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Evanich DJ, Ponnaluri VKC, Panchapakesa V, Erijman A, Campbell MA, Dai N, Langhorst BW, Vaisvila R, Williams L. Abstract 6018: Sequencing of 5-hydroxymethylcytosine to single base resolution. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
DNA methylation is an epigenetic regulator of gene expression with important functions in development and diseases such as cancer. The modified cytosines, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are identified using Illumina sequencing. Libraries are generated using either NEBNext® EM-seq™, an enzyme-based workflow, or by using sodium bisulfite conversion. These methods, however, cannot differentiate between 5mC and 5hmC. Distinguishing these modifications is important as there is increased interest in 5hmCs role in regulating gene expression. Methods currently exist to enable discrimination of 5mC and 5hmC, for example, oxBS-seq and TAB-seq. These methods still rely upon sodium bisulfite conversion and have reduced data quality due to fragmentation and loss of DNA. Here we describe an enzymatic method that enables specific detection of 5hmC. 5hmC is detected using two enzymatic steps. Firstly, 5hmCs are glucosylated, which protects them from subsequent deamination by APOBEC. In contrast, cytosines and 5mCs are deaminated resulting in their conversion to uracil and thymine, respectively. During Illumina sequencing deaminated cytosine and 5mC are read as thymine and the glucosylated 5hmC are read as cytosine. Subtractive analysis of 5hmC data from EM-seq data, which detects both 5mC and 5hmC, permits the identification of individual 5mC and 5hmC sites. 5hmC data were generated for inputs of 0.1 ng to 200 ng DNA isolated from E14 mouse embryonic stem cells and human brain. The 5hmC libraries had similar characteristics to EM-seq libraries, including expected insert sizes due to intact DNA molecules, low duplication rates and minimal GC bias. T4147 phage DNA was used as an internal control, as all cytosines are 5-hydroxymethylated, with 98-99% of cytosines identified as 5hmC. 5mC and 5hmC levels were also profiled during E14 cell differentiation for 10 days. Interestingly, 5hmC levels decreased whereas 5mC levels increased particularly during the first five days of differentiation. LC-MS/MS quantification of this same DNA mirrored the changes observed by sequencing. The ability to discriminate between 5mC and 5hmC will provide key insights into the role of these cytosine modifications in development and disease.
Citation Format: Daniel J. Evanich, V. K. Chaithanya Ponnaluri, Vaishnavi Panchapakesa, Ariel Erijman, Matthew A. Campbell, Nan Dai, Bradley W. Langhorst, Romualdas Vaisvila, Louise Williams. Sequencing of 5-hydroxymethylcytosine to single base resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6018.
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Affiliation(s)
| | | | | | | | | | - Nan Dai
- 1New England Biolabs, Inc., Ipswich, MA
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2
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Heider MR, Sun J, Sexton BS, Langhorst BW, Gray A, Higgins L, Chen L, Apone L, Evans TC, Nichols NM, Liu P. Abstract 249: A novel suite of enzyme mixes enable robust hybrid capture sequencing from low quality FFPE DNA. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
In cancer genomics, a common source of DNA is formalin-fixed, paraffin-embedded (FFPE) tissue from patient surgical samples, where in most cases high-quality fresh or frozen tissue samples are not available. FFPE DNA poses many notable challenges for preparing NGS libraries, including low input amounts and highly variable damage from fixation, storage, and extraction methods. Due to the high cost of sequencing and variability of coverage, regions of interest are often specifically enriched using hybrid capture-based approaches, but these methods require a high input of diverse, uniform DNA library to achieve the coverage required for somatic mutation identification in tumor samples. We developed a new DNA repair enzyme mix, enzymatic fragmentation mix, and library amplification PCR master mix, optimizing the activities of these mixes using FFPE samples ranging from DIN 1.8 to 6.8 to maximize yield, WGS library quality, and target enrichment library performance. Combining DNA damage repair and a novel enzymatic fragmentation mix upstream of library preparation reduced the false positive rate in somatic variant detection by repairing damage-derived mutations, and also improved the library yield, quality metrics (including mapping, chimeras, and properly-paired reads), complexity, coverage uniformity, and hybrid capture library quality metrics. The new PCR master mix boosts the library yield without compromising library quality in FFPE-derived samples, allowing flexibility in the PCR cycles used to accommodate high-throughput processing of FFPE samples of highly varied quality. This library prep workflow was evaluated with multiple sequencing platforms including Illumina, MGI, and Element Biosciences. This new suite of enzyme mixes allows even highly damaged FFPE samples to achieve high-quality libraries with sufficient input for hybrid capture. Increasing the useable reads and coverage enables robust detection of somatic variants as demonstrated using both reference standard DNA and patient-derived FFPE samples. Finally, the use of enzymatic fragmentation and a flexible PCR master mix make this FFPE library prep workflow compatible with high-throughput and automation-based workflows.
Citation Format: Margaret R. Heider, Jian Sun, Brittany S. Sexton, Bradley W. Langhorst, Andrew Gray, Lauren Higgins, Lixin Chen, Lynne Apone, Thomas C. Evans, Nicole M. Nichols, Pingfang Liu. A novel suite of enzyme mixes enable robust hybrid capture sequencing from low quality FFPE DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 249.
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Affiliation(s)
| | - Jian Sun
- 1New England Biolabs, Inc., Ipswich, MA
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3
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Bei Y, Pinet K, Vrtis KB, Borgaro JG, Sun L, Campbell M, Apone L, Langhorst BW, Nichols NM. Overcoming variant mutation-related impacts on viral sequencing and detection methodologies. Front Med (Lausanne) 2022; 9:989913. [PMID: 36388914 PMCID: PMC9650041 DOI: 10.3389/fmed.2022.989913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/05/2022] [Indexed: 11/30/2022] Open
Abstract
Prompt and accurate pathogen identification, by diagnostics and sequencing, is an effective tool for tracking and potentially curbing pathogen spread. Targeted detection and amplification of viral genomes depends on annealing complementary oligonucleotides to genomic DNA or cDNA. However, genomic mutations that occur during viral evolution may perturb annealing, which can result in incomplete sequence coverage of the genome and/or false negative diagnostic test results. Herein, we demonstrate how to assess, test, and optimize sequencing and detection methodologies to attenuate the negative impact of mutations on genome targeting efficiency. This evaluation was conducted using in vitro-transcribed (IVT) RNA as well as RNA extracted from clinical SARS-CoV-2 variant samples, including the heavily mutated Omicron variant. Using SARS-CoV-2 as a current example, these results demonstrate how to maintain reliable targeted pathogen sequencing and how to evaluate detection methodologies as new variants emerge.
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Afgan E, Nekrutenko A, Grüning BA, Blankenberg D, Goecks J, Schatz MC, Ostrovsky AE, Mahmoud A, Lonie AJ, Syme A, Fouilloux A, Bretaudeau A, Nekrutenko A, Kumar A, Eschenlauer AC, DeSanto AD, Guerler A, Serrano-Solano B, Batut B, Grüning BA, Langhorst BW, Carr B, Raubenolt BA, Hyde CJ, Bromhead CJ, Barnett CB, Royaux C, Gallardo C, Blankenberg D, Fornika DJ, Baker D, Bouvier D, Clements D, de Lima Morais DA, Tabernero DL, Lariviere D, Nasr E, Afgan E, Zambelli F, Heyl F, Psomopoulos F, Coppens F, Price GR, Cuccuru G, Corguillé GL, Von Kuster G, Akbulut GG, Rasche H, Hotz HR, Eguinoa I, Makunin I, Ranawaka IJ, Taylor JP, Joshi J, Hillman-Jackson J, Goecks J, Chilton JM, Kamali K, Suderman K, Poterlowicz K, Yvan LB, Lopez-Delisle L, Sargent L, Bassetti ME, Tangaro MA, van den Beek M, Čech M, Bernt M, Fahrner M, Tekman M, Föll MC, Schatz MC, Crusoe MR, Roncoroni M, Kucher N, Coraor N, Stoler N, Rhodes N, Soranzo N, Pinter N, Goonasekera NA, Moreno PA, Videm P, Melanie P, Mandreoli P, Jagtap PD, Gu Q, Weber RJM, Lazarus R, Vorderman RHP, Hiltemann S, Golitsynskiy S, Garg S, Bray SA, Gladman SL, Leo S, Mehta SP, Griffin TJ, Jalili V, Yves V, Wen V, Nagampalli VK, Bacon WA, de Koning W, Maier W, Briggs PJ. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res 2022; 50:W345-W351. [PMID: 35446428 PMCID: PMC9252830 DOI: 10.1093/nar/gkac247] [Citation(s) in RCA: 235] [Impact Index Per Article: 117.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 01/19/2023] Open
Abstract
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.
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Song C, Erijman A, Langhorst BW, Liu P, Dimalanta ET, Davis TB. Abstract 5628: Immune repertoire sequencing facilitates gamma delta T cell clonal determination. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Gamma-delta T cells are a small fraction of T lymphocytes with only 1-5% of the overall T cell population, but they are an important subset that have unique contributions to both innate and adaptive immunity. Gamma-delta T cells can recognize a broad range of antigens to provide rapid responses to pathogens, and can also interact with both immune cells and non-immune tissue cells triggering regulatory and cytotoxic responses. These unique features make them ideal candidates that could be targeted to induce durable immunity in the context of different pathologies. There has been growing interest in understanding the contributions of gamma-delta T cells to immunology and developing efficient gamma-delta T-cell-based therapies for cancer, infectious disease, and autoimmune disease. In this study, we have implemented T cell repertoire sequencing for high throughput characterization. Gamma-delta T cells were enriched from tissues and peripheral blood mononuclear cells (PBMCs). RNA was extracted and used to generate full length TCR libraries. Unique molecular identifiers (UMIs) were incorporated to discretely barcode each mRNA molecule, enabling absolute quantitative ranking of TCR clone abundance. Full length immune repertoire sequencing facilitates the detection of distinct and shared clones in tissue and blood samples, enabling the identification of disease specific clones to evaluate immunotherapy effects. In addition, RNA sequencing was performed for gene expression analysis of gamma-delta T cells to identify cell phenotypes.
Citation Format: Chen Song, Ariel Erijman, Bradley W. Langhorst, Pingfang Liu, Eileen T. Dimalanta, Theodore B. Davis. Immune repertoire sequencing facilitates gamma delta T cell clonal determination [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5628.
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Li Z, Bruce JL, Cohen B, Cunningham CV, Jack WE, Kunin K, Langhorst BW, Miller J, Moncion RA, Poole CB, Premsrirut PK, Ren G, Roberts RJ, Tanner NA, Zhang Y, Carlow CKS. Development and implementation of a simple and rapid extraction-free saliva SARS-CoV-2 RT-LAMP workflow for workplace surveillance. PLoS One 2022; 17:e0268692. [PMID: 35617204 PMCID: PMC9135294 DOI: 10.1371/journal.pone.0268692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 01/12/2023] Open
Abstract
Effective management of the COVID-19 pandemic requires widespread and frequent testing of the population for SARS-CoV-2 infection. Saliva has emerged as an attractive alternative to nasopharyngeal samples for surveillance testing as it does not require specialized personnel or materials for its collection and can be easily provided by the patient. We have developed a simple, fast, and sensitive saliva-based testing workflow that requires minimal sample treatment and equipment. After sample inactivation, RNA is quickly released and stabilized in an optimized buffer, followed by reverse transcription loop-mediated isothermal amplification (RT-LAMP) and detection of positive samples using a colorimetric and/or fluorescent readout. The workflow was optimized using 1,670 negative samples collected from 172 different individuals over the course of 6 months. Each sample was spiked with 50 copies/μL of inactivated SARS-CoV-2 virus to monitor the efficiency of viral detection. Using pre-defined clinical samples, the test was determined to be 100% specific and 97% sensitive, with a limit of detection of 39 copies/mL. The method was successfully implemented in a CLIA laboratory setting for workplace surveillance and reporting. From April 2021-February 2022, more than 30,000 self-collected samples from 755 individuals were tested and 85 employees tested positive mainly during December and January, consistent with high infection rates in Massachusetts and nationwide.
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Affiliation(s)
- Zhiru Li
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Barry Cohen
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - William E. Jack
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Katell Kunin
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Jacob Miller
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Reynes A. Moncion
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | | | - Guoping Ren
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Nathan A. Tanner
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Yinhua Zhang
- New England Biolabs, Ipswich, Massachusetts, United States of America
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7
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VijayKrishna N, Joshi J, Coraor N, Hillman-Jackson J, Bouvier D, van den Beek M, Eguinoa I, Coppens F, Davis J, Stolarczyk M, Sheffield NC, Gladman S, Cuccuru G, Grüning B, Soranzo N, Rasche H, Langhorst BW, Bernt M, Fornika D, de Lima Morais DA, Barrette M, van Heusden P, Petrillo M, Puertas-Gallardo A, Patak A, Hotz HR, Blankenberg D. Expanding the Galaxy's reference data. Bioinform Adv 2022; 2:vbac030. [PMID: 35669346 PMCID: PMC9155181 DOI: 10.1093/bioadv/vbac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/01/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023]
Abstract
Summary Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy. Availability and implementation The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 22.01, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull and released using an MIT license. Access to existing data is also available through CVMFS, with instructions at https://galaxyproject.org/admin/reference-data-repo/. No new data were generated or analyzed in support of this research.
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Affiliation(s)
| | - Jayadev Joshi
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Nate Coraor
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Jennifer Hillman-Jackson
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Dave Bouvier
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Marius van den Beek
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Ignacio Eguinoa
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - John Davis
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michał Stolarczyk
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | | | | | - Björn Grüning
- University of Freiburg, Freiburg im Breisgau, Germany
| | | | - Helena Rasche
- Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | | | - Matthias Bernt
- Department Computational Biology, Helmholtz Centre for Environmental Research, UFZ, 04318 Leipzig, Germany
| | - Dan Fornika
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | | | - Michel Barrette
- Centre de Calcul Scientifique, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Peter van Heusden
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | - Alex Patak
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Hans-Rudolf Hotz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- To whom correspondence should be addressed.
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Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 2021; 22:332. [PMID: 34872606 PMCID: PMC8650396 DOI: 10.1186/s13059-021-02529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group. RESULTS Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. CONCLUSIONS The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
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Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Claudia Lalancette
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Ting Gong
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | | | - Samantha Lent
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | | | | | | | - Raymond Cavalcante
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Anders Lundmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Justin Gurvitch
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mark Menor
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Caroline Sheridan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Gosia Golda
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Muszynska
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Paweł P Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Frank Wos
- New York Genome Center, New York, NY, 10013, USA
| | - Amanda Raine
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Ulrika Liljedahl
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Tomas Axelsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhaowei Yang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Li
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaopeng Yang
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Hongwei Wang
- Development of Medicine, the University of Chicago, Chicago, IL, 60637, USA
| | - Ari Melnick
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Shang Guo
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Alexander Blume
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Inmaculada Ibanez de Caceres
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Rocio Rosas
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Justin Wade Davis
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | - Dalila B Megherbi
- CMINDS Research Center, Francis College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Wenming Xiao
- Center for Devices and Radiological Health, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Will Liao
- New York Genome Center, New York, NY, 10013, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Yunliang Wang
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China.
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
- The Feil Family Brain and Mind Research Institute, New York, New York, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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9
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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10
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Vaisvila R, Ponnaluri VKC, Sun Z, Langhorst BW, Saleh L, Guan S, Dai N, Campbell MA, Sexton BS, Marks K, Samaranayake M, Samuelson JC, Church HE, Tamanaha E, Corrêa IR, Pradhan S, Dimalanta ET, Evans TC, Williams L, Davis TB. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res 2021; 31:1280-1289. [PMID: 34140313 PMCID: PMC8256858 DOI: 10.1101/gr.266551.120] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 05/06/2021] [Indexed: 01/15/2023]
Abstract
Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing data. To overcome these problems, enzymatic methyl-seq (EM-seq) was developed. This method detects 5mC and 5hmC using two sets of enzymatic reactions. In the first reaction, TET2 and T4-BGT convert 5mC and 5hmC into products that cannot be deaminated by APOBEC3A. In the second reaction, APOBEC3A deaminates unmodified cytosines by converting them to uracils. Therefore, these three enzymes enable the identification of 5mC and 5hmC. EM-seq libraries were compared with bisulfite-converted DNA, and each library type was ligated to Illumina adaptors before conversion. Libraries were made using NA12878 genomic DNA, cell-free DNA, and FFPE DNA over a range of DNA inputs. The 5mC and 5hmC detected in EM-seq libraries were similar to those of bisulfite libraries. However, libraries made using EM-seq outperformed bisulfite-converted libraries in all specific measures examined (coverage, duplication, sensitivity, etc.). EM-seq libraries displayed even GC distribution, better correlations across DNA inputs, increased numbers of CpGs within genomic features, and accuracy of cytosine methylation calls. EM-seq was effective using as little as 100 pg of DNA, and these libraries maintained the described advantages over bisulfite sequencing. EM-seq library construction, using challenging samples and lower DNA inputs, opens new avenues for research and clinical applications.
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Affiliation(s)
| | | | - Zhiyi Sun
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Lana Saleh
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Shengxi Guan
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Nan Dai
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Brittany S Sexton
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Katherine Marks
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Mala Samaranayake
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - James C Samuelson
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Heidi E Church
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Esta Tamanaha
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Sriharsa Pradhan
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Thomas C Evans
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Louise Williams
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Theodore B Davis
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
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11
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Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun 2021; 12:1660. [PMID: 33712587 PMCID: PMC7954844 DOI: 10.1038/s41467-021-21361-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- 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
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - 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
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ebrahim Afshinnekoo
- 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
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A Ivanov
- 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
- Clinical & Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Maria Sierra
- 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
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, Columbia, NY, USA
| | - Evan T Sholle
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Craig D Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ciaran Hassan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | | | - Dorottya Nagy-Szakal
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | | | | | - Niamh B O'Hara
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | - Jeffrey A Rosenfeld
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
- Department of Pathology, Robert Wood Johnson Medical School, New York, NJ, USA
| | - Ying Chen
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
| | - Peter A D Steel
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amos J Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Thomas R Campion
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Iman Hajirasouliha
- 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
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 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.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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12
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Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, Mason CE. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions. bioRxiv 2020:2020.04.20.048066. [PMID: 32511352 PMCID: PMC7255793 DOI: 10.1101/2020.04.20.048066] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.
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Affiliation(s)
- Daniel J. Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | | | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- Tri-Institutional Computational Biol. & Medicine Program, Weill Cornell Medicine, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
| | - Joel Rosiene
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Alon Shaiber
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A. Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- Clinical & Translational Science Center, Weill Cornell Medicine, NY, USA
| | - Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, NY, USA
| | - Craig D. Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | | | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- Tri-Institutional Computational Biol. & Medicine Program, Weill Cornell Medicine, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, NY, USA
| | | | - Amos J. Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, MD, USA
| | | | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | | | - Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Stacy M. Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, NC, USA
- Department of Medicine, Duke University Medical Center, NC, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Mirella Salvatore
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Marcin Imielinski
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, NY, USA
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13
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Potapov V, Ong JL, Langhorst BW, Bilotti K, Cahoon D, Canton B, Knight TF, Evans TC, Lohman GJS. A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining. Nucleic Acids Res 2019; 46:e79. [PMID: 29741723 PMCID: PMC6061786 DOI: 10.1093/nar/gky303] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 12/14/2022] Open
Abstract
DNA ligases are key enzymes in molecular and synthetic biology that catalyze the joining of breaks in duplex DNA and the end-joining of DNA fragments. Ligation fidelity (discrimination against the ligation of substrates containing mismatched base pairs) and bias (preferential ligation of particular sequences over others) have been well-studied in the context of nick ligation. However, almost no data exist for fidelity and bias in end-joining ligation contexts. In this study, we applied Pacific Biosciences Single-Molecule Real-Time sequencing technology to directly sequence the products of a highly multiplexed ligation reaction. This method has been used to profile the ligation of all three-base 5′-overhangs by T4 DNA ligase under typical ligation conditions in a single experiment. We report the relative frequency of all ligation products with or without mismatches, the position-dependent frequency of each mismatch, and the surprising observation that 5′-TNA overhangs ligate extremely inefficiently compared to all other Watson–Crick pairings. The method can easily be extended to profile other ligases, end-types (e.g. blunt ends and overhangs of different lengths), and the effect of adjacent sequence on the ligation results. Further, the method has the potential to provide new insights into the thermodynamics of annealing and the kinetics of end-joining reactions.
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Affiliation(s)
- Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Jennifer L Ong
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Bradley W Langhorst
- Applications and Product Development, New England Biolabs, Ipswich, MA 01938, USA
| | | | | | | | | | - Thomas C Evans
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
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Liu P, Krishnan K, Devoe CX, Langhorst BW, Dimalanta E, Davis TB. Abstract 3526: Incorporation of unique molecular identifiers (UMIs) into unique dual sample indexing (UDI) improves the accuracy of quantitative next generation sequencing. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Accurate analysis of quantitative NGS data is critical for low frequency variant detection, identification of differentially expressed transcripts, and correct diagnosis and patient care in a clinical NGS setting. Two major factors affecting sequencing accuracy are 1) PCR duplication arising from amplification of library molecules; and 2) errors introduced during library preparation and actual sequencing on the flow cell. Standard practice for identification and removal of PCR duplicates relies on aligning reads to the same genomic coordinates. However, this approach can not differentiate between PCR duplicates and reads originating from unique molecules with identical ends. The most effective method for error correction is Duplex Sequencing, which utilizes UMIs to tag both strands of each individual DNA duplex followed by building consensus sequences. Unfortunately, this approach is labor intensive and cost-prohibitive for complex genomes and large target panels. Therefore, a simple and reliable approach for duplicate removal and error correction would greatly facilitate the wider adoption of NGS technology for diagnostics and clinical applications.
In this study, we incorporate UMIs into UDI systems and assess the effect on the accuracy of quantitative sequencing assays. We first study the effectiveness of various computational methods to account for UMIs and remove base-calling errors introduced during sequencing. We then analyze the utility of UMIs for 1) unique and low abundance transcript identification and accurate transcript quantification; and 2) error correction in low frequency variant detection in genomic sequencing from both high quality cell line DNA and low quality FFPE DNA. In addition, we demonstrate that combining unique dual sample indexing with UMI molecular barcoding further improves data analysis accuracy, especially on patterned flow cells. Our approach involves a simple new UMI-containing UDI adaptor design that can also be applied to other sequencing methods and platforms.
Citation Format: Pingfang Liu, Keerthana Krishnan, Camille X. Devoe, Bradley W. Langhorst, Eileen Dimalanta, Theodore B. Davis. Incorporation of unique molecular identifiers (UMIs) into unique dual sample indexing (UDI) improves the accuracy of quantitative next generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3526.
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15
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Song C, Liu P, Barry A, Langhorst BW, Stewart FJ, Russello S, Davis TB, Dimalanta ET. Abstract 4046: Immune repertoire sequencing reveals tumor microenvironment and tracks clonally expanded B cell and T cell in blood. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The study of complex immunological diseases and tumor microenvironments has progressed through recent developments on sequencing of the immune repertoire. Using this approach, the interrogation of disease progression is facilitated through analysis of millions of V(D)J combinations from B cell antibodies (Igs) and T cell receptors (TCRs). One major challenge of immune repertoire sequencing is to accurately capture the structural and sequence complexities of antibodies and TCR genes. We have developed a method for accurate sequencing of full length immune gene repertoires of B cells and T cells. RNA extracted from tumor tissues containing tumor infiltrating lymphocytes, as well as matched peripheral blood mononuclear cells (PBMCs) were used to generate full length Ig and TCR libraries. Unique molecule index (UMI) was used to discretely barcode each mRNA molecule, enabling absolute quantitative ranking of antibody/TCR clone abundance. Full length immune repertoire sequencing facilitates detection of distinct and shared clones in tissue and blood samples, enabling identification of disease specific clones to evaluate immunotherapy effects. Highly expanded clones in tumor samples are also found in blood samples. RNA-seq libraries were also constructed from the same RNA for Ig and TCR libraries. The expression level of IGH/IGL/IGK and TRA/TRB in the immune sequencing libraries highly correlates with the RNA-seq data. In addition, both Ig and TCR libraries can be constructed in one tube to obtain a whole immune repertoire profile.Our immune repertoire sequencing approach allows accurate clonal determination for both Ig and TCR. This technique is applicable for investigation of lymphocytes infiltration of tumor microenvironments, tracing expanded B cell and T cells in blood samples, and monitoring of minimal residual disease.
Citation Format: Chen Song, Pingfang Liu, Andrew Barry, Bradley W. Langhorst, Fiona J. Stewart, Salvatore Russello, Theodore B. Davis, Eileen T. Dimalanta. Immune repertoire sequencing reveals tumor microenvironment and tracks clonally expanded B cell and T cell in blood [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4046.
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16
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Potapov V, Ong JL, Kucera RB, Langhorst BW, Bilotti K, Pryor JM, Cantor EJ, Canton B, Knight TF, Evans TC, Lohman GJS. Comprehensive Profiling of Four Base Overhang Ligation Fidelity by T4 DNA Ligase and Application to DNA Assembly. ACS Synth Biol 2018; 7:2665-2674. [PMID: 30335370 DOI: 10.1021/acssynbio.8b00333] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthetic biology relies on the manufacture of large and complex DNA constructs from libraries of genetic parts. Golden Gate and other Type IIS restriction enzyme-dependent DNA assembly methods enable rapid construction of genes and operons through one-pot, multifragment assembly, with the ordering of parts determined by the ligation of Watson-Crick base-paired overhangs. However, ligation of mismatched overhangs leads to erroneous assembly, and low-efficiency Watson Crick pairings can lead to truncated assemblies. Using sets of empirically vetted, high-accuracy junction pairs avoids this issue but limits the number of parts that can be joined in a single reaction. Here, we report the use of comprehensive end-joining ligation fidelity and bias data to predict high accuracy junction sets for Golden Gate assembly. The ligation profile accurately predicted junction fidelity in ten-fragment Golden Gate assembly reactions and enabled accurate and efficient assembly of a lac cassette from up to 24-fragments in a single reaction.
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Affiliation(s)
- Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Jennifer L. Ong
- Research Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Rebecca B. Kucera
- Applications and Product Development, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Bradley W. Langhorst
- Applications and Product Development, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Katharina Bilotti
- Research Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - John M. Pryor
- Research Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Eric J. Cantor
- Applications and Product Development, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Barry Canton
- Ginkgo Bioworks, Boston, Massachusetts 02210, United States
| | | | - Thomas C. Evans
- Research Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Gregory J. S. Lohman
- Research Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
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17
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Zhang A, Li S, Apone L, Sun X, Chen L, Ettwiller LM, Langhorst BW, Noren CJ, Xu MQ. Solid-phase enzyme catalysis of DNA end repair and 3' A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA. Sci Rep 2018; 8:15887. [PMID: 30367148 PMCID: PMC6203771 DOI: 10.1038/s41598-018-34079-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 10/06/2018] [Indexed: 01/28/2023] Open
Abstract
The use of next-generation sequencing (NGS) has been instrumental in advancing biological research and clinical diagnostics. To fully utilize the power of NGS, complete, uniform coverage of the entire genome is required. In this study, we identified the primary sources of bias observed in sequence coverage across AT-rich regions of the human genome with existing amplification-free DNA library preparation methods. We have found evidence that a major source of bias is the inefficient processing of AT-rich DNA in end repair and 3' A-tailing, causing under-representation of extremely AT-rich regions. We have employed immobilized DNA modifying enzymes to catalyze end repair and 3' A-tailing reactions, to notably reduce the GC bias observed with existing library construction methods.
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Affiliation(s)
- Aihua Zhang
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Shaohua Li
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Lynne Apone
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Xiaoli Sun
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Lixin Chen
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | | | | | | | - Ming-Qun Xu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.
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18
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Kovar L, Nageswara-Rao M, Ortega-Rodriguez S, Dugas DV, Straub S, Cronn R, Strickler SR, Hughes CE, Hanley KA, Rodriguez DN, Langhorst BW, Dimalanta ET, Bailey CD. PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing. Genome Biol Evol 2018; 10:2501-2517. [PMID: 30137422 PMCID: PMC6161758 DOI: 10.1093/gbe/evy179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2018] [Indexed: 12/31/2022] Open
Abstract
Reconstructions of vascular plant mitochondrial genomes (mt-genomes) are notoriously complicated by rampant recombination that has resulted in comparatively few plant mt-genomes being available. The dearth of plant mitochondrial resources has limited our understanding of mt-genome structural diversity, complex patterns of RNA editing, and the origins of novel mt-genome elements. Here, we use an efficient long read (PacBio) iterative assembly pipeline to generate mt-genome assemblies for Leucaena trichandra (Leguminosae: Caesalpinioideae: mimosoid clade), providing the first assessment of non-papilionoid legume mt-genome content and structure to date. The efficiency of the assembly approach facilitated the exploration of alternative structures that are common place among plant mitochondrial genomes. A compact version (729 kbp) of the recovered assemblies was used to investigate sources of mt-genome size variation among legumes and mt-genome sequence similarity to the legume associated root holoparasite Lophophytum. The genome and an associated suite of transcriptome data from select species of Leucaena permitted an in-depth exploration of RNA editing in a diverse clade of closely related species that includes hybrid lineages. RNA editing in the allotetraploid, Leucaena leucocephala, is consistent with co-option of nearly equal maternal and paternal C-to-U edit components, generating novel combinations of RNA edited sites. A preliminary investigation of L. leucocephala C-to-U edit frequencies identified the potential for a hybrid to generate unique pools of alleles from parental variation through edit frequencies shared with one parental lineage, those intermediate between parents, and transgressive patterns.
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Affiliation(s)
- Lynsey Kovar
- Department of Biology, New Mexico State University
| | | | | | | | - Shannon Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, New York
| | - Richard Cronn
- Pacific Northwest Research Station, Corvallis, Oregon
| | | | - Colin E Hughes
- Department of Systematic & Evolutionary Botany, University of Zurich, Switzerland
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19
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Yigit E, Feehery GR, Langhorst BW, Stewart FJ, Dimalanta ET, Pradhan S, Slatko B, Gardner AF, McFarland J, Sumner C, Davis TB. A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation. ACTA ACUST UNITED AC 2016; 115:7.26.1-7.26.14. [PMID: 27366894 DOI: 10.1002/cpmb.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
"Microbiome" is used to describe the communities of microorganisms and their genes in a particular environment, including communities in association with a eukaryotic host or part of a host. One challenge in microbiome analysis concerns the presence of host DNA in samples. Removal of host DNA before sequencing results in greater sequence depth of the intended microbiome target population. This unit describes a novel method of microbial DNA enrichment in which methylated host DNA such as human genomic DNA is selectively bound and separated from microbial DNA before next-generation sequencing (NGS) library construction. This microbiome enrichment technique yields a higher fraction of microbial sequencing reads and improved read quality resulting in a reduced cost of downstream data generation and analysis. © 2016 by John Wiley & Sons, Inc.
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20
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Munafó DB, Langhorst BW, Chater CL, Sumner CJ, Rodríguez DN, Russello S, Gardner AF, Slatko BE, Stewart FJ, Sinicropi D, Morlan J, Qu K, Dimalanta ET, Davis TB. Selective Depletion of Abundant RNAs to Enable Transcriptome Analysis of Low-Input and Highly Degraded Human RNA. ACTA ACUST UNITED AC 2016; 113:7.22.1-7.22.9. [PMID: 31773915 DOI: 10.1002/0471142727.mb0722s113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ribosomal RNAs (rRNAs) are extremely abundant, often constituting 80% to 90% of total RNA. Since rRNA sequences are often not of interest in genomic RNA sequencing experiments, rRNAs can be removed from the sample before the library preparation step, in order to prevent the majority of the library and the majority of sequencing reads from being rRNA. Removal of rRNA can be especially challenging for low quality and formalin-fixed paraffin-embedded (FFPE) RNA samples due to the fragmented nature of these RNA molecules. The NEBNext rRNA Depletion Kit (Human/Mouse/Rat) depletes both cytoplasmic (5 S rRNA, 5.8 S rRNA, 18 S rRNA, and 28 S rRNA) and mitochondrial rRNA (12 S rRNA and 16 S rRNA) from total RNA preparations from human, mouse, and rat samples. Due to the high similarity among mammalian rRNA sequences, it is likely that rRNA depletion can also be achieved for other mammals but has not been empirically tested. This product is compatible with both intact and degraded RNA (e.g., FFPE RNA). The resulting rRNA-depleted RNA is suitable for RNA-seq, random-primed cDNA synthesis, or other downstream RNA analysis applications. Regardless of the quality or amount of input RNA, this method efficiently removes rRNA, while retaining non-coding and other non-poly(A) RNAs. The NEBNext rRNA Depletion Kit thus provides a more complete picture of the transcript repertoire than oligo d(T) poly(A) mRNA enrichment methods. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - John Morlan
- Genomic Health, Inc, Redwood City, California
| | - Kunbin Qu
- Genomic Health, Inc, Redwood City, California
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Feehery GR, Yigit E, Oyola SO, Langhorst BW, Schmidt VT, Stewart FJ, Dimalanta ET, Amaral-Zettler LA, Davis T, Quail MA, Pradhan S. A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PLoS One 2013; 8:e76096. [PMID: 24204593 PMCID: PMC3810253 DOI: 10.1371/journal.pone.0076096] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/20/2013] [Indexed: 12/05/2022] Open
Abstract
DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we used a methyl-CpG binding domain (MBD) to separate methylated host DNA from microbial DNA based on differences in CpG methylation density. MBD fused to the Fc region of a human antibody (MBD-Fc) binds strongly to protein A paramagnetic beads, forming an effective one-step enrichment complex that was used to remove human or fish host DNA from bacterial and protistan DNA for subsequent sequencing and analysis. We report enrichment of DNA samples from human saliva, human blood, a mock malaria-infected blood sample and a black molly fish. When reads were mapped to reference genomes, sequence reads aligning to host genomes decreased 50-fold, while bacterial and Plasmodium DNA sequences reads increased 8-11.5-fold. The Shannon-Wiener diversity index was calculated for 149 bacterial species in saliva before and after enrichment. Unenriched saliva had an index of 4.72, while the enriched sample had an index of 4.80. The similarity of these indices demonstrates that bacterial species diversity and relative phylotype abundance remain conserved in enriched samples. Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types.
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Affiliation(s)
- George R. Feehery
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Erbay Yigit
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | | | | | - Victor T. Schmidt
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Fiona J. Stewart
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | | | - Linda A. Amaral-Zettler
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Department of Geological Sciences, Brown University, Providence, Rhode Island, United States of America
| | - Theodore Davis
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | | | - Sriharsa Pradhan
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
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Liu P, Lohman GJS, Cantor E, Langhorst BW, Yigit E, Apone LM, Munafo DB, Sumner C, Stewart FJ, Evans TC, Nichols NM, Dimalanta ET, Davis TB. A fast solution to NGS library preparation with low nanogram DNA input. BMC Proc 2012. [PMCID: PMC3467472 DOI: 10.1186/1753-6561-6-s6-p26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Langhorst BW, Nichols NM. Database of DNA polymerases. Curr Protoc Mol Biol 2012; Chapter 3:Unit3.25. [PMID: 22870860 DOI: 10.1002/0471142727.mb0325s99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The DNA Polymerase Database (Polbase) is intended to compile the wealth of existing DNA polymerase information from public and private records into an open, searchable database.
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Langhorst BW, Jack WE, Reha-Krantz L, Nichols NM. Polbase: a repository of biochemical, genetic and structural information about DNA polymerases. Nucleic Acids Res 2012; 40:D381-7. [PMID: 21993301 PMCID: PMC3245023 DOI: 10.1093/nar/gkr847] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 09/19/2011] [Accepted: 09/21/2011] [Indexed: 11/18/2022] Open
Abstract
Polbase (http://polbase.neb.com) is a freely accessible database of DNA polymerases and related references. It has been developed in a collaborative model with experts whose contributions reflect their varied backgrounds in genetics, structural biology and biochemistry. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software. With the contributions of many polymerase investigators, Polbase has become a powerful research tool covering most important aspects of polymerases, from sequence and structure to biochemistry.
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Affiliation(s)
- Bradley W. Langhorst
- New England Biolabs, 240 County Road, Ipswich, MA, USA and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - William E. Jack
- New England Biolabs, 240 County Road, Ipswich, MA, USA and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Linda Reha-Krantz
- New England Biolabs, 240 County Road, Ipswich, MA, USA and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole M. Nichols
- New England Biolabs, 240 County Road, Ipswich, MA, USA and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Cölfen H, Laue TM, Wohlleben W, Schilling K, Karabudak E, Langhorst BW, Brookes E, Dubbs B, Zollars D, Rocco M, Demeler B. The Open AUC Project. Eur Biophys J 2009; 39:347-59. [PMID: 19296095 PMCID: PMC2812709 DOI: 10.1007/s00249-009-0438-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/24/2009] [Accepted: 02/28/2009] [Indexed: 01/16/2023]
Abstract
Progress in analytical ultracentrifugation (AUC) has been hindered by obstructions to hardware innovation and by software incompatibility. In this paper, we announce and outline the Open AUC Project. The goals of the Open AUC Project are to stimulate AUC innovation by improving instrumentation, detectors, acquisition and analysis software, and collaborative tools. These improvements are needed for the next generation of AUC-based research. The Open AUC Project combines on-going work from several different groups. A new base instrument is described, one that is designed from the ground up to be an analytical ultracentrifuge. This machine offers an open architecture, hardware standards, and application programming interfaces for detector developers. All software will use the GNU Public License to assure that intellectual property is available in open source format. The Open AUC strategy facilitates collaborations, encourages sharing, and eliminates the chronic impediments that have plagued AUC innovation for the last 20 years. This ultracentrifuge will be equipped with multiple and interchangeable optical tracks so that state-of-the-art electronics and improved detectors will be available for a variety of optical systems. The instrument will be complemented by a new rotor, enhanced data acquisition and analysis software, as well as collaboration software. Described here are the instrument, the modular software components, and a standardized database that will encourage and ease integration of data analysis and interpretation software.
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Affiliation(s)
- Helmut Cölfen
- Colloid Chemistry, Max-Planck-Institute of Colloids and Interfaces, Research Campus Golm, Am Mühlenberg, 14424 Potsdam, Germany
| | - Thomas M. Laue
- Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, NH 03824 USA
| | | | - Kristian Schilling
- Nanolytics, Gesellschaft für Kolloidanalytik mbH, Am Mühlenberg 11, 14476 Potsdam, Germany
| | - Engin Karabudak
- Colloid Chemistry, Max-Planck-Institute of Colloids and Interfaces, Research Campus Golm, Am Mühlenberg, 14424 Potsdam, Germany
| | - Bradley W. Langhorst
- Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, NH 03824 USA
| | - Emre Brookes
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Bruce Dubbs
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Dan Zollars
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Mattia Rocco
- Istituto Nazionale per la Ricerca sul Cancro (IST), 16132 Genova, Italy
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229 USA
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