Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA Jennifer Reiner, Lisa Karger, Ninette Cohen, Lakshmi Mehta,

Slides:

Advertisements

Similar presentations

Martina I. Lefterova, Peidong Shen, Justin I

Advertisements

A Genome-Wide High-Resolution Array-CGH Analysis of Cutaneous Melanoma and Comparison of Array-CGH to FISH in Diagnostic Evaluation Lu Wang, Mamta Rao,

Bone Marrow Transplant Engraftment Analysis with Loss of an Informative Allele Steven A. Schichman, Pei Lin, Lori J. Gilbrech, Pamela S. Gray, Carla S.

In Vitro Transcription Amplification and Labeling Methods Contribute to the Variability of Gene Expression Profiling with DNA Microarrays Changqing Ma,

Ane Y. Schmidt, Thomas v. O. Hansen, Lise B

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

High-Resolution Genomic Profiling of Disseminated Tumor Cells in Prostate Cancer Yu Wu, Jamie R. Schoenborn, Colm Morrissey, Jing Xia, Sandy Larson, Lisha.

Carol Beadling, Tanaya L. Neff, Michael C

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

Martina I. Lefterova, Peidong Shen, Justin I

Emily M. Kudalkar, Naif A. M

Haley J. Abel, Hussam Al-Kateb, Catherine E. Cottrell, Andrew J

Real-Time Polymerase Chain Reaction for Detecting Bacterial DNA Directly from Blood of Neonates Being Evaluated for Sepsis Jeanne A. Jordan, Mary Beth.

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

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

Da Eun Lee, Ji Hyae Lim, Min Hyoung Kim, So Yeon Park, Hyun Mee Ryu

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

Precision Profiling and Components of Variability Analysis for Affymetrix Microarray Assays Run in a Clinical Context Thomas M. Daly, Carmen M. Dumaual,

Influence of RNA Labeling on Expression Profiling of MicroRNAs

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

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.

Molecular Diagnosis of Autosomal Dominant Polycystic Kidney Disease Using Next- Generation Sequencing Adrian Y. Tan, Alber Michaeel, Genyan Liu, Olivier.

Copy Number Variation Sequencing for Comprehensive Diagnosis of Chromosome Disease Syndromes Desheng Liang, Ying Peng, Weigang Lv, Linbei Deng, Yanghui.

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

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

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

Jennifer Kerkhof, Laila C

A DNA Microarray for the Detection of Point Mutations and Copy Number Variation Causing Familial Hypercholesterolemia in Europe Marianne A. Stef, Lourdes.

Patrick R. Murray The Journal of Molecular Diagnostics

Bone Marrow Transplant Engraftment Analysis with Loss of an Informative Allele Steven A. Schichman, Pei Lin, Lori J. Gilbrech, Pamela S. Gray, Carla S.

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

Eric Samorodnitsky, Jharna Datta, Benjamin M

Real-Time Polymerase Chain Reaction for Detecting Bacterial DNA Directly from Blood of Neonates Being Evaluated for Sepsis Jeanne A. Jordan, Mary Beth.

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

A Genome-Wide High-Resolution Array-CGH Analysis of Cutaneous Melanoma and Comparison of Array-CGH to FISH in Diagnostic Evaluation Lu Wang, Mamta Rao,

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

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

Jamal H. Carter, Samantha N. McNulty, Patrick J. Cimino, Catherine E

A 39-bp Deletion Polymorphism in PTEN in African American Individuals

Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer Kazimierz.

Gene-Expression Variation Within and Among Human Populations

Chimerism Analysis in the Pediatric Setting

The Molecular Pathology of Primary Immunodeficiencies

Performance of Whole-Genome Amplified DNA Isolated from Serum and Plasma on High-Density Single Nucleotide Polymorphism Arrays Daniel T. Croft, Rick.

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

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

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

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

Bassem A. Bejjani, Lisa G. Shaffer

Microarray Gene Expression Analysis of Fixed Archival Tissue Permits Molecular Classification and Identification of Potential Therapeutic Targets in Diffuse.

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,

Anu Aggarwal, Manu Jamwal, Ganesh K

Mamoru Kato, Yusuke Nakamura, Tatsuhiko Tsunoda

A Variant Detection Pipeline for Inherited Cardiomyopathy–Associated Genes Using Next-Generation Sequencing Théo G.M. Oliveira, Miguel Mitne-Neto, Louise.

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

Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement.

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

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

Association of MicroRNA Expression with Microsatellite Instability Status in Colorectal Adenocarcinoma Jonathan S.L. Earle, Rajyalakshmi Luthra, Angela.

Intratumoral Heterogeneity of MicroRNA Expression in Breast Cancer

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

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

Template-Directed Dye-Terminator Incorporation with Fluorescence Polarization Detection for Analysis of Single Nucleotide Polymorphisms Implicated in.

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

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

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

In Vitro Transcription Amplification and Labeling Methods Contribute to the Variability of Gene Expression Profiling with DNA Microarrays Changqing Ma,

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:

Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA Jennifer Reiner, Lisa Karger, Ninette Cohen, Lakshmi Mehta, Lisa Edelmann, Stuart A. Scott The Journal of Molecular Diagnostics Volume 19, Issue 3, Pages 397-403 (May 2017) DOI: 10.1016/j.jmoldx.2016.11.006 Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Evaluation of overall saliva DNA quality. All 20 blood and saliva DNA samples were assessed for quality by measuring UV spectrophotometry absorbance. Illustrated are box-and-whisker plots of the A260/280 (A) and A260/230 (B) values for blood and saliva DNA, with medians denoted by horizontal lines and 95th percentiles denoted by vertical lines. Data are expressed as median box-and-whisker plots. The Journal of Molecular Diagnostics 2017 19, 397-403DOI: (10.1016/j.jmoldx.2016.11.006) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Effect of bacterial content on chromosomal microarray (CMA) quality. The effect of bacterial content on CMA quality was assessed using the following platform-specific quality metrics: derivative log ratio (dLR; Agilent; A), log R deviation (Illumina; B), and median absolute pairwise difference (MAPD; Affymetrix; C). The scatter plots indicate that increasing bacterial content does not influence CMA quality metrics. The Journal of Molecular Diagnostics 2017 19, 397-403DOI: (10.1016/j.jmoldx.2016.11.006) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Comparison of chromosomal microarray (CMA) and single-nucleotide polymorphism (SNP) quality metrics between blood and saliva DNA. CMA quality was assessed using the derivative log ratio (dLR; Agilent), log R deviation (Illumina), and median absolute pairwise difference (MAPD; Affymetrix), and SNP genotyping quality metrics were assessed using the SNP call rate (Agilent), median B allele frequency (BAF; Illumina), and SNP quality control (snpQC; Affymetrix). Illustrated are box-and-whisker plots of the CMA (A) and SNP (B) quality values for blood and saliva DNA, with medians denoted by horizontal lines and 95th percentiles denoted by vertical lines. The Journal of Molecular Diagnostics 2017 19, 397-403DOI: (10.1016/j.jmoldx.2016.11.006) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Copy number variant (CNV) concordance between paired blood and saliva DNA. Illustrated are box-and-whisker plots for raw CNV calls (>100 kb; A) and percentage overlap of CNV calls for the three chromosomal microarray (CMA) platforms (B). Medians are denoted by horizontal lines, and 95th percentiles denoted by vertical lines. Although comparable numbers of CNVs were detected in paired blood and saliva DNA, the percentage overlap of identified CNVs was variable across all CMA platforms. The Journal of Molecular Diagnostics 2017 19, 397-403DOI: (10.1016/j.jmoldx.2016.11.006) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 5 Absence of heterozygosity (AOH) concordance between blood and saliva DNA. Illustrated are median box-and-whisker plots for the number of detected AOH calls (>2 Mb), medians denoted by horizontal lines and 95th percentiles denoted by vertical lines. The numbers of AOH calls detected in paired blood and saliva DNA were comparable by chromosomal microarray (CMA) testing; however, CMA platforms based on single-nucleotide polymorphism genotyping chemistry were most consistent. The Journal of Molecular Diagnostics 2017 19, 397-403DOI: (10.1016/j.jmoldx.2016.11.006) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions