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

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.
Nat Biotechnol. 2021 Sep;39(9):1129-1140. doi: 10.1038/s41587-021-01049-5.

Authors

Other Contributors

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}

¹Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

²The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.

³University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA.

⁴Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

⁵Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.

⁶New York Genome Center, New York, NY, USA.

⁷Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.

⁸Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

⁹Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA.

¹⁰DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA.

¹¹Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.

¹²Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.

¹³HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.

¹⁴BGI-Shenzhen, Shenzhen, China.

¹⁵MGI, BGI-Shenzhen, Shenzhen, China.

¹⁶Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.

¹⁷Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.

¹⁸Illumina, Inc., San Diego, CA, USA.

¹⁹Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA.

²⁰Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.

²¹Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

²²Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA.

²³Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

²⁴The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.

²⁵The Feil Family Brain and Mind Research Institute, New York, NY, USA.

²⁶The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.

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