Mass Spectrometry-Based Loss of Heterozygosity Analysis of Single-Nucleotide Polymorphism Loci in Paraffin Embedded Tumors Using the MassEXTEND Assay

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

CyclinD1/CyclinD3 Ratio by Real-Time PCR Improves Specificity for the Diagnosis of Mantle Cell Lymphoma Carol D. Jones, Katherine H. Darnell, Roger A.

High-Quality Genotyping Data from Formalin-Fixed, Paraffin-Embedded Tissue on the Drug Metabolizing Enzymes and Transporters Plus Array Hanneke I. Vos,

An Enhanced Polymerase Chain Reaction Assay to Detect Pre- and Full Mutation Alleles of the Fragile X Mental Retardation 1 Gene Alessandro Saluto, Alessandro.

Droplet Digital PCR for Absolute Quantification of EML4-ALK Gene Rearrangement in Lung Adenocarcinoma Qiushi Wang, Xin Yang, Yong He, Qiang Ma, Li Lin,

Novel Functional Single Nucleotide Polymorphisms in the Latent Transforming Growth Factor-β Binding Protein-1L Promoter Tomomi Higashi, Satoru Kyo, Masaki.

Genotyping of DNA Samples Isolated from Formalin-Fixed Paraffin-Embedded Tissues Using Preamplification Renee Baak-Pablo, Vincent Dezentje, Henk-Jan.

Sensitive Detection of KRAS Mutations in Archived Formalin-Fixed Paraffin-Embedded Tissue Using Mutant-Enriched PCR and Reverse-Hybridization Christoph.

RT-PCR Analysis of RNA Extracted from Bouin-Fixed and Paraffin-Embedded Lymphoid Tissues Annunziata Gloghini, Barbara Canal, Ulf Klein, Luigino Dal Maso,

Detection of Low-Level KRAS Mutations Using PNA-Mediated Asymmetric PCR Clamping and Melting Curve Analysis with Unlabeled Probes Ji Eun Oh, Hee Sun.

Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe–Based Single-

High-Throughput, Multiplex Genotyping Directly from Blood or Dried Blood Spot without DNA Extraction for the Screening of Multiple G6PD Gene Variants.

Hendrikus J. Dubbink, Peggy N. Atmodimedjo, Ronald van Marion, Niels M

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

Rapid Genotyping of Single Nucleotide Polymorphisms Influencing Warfarin Drug Response by Surface-Enhanced Laser Desorption and Ionization Time-of-Flight.

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

Establishment and Study of Different Real-Time Polymerase Chain Reaction Assays for the Quantification of Cells with Deletions of Chromosome 7 Elia Mattarucchi,

IgH PCR of Zinc Formalin-Fixed, Paraffin-Embedded Non-Lymphomatous Gastric Samples Produces Artifactual “Clonal” Bands Not Observed in Paired Tissues.

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

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

Homogeneous Polymerase Chain Reaction Nucleobase Quenching Assay to Detect the 1-kbp Deletion in CLN3 That Causes Batten Disease Paul G. Rothberg, Denia.

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

Silke Lassmann, Ulrike V

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

Multiplex Pyrosequencing of Two Polymorphisms in DNA Repair Gene XRCC1

A Tumor Sorting Protocol that Enables Enrichment of Pancreatic Adenocarcinoma Cells and Facilitation of Genetic Analyses Zachary S. Boyd, Rajiv Raja,

Sensitive Detection of KRAS Mutations in Archived Formalin-Fixed Paraffin-Embedded Tissue Using Mutant-Enriched PCR and Reverse-Hybridization Christoph.

Detection of KRAS and BRAF Mutations in Colorectal Carcinoma

Patrick R. Murray The Journal of Molecular Diagnostics

Andrea Gaedigk, Amanda K. Riffel, J. Steven Leeder

Low Copy Number DNA Template Can Render Polymerase Chain Reaction Error Prone in a Sequence-Dependent Manner Mansour Akbari, Marianne Doré Hansen, Jostein.

An Enhanced Polymerase Chain Reaction Assay to Detect Pre- and Full Mutation Alleles of the Fragile X Mental Retardation 1 Gene Alessandro Saluto, Alessandro.

Triplex High-Resolution Melting Assay for the Simultaneous Assessment of IFNL3 rs , ABCB11 rs , and RNF7 rs Genotypes in Chronic.

High-Quality Genotyping Data from Formalin-Fixed, Paraffin-Embedded Tissue on the Drug Metabolizing Enzymes and Transporters Plus Array Hanneke I. Vos,

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

Evaluation of BRAF Mutation Testing Methodologies in Formalin-Fixed, Paraffin- Embedded Cutaneous Melanomas Johanne Lade-Keller, Kirsten M. Rømer, Per.

Molecular Aspects of Melanocytic Dysplastic Nevi

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

Rapid and Inexpensive Detection of α1-Antitrypsin Deficiency-Related Alleles S and Z by a Real-Time Polymerase Chain Reaction Suitable for a Large-Scale.

John A. Tynan, Payam Mahboubi, Lesley L

Iris Schrijver, Tiffanee J. Lenzi, Carol D. Jones, Marla J

Molecular Inversion Probe Array for the Genetic Evaluation of Stillbirth Using Formalin- Fixed, Paraffin-Embedded Tissue Leslie R. Rowe, Harshwardhan.

Deamination Effects in Formalin-Fixed, Paraffin-Embedded Tissue Samples in the Era of Precision Medicine Seokhwi Kim, Charny Park, Yongick Ji, Deok G.

