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Larivière D, Wickham L, Keiler K, Nekrutenko A. Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses. BMC Microbiol 2021; 21:168. [PMID: 34090324 PMCID: PMC8178898 DOI: 10.1186/s12866-021-02184-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/08/2020] [Accepted: 04/08/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Significant progress has been made in advancing and standardizing tools for human genomic and biomedical research. Yet, the field of next-generation sequencing (NGS) analysis for microorganisms (including multiple pathogens) remains fragmented, lacks accessible and reusable tools, is hindered by local computational resource limitations, and does not offer widely accepted standards. One such "problem areas" is the analysis of Transposon Insertion Sequencing (TIS) data. TIS allows probing of almost the entire genome of a microorganism by introducing random insertions of transposon-derived constructs. The impact of the insertions on the survival and growth under specific conditions provides precise information about genes affecting specific phenotypic characteristics. A wide array of tools has been developed to analyze TIS data. Among the variety of options available, it is often difficult to identify which one can provide a reliable and reproducible analysis. RESULTS Here we sought to understand the challenges and propose reliable practices for the analysis of TIS experiments. Using data from two recent TIS studies, we have developed a series of workflows that include multiple tools for data de-multiplexing, promoter sequence identification, transposon flank alignment, and read count repartition across the genome. Particular attention was paid to quality control procedures, such as determining the optimal tool parameters for the analysis and removal of contamination. CONCLUSIONS Our work provides an assessment of the currently available tools for TIS data analysis. It offers ready to use workflows that can be invoked by anyone in the world using our public Galaxy platform ( https://usegalaxy.org ). To lower the entry barriers, we have also developed interactive tutorials explaining details of TIS data analysis procedures at https://bit.ly/gxy-tis .
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Affiliation(s)
- Delphine Larivière
- Biochemistry and Molecular Biology Department, Eberly College of Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- The Galaxy Project
| | - Laura Wickham
- Biochemistry and Molecular Biology Department, Eberly College of Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kenneth Keiler
- Biochemistry and Molecular Biology Department, Eberly College of Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Anton Nekrutenko
- Biochemistry and Molecular Biology Department, Eberly College of Science, The Pennsylvania State University, University Park, Pennsylvania, USA.
- The Galaxy Project, .
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Abstract
The NovaSeq 6000 is a sequencing platform from Illumina that enables the sequencing of short reads with an output up to 6 Tb. The NovaSeq 6000 uses the typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000. Several types of sequencing kits coupled with dual flow cell mode enable high scalability of sequencing outputs to match a wide range of applications from complete genome sequencing to metagenomics analysis. In this chapter, after explaining how to assemble a normalized pool of libraries for sequencing, we will describe the experimental steps required to run the pools on the NovaSeq 6000 platform.
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Affiliation(s)
- Alessandra Modi
- Department of Biology, University of Firenze, Firenze, Italy
| | - Stefania Vai
- Department of Biology, University of Firenze, Firenze, Italy
| | - David Caramelli
- Department of Biology, University of Firenze, Firenze, Italy
| | - Martina Lari
- Department of Biology, University of Firenze, Firenze, Italy.
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Abstract
Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.
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Affiliation(s)
- Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Colton J Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Herruzo JM, Gonzalez-Navarro S, Ibanez-Marin P, Vinals-Yufera V, Alastruey-Benede J, Plata O. Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:1093-1104. [PMID: 30530369 DOI: 10.1109/tcbb.2018.2884701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in a memory bound problem. This paper analyzes different FM-index versions presented in the literature, focusing on those computing aspects related to the data access. As a result of the analysis, we propose a new organization of FM-index that minimizes the demand for memory bandwidth, allowing a great improvement of performance on processors with high-bandwidth memory, such as the second-generation Intel Xeon Phi (Knights Landing, or KNL), integrating ultra high-bandwidth stacked memory technology. As the roofline model shows, our implementation reaches 95 percent of the peak random access bandwidth limit when executed on the KNL and almost all of the available bandwidth when executed on other Intel Xeon architectures with conventional DDR memory. In addition, the obtained throughput in KNL is much higher than the results reported for GPUs in the literature.
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Grogan KE, Perry GH. Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools. Evol Anthropol 2020; 29:143-158. [PMID: 32142200 PMCID: PMC10574139 DOI: 10.1002/evan.21825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.
