Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

. 2021 Sep;39(9):1129-1140.

doi: 10.1038/s41587-021-01049-5.

Epub 2021 Sep 9.

Jonathan Foox^{1

2}, Scott W Tighe³, Charles M Nicolet⁴, Justin M Zook⁵, Marta Byrska-Bishop⁶, Wayne E Clarke⁶, Michael M Khayat^{7

8}, Medhat Mahmoud^{7

8}, Phoebe K Laaguiby³, Zachary T Herbert⁹, Derek Warner¹⁰, George S Grills¹¹, Jin Jen¹², Shawn Levy¹³, Jenny Xiang¹, Alicia Alonso¹, Xia Zhao^{14

15}, Wenwei Zhang¹⁴, Fei Teng¹⁴, Yonggang Zhao^{14

16}, Haorong Lu^{14

17}, Gary P Schroth¹⁸, Giuseppe Narzisi⁶, William Farmerie¹⁹, Fritz J Sedlazeck^{20

21}, Don A Baldwin²², Christopher E Mason^{23

24

25

26}

Affiliations

¹ Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
² The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
³ University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA.
⁴ Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁵ Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
⁶ New York Genome Center, New York, NY, USA.
⁷ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
⁸ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
⁹ Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA.
¹⁰ DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA.
¹¹ Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
¹² Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
¹³ HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
¹⁴ BGI-Shenzhen, Shenzhen, China.
¹⁵ MGI, BGI-Shenzhen, Shenzhen, China.
¹⁶ Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
¹⁷ Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
¹⁸ Illumina, Inc., San Diego, CA, USA.
¹⁹ Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA.
²⁰ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. fritz.sedlazeck@bcm.edu.
²¹ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. fritz.sedlazeck@bcm.edu.
²² Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA. donald.baldwin@fccc.edu.
²³ Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.
²⁴ The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.
²⁵ The Feil Family Brain and Mind Research Institute, New York, NY, USA. chm2042@med.cornell.edu.
²⁶ The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.

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Jonathan Foox et al.

Nat Biotechnol.

2021 Sep.

. 2021 Sep;39(9):1129-1140.

doi: 10.1038/s41587-021-01049-5.

Epub 2021 Sep 9.

Authors

Affiliations

¹ Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
² The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
³ University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA.
⁴ Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁵ Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
⁶ New York Genome Center, New York, NY, USA.
⁷ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
⁸ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
⁹ Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA.
¹⁰ DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA.
¹¹ Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
¹² Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
¹³ HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
¹⁴ BGI-Shenzhen, Shenzhen, China.
¹⁵ MGI, BGI-Shenzhen, Shenzhen, China.
¹⁶ Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
¹⁷ Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
¹⁸ Illumina, Inc., San Diego, CA, USA.
¹⁹ Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA.
²⁰ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. fritz.sedlazeck@bcm.edu.
²¹ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. fritz.sedlazeck@bcm.edu.
²² Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA. donald.baldwin@fccc.edu.
²³ Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.
²⁴ The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.
²⁵ The Feil Family Brain and Mind Research Institute, New York, NY, USA. chm2042@med.cornell.edu.
²⁶ The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.

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Abstract

Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. The long-read instrument PacBio CCS had the highest reference-based mapping rate and lowest non-mapping rate. The two long-read platforms PacBio CCS and PromethION/MinION showed the best sequence mapping in repeat-rich areas and across homopolymers. NovaSeq 6000 using 2 × 250-bp read chemistry was the most robust instrument for capturing known insertion/deletion events. This study serves as a benchmark for current genomics technologies, as well as a resource to inform experimental design and next-generation sequencing variant calling.

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