Accurate single cell 24 chromosome aneuploidy screening using whole genome amplification and single nucleotide polymorphism microarrays Nathan R. Treff,

Sensitive and Specific KRAS Somatic Mutation Analysis on Whole-Genome Amplified DNA from Archival Tissues Ronald van Eijk, Marjo van Puijenbroek, Amiet.

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

Julie Di Cristofaro, Monique Silvy, Jacques Chiaroni, Pascal Bailly

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

Multifocal Myxoid Liposarcoma—Metastasis or Second Primary Tumor?

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.

Accurate Detection of Copy Number Changes in DNA Extracted from Formalin-Fixed, Paraffin-Embedded Melanoma Tissue Using Duplex Ratio Tests David A. Moore,

Detection of KIAA1549-BRAF Fusion Transcripts in Formalin-Fixed Paraffin-Embedded Pediatric Low-Grade Gliomas Yongji Tian, Benjamin E. Rich, Natalie.

Mutation Detection of Epidermal Growth Factor Receptor and KRAS Genes Using the Smart Amplification Process Version 2 from Formalin-Fixed, Paraffin-Embedded.

Rapid and Sensitive Real-Time Polymerase Chain Reaction Method for Detection and Quantification of 3243A>G Mitochondrial Point Mutation Rinki Singh,

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

Amplification Refractory Mutation System, a Highly Sensitive and Simple Polymerase Chain Reaction Assay, for the Detection of JAK2 V617F Mutation in Chronic.

Katy Hanlon, Lorna W. Harries, Sian Ellard, Claudius E. Rudin

A Rapid and Reliable Test for BRCA1 and BRCA2 Founder Mutation Analysis in Paraffin Tissue Using Pyrosequencing Liying Zhang, Tomas Kirchhoff, Cindy.

A Real-Time PCR Assay for the Simultaneous Detection of Functional N284I and L412F Polymorphisms in the Human Toll-Like Receptor 3 Gene Robert A. Brown,

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

Genotyping of Human Platelet Antigens 1 to 6 and 15 by High-Resolution Amplicon Melting and Conventional Hybridization Probes Michael Liew, Lesa Nelson,

JAZF1/JJAZ1 Gene Fusion in Endometrial Stromal Sarcomas

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.

Triplet Repeat Primed PCR (TP PCR) in Molecular Diagnostic Testing for Friedreich Ataxia Paola Ciotti, Emilio Di Maria, Emilia Bellone, Franco Ajmar,

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

Detection of BRCA1 and BRCA2 Ashkenazi Jewish Founder Mutations in Formalin- Fixed Paraffin-Embedded Tissues Using Conventional PCR and Heteroduplex/Amplicon.

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:

Mass Spectrometry-Based Loss of Heterozygosity Analysis of Single-Nucleotide Polymorphism Loci in Paraffin Embedded Tumors Using the MassEXTEND Assay Marjo van Puijenbroek, Jan Willem F. Dierssen, Patrick Stanssens, Ronald van Eijk, Anne Marie Cleton-Jansen, Tom van Wezel, Hans Morreau The Journal of Molecular Diagnostics Volume 7, Issue 5, Pages 623-630 (November 2005) DOI: 10.1016/S1525-1578(10)60596-X Copyright © 2005 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Design of the MassEXTEND genotyping of c.827A>C SNP assay. 1) PCR amplification generated a product including the c.827A>C SNP. 2) MassEXTEND reaction that results in two products with different mass: c.827C allele, 6558.3 d, and c.827A allele, 7199.8 d. The Journal of Molecular Diagnostics 2005 7, 623-630DOI: (10.1016/S1525-1578(10)60596-X) Copyright © 2005 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Mass spectra of the three c.827A>C SNP genotypes (A, A/A; B, C/C; C, A/C) and tumor 02031 with loss of the A allele (D). The alleles are indicated with thick horizontal arrows. Pausing and probe peaks are indicated above the graph. The Journal of Molecular Diagnostics 2005 7, 623-630DOI: (10.1016/S1525-1578(10)60596-X) Copyright © 2005 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Sequence analysis of the c.827A>C SNP of PTPRJ of flow-sorted cell populations. Distinct cell populations were flow-sorted from the formalin-fixed paraffin-embedded primary tumor and lymph-node metastasis of case 02031. A–F: Primary tumor. A: Keratin positive (K pos.) cells can be clearly identified in the forward scatter versus keratin dot plot, compared with a negative control (C). B: After gating on the K pos. cells, a bimodal DNA histogram can be observed with two dominant cycling populations with a DNA index of 1.7 and 2.6, respectively. D: The Keratin negative (K neg.) cells, comprising inflammatory and stromal cells, revealed an unimodal DNA diploid histogram.17 E and F: Sequence analysis of fraction ID 1.7 and fraction ID 2.6 showed loss of the A allele in both populations. G–L: Lymph-node metastasis. G: Forward scatter versus keratin dot plot. I: Negative control. H: Gating on the K pos. cells shows an unimodal DNA histogram with a DNA index of 2.6. These cells probably branched from the second DNA aneuploid population (DI = 2.6) of the primary tumor. J: Unimodal DNA diploid histogram of the K neg. cells. K: Sequence analysis of ID 2.6 fraction showed loss of the A allele. L: The K neg. cells are diploid and show the normal A/C genotype. The Journal of Molecular Diagnostics 2005 7, 623-630DOI: (10.1016/S1525-1578(10)60596-X) Copyright © 2005 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions