Development and Validation of a Mass Spectrometry–Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease Brendan Blumenstiel, Matthew DeFelice,

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.

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

Simple, Efficient, and Cost-Effective Multiplex Genotyping with Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of Hemoglobin.

Martina I. Lefterova, Peidong Shen, Justin I

KRAS and BRAF Mutation Analysis in Routine Molecular Diagnostics

Volume 67, Issue 6, Pages (June 2005)

Performance Evaluation of the TheraTyper-GJB2 Assay for Detection of GJB2 Gene Mutations Ji-Yong Chun, Soo-Kyung Shin, Kyung Tae Min, Woojae Cho, Jaeil.

High-Throughput Homogeneous Mass Cleave Assay Technology for the Diagnosis of Autosomal Recessive Parkinson's Disease Christopher Schroeder, Michael.

Carol Beadling, Tanaya L. Neff, Michael C

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

Simultaneous Genotyping of α-Thalassemia Deletional and Nondeletional Mutations by Real-Time PCR–Based Multicolor Melting Curve Analysis Qiuying Huang,

Martina I. Lefterova, Peidong Shen, Justin I

Todd S. Laughlin, Michael W. Becker, Jane L. Liesveld, Deborah A

KRAS and BRAF Mutation Analysis in Routine Molecular Diagnostics

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

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

PCR–Electrospray Ionization Mass Spectrometry

Pyrosequencing Is an Accurate and Reliable Method for the Analysis of Heteroplasmy of the A3243G Mutation in Patients with Mitochondrial Diabetes Jing-bin.

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

Laboratory Diagnosis of Clostridium difficile Infection

Joanna Wang, Chetan Bettegowda The Journal of Molecular Diagnostics

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

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

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

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

Simultaneous Genotyping of α-Thalassemia Deletional and Nondeletional Mutations by Real-Time PCR–Based Multicolor Melting Curve Analysis Qiuying Huang,

Detection of KRAS and BRAF Mutations in Colorectal Carcinoma

Patrick R. Murray The Journal of Molecular Diagnostics

Performance Evaluation of the TheraTyper-GJB2 Assay for Detection of GJB2 Gene Mutations Ji-Yong Chun, Soo-Kyung Shin, Kyung Tae Min, Woojae Cho, Jaeil.

Detection and Typing of Viruses Using Broadly Sensitive Cocktail-PCR and Mass Spectrometric Cataloging Charul Gijavanekar, Rafal Drabek, Mithil Soni,

Validation of Circulating miRNA Biomarkers for Predicting Lymph Node Metastasis in Gastric Cancer Shine Young Kim, Tae Yong Jeon, Chang In Choi, Dae.

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,

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

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

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

Direct Bacterial Profiling by Matrix-Assisted Laser Desorption−Ionization Time-of-Flight Mass Spectrometry for Identification of Pathogenic Neisseria

PCR–Electrospray Ionization Mass Spectrometry

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

Olivier Gruselle, Thierry Coche, Jamila Louahed

F. Bittar, J.-M. Rolain Clinical Microbiology and Infection

Development of a Quantitative Real-Time Polymerase Chain Reaction Assay for the Detection of the JAK2 V617F Mutation Elizabeth C. Wolstencroft, Katy.

John A. Tynan, Payam Mahboubi, Lesley L

The Molecular Pathology of Primary Immunodeficiencies

The Suitability of Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry in a Laboratory Developed Test Using Cystic Fibrosis Carrier.

Evaluation of a Novel Chlamydia trachomatis Microsphere Suspension Assay for Detection and Genotyping of the Different Serovars in Clinical Samples Koen.

Application of Nuclear Magnetic Resonance to Detect Toxigenic Clostridium difficile from Stool Specimens Paul Yang, Sara Hash, Katherine Park, Charlene.

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

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

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

Novel, Improved Sample Preparation for Rapid, Direct Identification from Positive Blood Cultures Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight.

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.

Detection of the JAK2 V617F Mutation by LightCycler PCR and Probe Dissociation Analysis Marla Lay, Rajan Mariappan, Jason Gotlib, Lisa Dietz, Siby Sebastian,

Simple, Efficient, and Cost-Effective Multiplex Genotyping with Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of Hemoglobin.

Maria Erali, David C. Pattison, Carl T. Wittwer, Cathy A. Petti

A Clinically Validated Diagnostic Second-Generation Sequencing Assay for Detection of Hereditary BRCA1 and BRCA2 Mutations Ian E. Bosdet, T. Roderick.

Analytical Validation of a Personalized Medicine APOL1 Genotyping Assay for Nondiabetic Chronic Kidney Disease Risk Assessment Jinglan Zhang, Anastasia.

Development of an Allele-Specific Real-Time PCR Assay for Discrimination and Quantification of p63 R279H Mutation in EEC Syndrome Vanessa Barbaro, Letizia.

Performance and Clinical Evaluation of a Sensitive Multiplex Assay for the Rapid Detection of Common NPM1 Mutations Michael Hafez, Fei Ye, Keith Jackson,

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

Avoiding Pitfalls in Molecular Genetic Testing

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

Novel Method for PIK3CA Mutation Analysis

Mangalathu S. Rajeevan, Suzanne D

Statistical Treatment of Fluorescence in Situ Hybridization Validation Data to Generate Normal Reference Ranges Using Excel Functions Allison L. Ciolino,

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

Identification of Evidence-Based Biospecimen Quality-Control Tools

Volume 67, Issue 6, Pages (June 2005)

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

Presentation transcript:

Development and Validation of a Mass Spectrometry–Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease Brendan Blumenstiel, Matthew DeFelice, Ozge Birsoy, Anthony J. Bleyer, Stanislav Kmoch, Todd A. Carter, Andreas Gnirke, Kendrah Kidd, Heidi L. Rehm, Lucienne Ronco, Eric S. Lander, Stacey Gabriel, Niall J. Lennon The Journal of Molecular Diagnostics Volume 18, Issue 4, Pages 566-571 (July 2016) DOI: 10.1016/j.jmoldx.2016.03.003 Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectra readout of a wild-type negative sample (A) and +C positive sample (B). Unextended probe products are indicated by asterisks. Successful restriction digestion is indicated by a strong peak at 4889.21 Da and low-intensity peak at 5162.4 Da (MwoI control). Reaction performance is indicated by the GAPDH control extension product at 5557.63 Da. +C insertion event indicated by a peak at 5904.83 Da (shaded area). The Journal of Molecular Diagnostics 2016 18, 566-571DOI: (10.1016/j.jmoldx.2016.03.003) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Flowchart of mucin-1 kidney disease (MKD) calling. Signal to noise ratios (SNRs) for four potential peaks are used to determine the test result. Conclusive calls of wild-type (negative) or +C (positive) are only reported when both the GAPDH and MwoI (−) controls pass the set thresholds. Samples with low but detectable signal for the MKD extension product (SNR, 1.5 to 15) are called inconclusive. The Journal of Molecular Diagnostics 2016 18, 566-571DOI: (10.1016/j.jmoldx.2016.03.003) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 A: The distribution of peak signal to noise ratios (SNRs) for the mucin-1 kidney disease +C analyte at 5904.83 Da was observed for all 384 validation reactions. Results binned by known sample reference. Eleven of 384 reactions generated a SNR between 1.5 and 15 (shaded area) and were called inconclusive. B: Distribution of GAPDH control extension analyte SNR at 5557.63 Da for 384 assays performed during validation. Three of 384 wells failed because the signal was below the set SNR threshold of 15 (dotted line). C: Successful MwoI restriction digestion is determined by assessing the two potential extension products of a probe interrogating the restriction site of a synthetic amplicon spike in. One of 384 assays failed the MwoI control with a signal below the SNR threshold of 10 (dotted line) at mass 4889.21 Da. Both peak values are plotted for 384 assay wells run in the validation. Data presented as distributions with outlier box plots. The Journal of Molecular Diagnostics 2016 18, 566-571DOI: (10.1016/j.jmoldx.2016.03.003) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions