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Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol 2021; 39:1466. [PMID: 34635840 DOI: 10.1038/s41587-021-01122-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott W Tighe
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Charles M Nicolet
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin M Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Michael M Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Phoebe K Laaguiby
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derek Warner
- DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenny Xiang
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Xia Zhao
- BGI-Shenzhen, Shenzhen, China.,MGI, BGI-Shenzhen, Shenzhen, China
| | | | | | - Yonggang Zhao
- BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | | | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Don A Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. .,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. .,The Feil Family Brain and Mind Research Institute, New York, NY, USA. .,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol 2021; 39:1129-1140. [PMID: 34504351 PMCID: PMC8985210 DOI: 10.1038/s41587-021-01049-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
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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Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott W. Tighe
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Charles M. Nicolet
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Michael M. Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Phoebe K. Laaguiby
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Zachary T. Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derek Warner
- DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenny Xiang
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Xia Zhao
- BGI-Shenzhen, Shenzhen, China.,MGI, BGI-Shenzhen, Shenzhen, China
| | | | | | - Yonggang Zhao
- BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | | | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
| | - Don A. Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute, New York, NY, USA.,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
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