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Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

Jonathan Foox, Scott W. Tighe, Charles M. Nicolet, Justin M. Zook, Marta Byrska-Bishop, Wayne E. Clarke, Michael M. Khayat, Medhat Mahmoud, Phoebe K. Laaguiby, Zachary T. Herbert, Derek Warner, George S. Grills, Jin Jen, Shawn Levy, Jenny Xiang, Alicia Alonso, Gary P. Schroth, Fritz J. Sedlazeck, Giuseppe Narzisi, William Farmerie, Don A. Baldwin, View ORCID ProfileChristopher E. Mason
doi: https://doi.org/10.1101/2020.07.23.218602
Jonathan Foox
1Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
2The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
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Scott W. Tighe
3University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, Vermont, USA
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Charles M. Nicolet
4Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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Justin M. Zook
5Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
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Marta Byrska-Bishop
6New York Genome Center, New York, NY, 10013, USA
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Wayne E. Clarke
6New York Genome Center, New York, NY, 10013, USA
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Michael M. Khayat
7Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
8Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Medhat Mahmoud
7Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
8Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Phoebe K. Laaguiby
3University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, Vermont, USA
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Zachary T. Herbert
9Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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Derek Warner
10DNA Sequencing Core, University of Utah, Salt Lake City, Utah, USA
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George S. Grills
11Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
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Jin Jen
12Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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Shawn Levy
13HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
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Jenny Xiang
1Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
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Alicia Alonso
1Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
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Gary P. Schroth
14Illumina, Inc., San Diego, CA, USA
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Fritz J. Sedlazeck
7Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
8Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Giuseppe Narzisi
6New York Genome Center, New York, NY, 10013, USA
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William Farmerie
15Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
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Don A. Baldwin
16Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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  • For correspondence: donald.baldwin@fccc.edu chm2042@med.cornell.edu
Christopher E. Mason
1Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
2The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
17The Feil Family Brain and Mind Research Institute, New York, New York, USA
18The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
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  • ORCID record for Christopher E. Mason
  • For correspondence: donald.baldwin@fccc.edu chm2042@med.cornell.edu
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Abstract

Massively parallel DNA sequencing is a critical tool for genomics research and clinical diagnostics. Here, we describe the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Phase II Study to measure quality and reproducibility of DNA sequencing. Replicates of human and bacterial reference DNA samples were generated across multiple sequencing platforms, including well-established technologies such as Illumina, ThermoFisher Ion Torrent, and Pacific Biosciences, as well as emerging technologies such as BGI, Genapsys, and Oxford Nanopore. A total of 202 datasets were generated to investigate the performance of a total of 16 sequencing platforms, including mappability of reads, coverage and error rates in difficult genomic regions, and detection of small-scale polymorphisms and large-scale structural variants. This study provides a comprehensive baseline resource for continual benchmarking as chemistries, methods, and platforms evolve for DNA sequencing.

Competing Interest Statement

G.P.S is employed by Illumina Inc. All other authors declare no competing financial interests.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 24, 2020.
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Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study
Jonathan Foox, Scott W. Tighe, Charles M. Nicolet, Justin M. Zook, Marta Byrska-Bishop, Wayne E. Clarke, Michael M. Khayat, Medhat Mahmoud, Phoebe K. Laaguiby, Zachary T. Herbert, Derek Warner, George S. Grills, Jin Jen, Shawn Levy, Jenny Xiang, Alicia Alonso, Gary P. Schroth, Fritz J. Sedlazeck, Giuseppe Narzisi, William Farmerie, Don A. Baldwin, Christopher E. Mason
bioRxiv 2020.07.23.218602; doi: https://doi.org/10.1101/2020.07.23.218602
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Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study
Jonathan Foox, Scott W. Tighe, Charles M. Nicolet, Justin M. Zook, Marta Byrska-Bishop, Wayne E. Clarke, Michael M. Khayat, Medhat Mahmoud, Phoebe K. Laaguiby, Zachary T. Herbert, Derek Warner, George S. Grills, Jin Jen, Shawn Levy, Jenny Xiang, Alicia Alonso, Gary P. Schroth, Fritz J. Sedlazeck, Giuseppe Narzisi, William Farmerie, Don A. Baldwin, Christopher E. Mason
bioRxiv 2020.07.23.218602; doi: https://doi.org/10.1101/2020.07.23.218602

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