lane 11 is 100-bp marker. DNA quality control, 350-bp RAG2 PCR product from the first round of PCR, is visible in patient sample lanes where BCL2/JH did not amplify. The Journal of Molecular Diagnostics 2006 8, 40-50DOI: (10.2353/jmoldx.2006.050050) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 RQ-PCR analysis of patient 009 with primer set MBRB/JH. a: Tenfold serial dilutions of LY8 cell line calibration standard. The highest concentration produces detectable PCR at 22 cycles, whereas the lowest requires ∼41 cycles. b: The log quantity of sample is plotted versus cycle threshold (Ct) to generate the standard curve from which unknown samples are quantified. c: Follow-up samples from patient 009 at 42 months amplified at 40 cycles, whereas triplicate samples from 48 months required only 36 cycles, indicating ∼10-fold higher concentration. d: Melt peaks generated from plotting −dI/dt versus temperature, show coincident peaks from baseline and follow-up patient 009 samples at 82.8°C while the control LY8 cell line peaks at 84.8°C. The Journal of Molecular Diagnostics 2006 8, 40-50DOI: (10.2353/jmoldx.2006.050050) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Standard curves of RQ-PCR BCL2/JH and RAG2 reactions. The log of initial cell equivalents is plotted versus cycle threshold for each RQ-PCR reaction. All curves have slopes of close to −3.9 and r2 values equal to 0.998, indicating similar amplification efficiencies in each reaction. The PCR primers and conditions for each reaction are listed in Tables 2 and 3. The Journal of Molecular Diagnostics 2006 8, 40-50DOI: (10.2353/jmoldx.2006.050050) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 5 Standard curves for RQ-PCR for ASO (patient-specific) reactions and RAG2. The log of initial cell equivalents is plotted versus cycle threshold for patient 004 ASO RQ-PCR reactions. A curve generated from dilutions of patient 004 LN DNA is similar to a curve generated from dilutions of purified, quantified PCR product. In all three curves, slopes are −3.5 and r2 = 1.0. This demonstrated that PCR products with known copy number can be used to generate a valid standard curve for the quantification of ASO-specific reactions. The Journal of Molecular Diagnostics 2006 8, 40-50DOI: (10.2353/jmoldx.2006.050050) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 6 Small and large amplicons are RQ-PCR amplified with similar efficiencies. MBRB-JH primers were used to amplify the BCL2-JH junctions in highly infiltrated baseline BM samples from patients 002 and 110. a: The resulting products were sized against 100-bp ladder (M1) and 10-bp ladder (M2) on a 3% agarose gel and estimated to be 150 bp and 230 bp in length. LY8 amplicons were 210 bp. b: Tenfold serial dilutions (200 to 0.2 ng) of the patient samples and the LY8-positive control cell line were RQ-PCR amplified. Resulting cycle thresholds were plotted against log DNA concentrations and showed r2 = 0.99 for all three dilution sets. The slopes for LY8, patient 110 and patient 002 were −4.2, −4.1, and −3.7, respectively, demonstrating similar amplification efficiencies. The Journal of Molecular Diagnostics 2006 8, 40-50DOI: (10.2353/jmoldx.2006.050050) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 7 Serial analysis of 12 patients with molecular markers. All patient samples were initially analyzed with qualitative nested PCR as described in Materials and Methods. The samples were then reanalyzed with RQ-PCR. All samples shown as PCR-negative were negative by both techniques. All samples that were positive with nested PCR were quantifiable with RQ-PCR with the exception of some samples for patient 021 (detail in text) shown only as nested PCR+. The calculated percentages of contamination were converted to cell equivalents per million cells and rounded to the nearest log for ease of representation. Each log concentration is represented by a separate color. Clinical relapse occurred, as indicated with R, only in patients with increasing proportions of PCR-positive cells. The Journal of Molecular Diagnostics 2006 8, 40-50DOI: (10.2353/jmoldx.2006.050050) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions