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2 results on '"Matthew C. Hiemenz"'

1. Building a Robust Tumor Profiling Program: Synergy between Next-Generation Sequencing and Targeted Single-Gene Testing.

Author

Matthew C Hiemenz, Stephan Kadauke, David B Lieberman, David B Roth, Jianhua Zhao, Christopher D Watt, Robert D Daber, and Jennifer J D Morrissette

Subjects
Medicine, Science
Abstract

Next-generation sequencing (NGS) is a powerful platform for identifying cancer mutations. Routine clinical adoption of NGS requires optimized quality control metrics to ensure accurate results. To assess the robustness of our clinical NGS pipeline, we analyzed the results of 304 solid tumor and hematologic malignancy specimens tested simultaneously by NGS and one or more targeted single-gene tests (EGFR, KRAS, BRAF, NPM1, FLT3, and JAK2). For samples that passed our validated tumor percentage and DNA quality and quantity thresholds, there was perfect concordance between NGS and targeted single-gene tests with the exception of two FLT3 internal tandem duplications that fell below the stringent pre-established reporting threshold but were readily detected by manual inspection. In addition, NGS identified clinically significant mutations not covered by single-gene tests. These findings confirm NGS as a reliable platform for routine clinical use when appropriate quality control metrics, such as tumor percentage and DNA quality cutoffs, are in place. Based on our findings, we suggest a simple workflow that should facilitate adoption of clinical oncologic NGS services at other institutions.

Published
2016
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2. Building a Robust Tumor Profiling Program: Synergy between Next-Generation Sequencing and Targeted Single-Gene Testing

Author

Stephan Kadauke, Matthew C. Hiemenz, Christopher D. Watt, Robert Daber, David B. Lieberman, Jianhua Zhao, David Roth, and Jennifer J.D. Morrissette

Subjects
0301 basic medicine, Molecular biology, Physiology, Gene Identification and Analysis, lcsh:Medicine, Artificial Gene Amplification and Extension, Bioinformatics, medicine.disease_cause, Polymerase Chain Reaction, 0302 clinical medicine, Sequencing techniques, Neoplasms, Medicine and Health Sciences, Profiling (information science), DNA sequencing, lcsh:Science, Fluids, Multidisciplinary, medicine.diagnostic_test, Physics, High-Throughput Nucleotide Sequencing, Genomics, Hematology, Body Fluids, Blood, 030220 oncology & carcinogenesis, Physical Sciences, Engineering and Technology, KRAS, Anatomy, Transcriptome Analysis, Nucleophosmin, Research Article, Next-Generation Sequencing, Quality Control, States of Matter, Concordance, Single gene, Computational biology, Biology, 03 medical and health sciences, Industrial Engineering, medicine, Genetics, Biomarkers, Tumor, Point Mutation, Humans, Genetic Testing, Mutation Detection, Genetic testing, Biology and life sciences, lcsh:R, Computational Biology, Liquids, Genome Analysis, Research and analysis methods, 030104 developmental biology, Workflow, Molecular biology techniques, Mutation, lcsh:Q
Abstract

Next-generation sequencing (NGS) is a powerful platform for identifying cancer mutations. Routine clinical adoption of NGS requires optimized quality control metrics to ensure accurate results. To assess the robustness of our clinical NGS pipeline, we analyzed the results of 304 solid tumor and hematologic malignancy specimens tested simultaneously by NGS and one or more targeted single-gene tests (EGFR, KRAS, BRAF, NPM1, FLT3, and JAK2). For samples that passed our validated tumor percentage and DNA quality and quantity thresholds, there was perfect concordance between NGS and targeted single-gene tests with the exception of two FLT3 internal tandem duplications that fell below the stringent pre-established reporting threshold but were readily detected by manual inspection. In addition, NGS identified clinically significant mutations not covered by single-gene tests. These findings confirm NGS as a reliable platform for routine clinical use when appropriate quality control metrics, such as tumor percentage and DNA quality cutoffs, are in place. Based on our findings, we suggest a simple workflow that should facilitate adoption of clinical oncologic NGS services at other institutions.

Published
2016

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