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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.
Foox, Jonathan; Tighe, Scott W; Nicolet, Charles M; Zook, Justin M; Byrska-Bishop, Marta; Clarke, Wayne E; Khayat, Michael M; Mahmoud, Medhat; Laaguiby, Phoebe K; Herbert, Zachary T; Warner, Derek; Grills, George S; Jen, Jin; Levy, Shawn; Xiang, Jenny; Alonso, Alicia; Zhao, Xia; Zhang, Wenwei; Teng, Fei; Zhao, Yonggang; Lu, Haorong; Schroth, Gary P; Narzisi, Giuseppe; Farmerie, William; Sedlazeck, Fritz J; Baldwin, Don A; Mason, Christopher E.
Afiliação
  • Foox J; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
  • Tighe SW; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
  • Nicolet CM; University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA.
  • Zook JM; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
  • Byrska-Bishop M; Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • Clarke WE; New York Genome Center, New York, NY, USA.
  • Khayat MM; New York Genome Center, New York, NY, USA.
  • Mahmoud M; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
  • Laaguiby PK; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
  • Herbert ZT; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
  • Warner D; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
  • Grills GS; University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA.
  • Jen J; Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Levy S; DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA.
  • Xiang J; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
  • Alonso A; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
  • Zhao X; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Zhang W; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
  • Teng F; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
  • Zhao Y; BGI-Shenzhen, Shenzhen, China.
  • Lu H; MGI, BGI-Shenzhen, Shenzhen, China.
  • Schroth GP; BGI-Shenzhen, Shenzhen, China.
  • Narzisi G; BGI-Shenzhen, Shenzhen, China.
  • Farmerie W; BGI-Shenzhen, Shenzhen, China.
  • Sedlazeck FJ; Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
  • Baldwin DA; BGI-Shenzhen, Shenzhen, China.
  • Mason CE; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
Nat Biotechnol ; 39(9): 1129-1140, 2021 09.
Article em En | MEDLINE | ID: mdl-34504351
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.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Análise de Sequência de DNA / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans Idioma: En Revista: Nat Biotechnol Assunto da revista: BIOTECNOLOGIA Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Análise de Sequência de DNA / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans Idioma: En Revista: Nat Biotechnol Assunto da revista: BIOTECNOLOGIA Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos