BPHL SARS-CoV-2 Tiled Amplicon Illumina Sequencing v2

Illumina Sequencing ◽

Library Preparation ◽

Next Generation ◽

Florida Department ◽

Wet Lab ◽

This protocol details the Florida Department of Health's Bureau of Public Health Laboratories' (BPHL) wet lab portion of our SARS-CoV-2 next generation sequencing workflow. The method is a tiled amplicon approach using ARTIC V3 primers. The amplicon generation was adapted from the Matteson protocol1. The library preparation is Illumina NexteraXT. Library pooling and normalization were adapted from the Gohl protocol3. This protocol is for loading a MiSeq, but we have had equal success running on iSeqs and NextSeqs as well. Up to 96 libraries can be run on a MiSeq and up to 384 on a NextSeq.

Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing

BMC Genomics ◽

10.1186/s12864-018-4677-y ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 7

Author(s):

Wells W. Wu ◽

Je-Nie Phue ◽

Chun-Ting Lee ◽

Changyi Lin ◽

Lai Xu ◽

...

Keyword(s):

High Throughput ◽

Library Preparation ◽

Next Generation ◽

Laboratory diagnosis of bacterial meningitis by direct detection, serotyping and Next Generation Sequencing: How 10 years of testing in New York State has evolved to improve laboratory diagnosis and public health

Molecular and Cellular Probes ◽

10.1016/j.mcp.2021.101786 ◽

2021 ◽

pp. 101786

Author(s):

James R. Long ◽

Kara Mitchell ◽

Justine Edwards ◽

Danielle Wroblewski ◽

Elizabeth Luke ◽

...

Keyword(s):

Public Health ◽

New York ◽

Bacterial Meningitis ◽

Direct Detection ◽

New York State ◽

Laboratory Diagnosis ◽

Next Generation ◽

York State ◽

Sample Preparation, Standards, and Library Preparation for Next Generation Sequencing

Next Generation Sequencing in Forensic Science ◽

10.4324/9781003196464-3 ◽

2021 ◽

pp. 31-45

Author(s):

Kelly M. Elkins ◽

Cynthia B. Zeller

Keyword(s):

Sample Preparation ◽

Library Preparation ◽

Next Generation ◽

Application of Next-Generation Sequencing in Public Health Epidemiology and Outbreak Investigation

Advances in Molecular Pathology ◽

10.1016/j.yamp.2019.07.007 ◽

2019 ◽

Vol 2 (1) ◽

pp. 89-97 ◽

Cited By ~ 1

Author(s):

Anthony Tran ◽

Marie-Claire Rowlinson

Keyword(s):

Public Health ◽

Outbreak Investigation ◽

Next Generation ◽

Public Health Epidemiology ◽

Next-Generation Sequencing Library Preparation for 16S rRNA Microbiome Analysis After Serpin Treatment

Methods in Molecular Biology - Serpins ◽

10.1007/978-1-4939-8645-3_14 ◽

2018 ◽

pp. 213-221 ◽

Cited By ~ 1

Author(s):

Juan Maldonado ◽

Jordan R. Yaron ◽

Liqiang Zhang ◽

Alexandra Lucas

Keyword(s):

16S Rrna ◽

Library Preparation ◽

Next Generation ◽

Microbiome Analysis ◽

Sequencing Library ◽

Sequencing Library Preparation ◽

CleanTag Adapters Improve Small RNA Next-Generation Sequencing Library Preparation by Reducing Adapter Dimers

Methods in Molecular Biology - Next Generation Sequencing ◽

10.1007/978-1-4939-7514-3_10 ◽

2017 ◽

pp. 145-161

Author(s):

Sabrina Shore ◽

Jordana M. Henderson ◽

Anton P. McCaffrey

Keyword(s):

Small Rna ◽

Library Preparation ◽

Next Generation ◽

Sequencing Library ◽

Sequencing Library Preparation ◽

Rapid, high-throughput library preparation for next-generation sequencing

Nature Methods ◽

10.1038/nmeth.f.310 ◽

2010 ◽

Vol 7 (8) ◽

pp. iii-iv ◽

Cited By ~ 7

Author(s):

Haiying Grunenwald ◽

Brad Baas ◽

Nicholas Caruccio ◽

Fraz Syed

Keyword(s):

High Throughput ◽

Library Preparation ◽

Next Generation ◽

Practical Guidance to Implementing Quality Management Systems in Public Health Laboratories Performing Next-Generation Sequencing: Personnel, Equipment, and Process Management (Phase 1)

Journal of Clinical Microbiology ◽

10.1128/jcm.00261-19 ◽

2019 ◽

Vol 57 (8) ◽

Cited By ~ 3

Author(s):

Rebecca J. Hutchins ◽

Kristy L. Phan ◽

Adeeba Saboor ◽

Joseph D. Miller ◽

Atis Muehlenbachs

Keyword(s):

Public Health ◽

Quality Management ◽

Process Management ◽

Quality Management System ◽

Phase 1 ◽

Quality System ◽

Clinical Diagnostics ◽

Next Generation ◽

ABSTRACT Quality standards as part of an effective quality management system (QMS) are the cornerstone for generating high-quality test results. Next-generation sequencing (NGS) has the potential to improve both clinical diagnostics and public health surveillance efforts in multiple areas, including infectious diseases. However, the laboratories adopting NGS methods face significant challenges due to the complex and modular process design. This document summarizes the first phase of quality system guidance developed by the Centers for Disease Control and Prevention (CDC) NGS Quality Workgroup. The quality system essentials of personnel, equipment, and process management (quality control and validation) were prioritized based on a risk assessment using information gathered from participating CDC laboratories. Here, we present a prioritized QMS framework, including procedures and documentation tools, to assist laboratory implementation and maintenance of quality practices for NGS workflows.