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Affiliation(s)
- Kathleen E. Grogan
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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Graham G, Csicsery N, Stasiowski E, Thouvenin G, Mather WH, Ferry M, Cookson S, Hasty J. Genome-scale transcriptional dynamics and environmental biosensing. Proc Natl Acad Sci U S A 2020; 117:3301-3306. [PMID: 31974311 PMCID: PMC7022183 DOI: 10.1073/pnas.1913003117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome-scale technologies have enabled mapping of the complex molecular networks that govern cellular behavior. An emerging theme in the analyses of these networks is that cells use many layers of regulatory feedback to constantly assess and precisely react to their environment. The importance of complex feedback in controlling the real-time response to external stimuli has led to a need for the next generation of cell-based technologies that enable both the collection and analysis of high-throughput temporal data. Toward this end, we have developed a microfluidic platform capable of monitoring temporal gene expression from over 2,000 promoters. By coupling the "Dynomics" platform with deep neural network (DNN) and associated explainable artificial intelligence (XAI) algorithms, we show how machine learning can be harnessed to assess patterns in transcriptional data on a genome scale and identify which genes contribute to these patterns. Furthermore, we demonstrate the utility of the Dynomics platform as a field-deployable real-time biosensor through prediction of the presence of heavy metals in urban water and mine spill samples, based on the the dynamic transcription profiles of 1,807 unique Escherichia coli promoters.
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Affiliation(s)
- Garrett Graham
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Nicholas Csicsery
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth Stasiowski
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Gregoire Thouvenin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | | | | | | | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093;
- Quantitative BioSciences, Inc., San Diego, CA 92121
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- BioCircuits Institute, University of California San Diego, La Jolla, CA 92093
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Boykin LM, Sseruwagi P, Alicai T, Ateka E, Mohammed IU, Stanton JAL, Kayuki C, Mark D, Fute T, Erasto J, Bachwenkizi H, Muga B, Mumo N, Mwangi J, Abidrabo P, Okao-Okuja G, Omuut G, Akol J, Apio HB, Osingada F, Kehoe MA, Eccles D, Savill A, Lamb S, Kinene T, Rawle CB, Muralidhar A, Mayall K, Tairo F, Ndunguru J. Tree Lab: Portable genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa. Genes (Basel) 2019; 10:genes10090632. [PMID: 31438604 PMCID: PMC6769854 DOI: 10.3390/genes10090632] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 02/01/2023] Open
Abstract
In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell wall-degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This closed system delivers purified DNA with no cross-contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output into nucleotide base called data locally in real-time, removing the need for high-specification computers and large file transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and setup. To evaluate and validate capability of the system for unbiased pathogen identification by real-time sequencing in a farmer’s field setting, we analysed samples collected from cassava plants grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya). A range of viral pathogens, all with similar symptoms, greatly reduce yield or destroy cassava crops. Eight hundred (800) million people worldwide depend on cassava for food and yearly income, and viral diseases are a significant constraint to its production. Early pathogen detection at a molecular level has great potential to rescue crops within a single growing season by providing results that inform decisions on disease management, use of appropriate virus-resistant or replacement planting. This case study presented conditions of working in-field with limited or no access to mains power, laboratory infrastructure, Internet connectivity and highly variable ambient temperature. An additional challenge is that, generally, plant material contains inhibitors of downstream molecular processes making effective DNA purification critical. We successfully undertook real-time on-farm genome sequencing of samples collected from cassava plants on three farms, one in each country. Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis, including sample collection, processing and provisional sequencing results was complete in under 3 h. The need for accurate, rapid and on-site diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications that are relevant to human and animal health, environmental management and conservation.
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Affiliation(s)
- Laura M Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia.
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Titus Alicai
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Elijah Ateka
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
| | - Ibrahim Umar Mohammed
- Department of Crop Science, Faculty of Agriculture, Kebbi State University of Science and Technology, Aliero P.O. Box 1144, Nigeria
| | - Jo-Ann L Stanton
- Department of Anatomy, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Charles Kayuki
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Deogratius Mark
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Tarcisius Fute
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Joel Erasto
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Hilda Bachwenkizi
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Brenda Muga
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
| | - Naomi Mumo
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
| | - Jenniffer Mwangi
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
| | - Phillip Abidrabo
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Geoffrey Okao-Okuja
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Geresemu Omuut
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Jacinta Akol
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Hellen B Apio
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Francis Osingada
- National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
| | - Monica A Kehoe
- Department of Primary Industries and Regional Development Diagnostic Laboratory Services, Plant Pathology, South Perth, WA 6151, Australia
| | - David Eccles
- Malaghan Institute of Medical Research, P.O. Box 7060, Newtown, Wellington 6242, New Zealand
| | - Anders Savill
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Stephen Lamb
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Tonny Kinene
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Christopher B Rawle
- Department of Anatomy, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | | | - Kirsty Mayall
- MicroGEM Ltd., 9 Melody Ln, Ruakura, Hamilton 3216, New Zealand
| | - Fred Tairo
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
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Wang J, Liu Z, Bellen HJ, Yamamoto S. Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information. J Vis Exp 2019:10.3791/59542. [PMID: 31475990 PMCID: PMC7401700 DOI: 10.3791/59542] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Through whole-exome/genome sequencing, human geneticists identify rare variants that segregate with disease phenotypes. To assess if a specific variant is pathogenic, one must query many databases to determine whether the gene of interest is linked to a genetic disease, whether the specific variant has been reported before, and what functional data is available in model organism databases that may provide clues about the gene's function in human. MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) is a one-stop data collection tool for human genes and variants and their orthologous genes in seven model organisms including in mouse, rat, zebrafish, fruit fly, nematode worm, fission yeast, and budding yeast. In this Protocol, we provide an overview of what MARRVEL can be used for and discuss how different datasets can be used to assess whether a variant of unknown significance (VUS) in a known disease-causing gene or a variant in a gene of uncertain significance (GUS) may be pathogenic. This protocol will guide a user through searching multiple human databases simultaneously starting with a human gene with or without a variant of interest. We also discuss how to utilize data from OMIM, ExAC/gnomAD, ClinVar, Geno2MP, DGV and DECHIPHER. Moreover, we illustrate how to interpret a list of ortholog candidate genes, expression patterns, and GO terms in model organisms associated with each human gene. Furthermore, we discuss the value protein structural domain annotations provided and explain how to use the multiple species protein alignment feature to assess whether a variant of interest affects an evolutionarily conserved domain or amino acid. Finally, we will discuss three different use-cases of this website. MARRVEL is an easily accessible open access website designed for both clinical and basic researchers and serves as a starting point to design experiments for functional studies.
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Affiliation(s)
- Julia Wang
- Program in Developmental Biology, Baylor College of Medicine; Medical Scientist Training Program, Baylor College of Medicine
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Molecular and Human Genetics, Baylor College of Medicine; Department of Neuroscience, Baylor College of Medicine; Howard Hughes Medical Institute, Baylor College of Medicine
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital; Department of Molecular and Human Genetics, Baylor College of Medicine; Department of Neuroscience, Baylor College of Medicine;
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Fredrich B, Schmöhl M, Junge O, Gundlach S, Ellinghaus D, Pfeufer A, Bettecken T, Siddiqui R, Franke A, Wienker TF, Hoeppner MP, Krawczak M. VarWatch-A stand-alone software tool for variant matching. PLoS One 2019; 14:e0215618. [PMID: 31022234 PMCID: PMC6483337 DOI: 10.1371/journal.pone.0215618] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022] Open
Abstract
Massively parallel DNA sequencing of clinical samples holds great promise for the gene-based diagnosis of human inherited diseases because it allows rapid detection of putatively causative mutations at genome-wide level. Without additional evidence complementing their initial bioinformatics evaluation, however, the clinical relevance of such candidate genetic variants often remains unclear. In consequence, dedicated 'matching' services have been established in recent years that aim at the discovery of other, comparable case reports to facilitate individual diagnoses. However, legal concerns have been raised about the global sharing of genetic data, particularly in Europe where the recently enacted General Data Protection Regulation EU-2016/679 classifies genetic data as highly sensitive. Hence, unrestricted sharing of genetic data from clinical cases on platforms outside the national jurisdiction increasingly may be perceived as problematic. To allow collaborative data producers, particularly large consortia of diagnostic laboratories, to acknowledge these concerns while still practicing efficient case matching internally, novel tools are required. To this end, we developed VarWatch, an easy-to-deploy and highly scalable case matching software that provides users with comprehensive programmatic tools and a user-friendly interface to fulfil said purpose.
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Affiliation(s)
- Broder Fredrich
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marcus Schmöhl
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sven Gundlach
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Arne Pfeufer
- Humangenetische Praxis PD Dr. Pfeufer, München, Germany
- MVZ für Molekulardiagnostik GmbH, München, Germany
- Myriad GmbH, Martinsried, Germany
| | | | - Roman Siddiqui
- TMF – Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V., Berlin, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Marc P. Hoeppner
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
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10
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Bowden R, Davies RW, Heger A, Pagnamenta AT, de Cesare M, Oikkonen LE, Parkes D, Freeman C, Dhalla F, Patel SY, Popitsch N, Ip CLC, Roberts HE, Salatino S, Lockstone H, Lunter G, Taylor JC, Buck D, Simpson MA, Donnelly P. Sequencing of human genomes with nanopore technology. Nat Commun 2019; 10:1869. [PMID: 31015479 PMCID: PMC6478738 DOI: 10.1038/s41467-019-09637-5] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [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: 08/30/2018] [Accepted: 03/19/2019] [Indexed: 12/17/2022] Open
Abstract
Whole-genome sequencing (WGS) is becoming widely used in clinical medicine in diagnostic contexts and to inform treatment choice. Here we evaluate the potential of the Oxford Nanopore Technologies (ONT) MinION long-read sequencer for routine WGS by sequencing the reference sample NA12878 and the genome of an individual with ataxia-pancytopenia syndrome and severe immune dysregulation. We develop and apply a novel reference panel-free analytical method to infer and then exploit phase information which improves single-nucleotide variant (SNV) calling performance from otherwise modest levels. In the clinical sample, we identify and directly phase two non-synonymous de novo variants in SAMD9L, (OMIM #159550) inferring that they lie on the same paternal haplotype. Whilst consensus SNV-calling error rates from ONT data remain substantially higher than those from short-read methods, we demonstrate the substantial benefits of analytical innovation. Ongoing improvements to base-calling and SNV-calling methodology must continue for nanopore sequencing to establish itself as a primary method for clinical WGS.
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Affiliation(s)
- Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Robert W Davies
- Genomics plc, Oxford, OX1 1JD, UK
- Program in Genetics and Genomic Biology and The Centre for Applied Genomics, Hospital for Sick Children, Toronto, M5G 0A4, Canada
| | | | - Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | | | - Laura E Oikkonen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Duncan Parkes
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Colin Freeman
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Fatima Dhalla
- Department of Clinical Immunology, Oxford University Hospitals, Oxford, OX3 9DU, UK
- Developmental Immunology Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Smita Y Patel
- Department of Clinical Immunology, Oxford University Hospitals, Oxford, OX3 9DU, UK
- Clinical Immunology Group, National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - Niko Popitsch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Camilla L C Ip
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hannah E Roberts
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Silvia Salatino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Helen Lockstone
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Gerton Lunter
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Genomics plc, Oxford, OX1 1JD, UK
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - David Buck
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | | | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Genomics plc, Oxford, OX1 1JD, UK.
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK.
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11
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Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-based technology enables efficient and precise perturbations of target genomic sites. Combining the endonuclease Cas9 and a pooled guide RNA library allows for systematic screenings of genes associated with a growth disadvantage or lethal phenotype under various conditions in organisms and tissues. Here, we describe a complete protocol for scalable CRISPR/Cas9-based dropout screening for essential genes from focused genomic regions to whole genomes.
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Affiliation(s)
- Kai Wu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sami N Malek
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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12
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Abstract
Chromium 10× 3' V2 protocol is a 3' end counting single-cell mRNA sequencing protocol that allows to process and sequence RNA from thousands of cells in parallel. Chromium10× by 10× Genomics is an emulsion-based device that enables to compartmentalize single cells along with sets of uniquely barcoded primers and reverse transcription reagents into nanoscale droplets that are used as reaction chambers to generate barcoded full-length cDNA from single cells. After RT reaction single-stranded barcoded cDNAs are pooled together and processed to generate sequencing libraries compatible with the standard Illumina platforms. Here we show in detail the main steps of the protocol applied to the analysis of tumor-infiltrating T lymphocytes (TILs). The main steps are cell preparation, cDNA synthesis, library construction, and sequencing.This protocol refers specifically to the CG00052_SingleCell3_ReagentKitv2UserGuide_RevD downloadable from 10× Genomics website ( https://www.10xgenomics.com ) and does not substitute it. Always refer to this guide, paying attention to updates and revisions.
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Affiliation(s)
- Marco De Simone
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.
| | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.
- Department of Medical Biotechnology and Translational Medicine, Università Degli Studi di Milano, Milan, Italy.
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13
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Abstract
Dysregulation of miRNA-mRNA regulatory networks is very common phenomenon in any diseases including cancer. Altered expression of biomarkers leads to these gynecologic cancers. Therefore, understanding the underlying biological mechanisms may help in developing a robust diagnostic as well as a prognostic tool. It has been demonstrated in various studies that the pathways associated with gynecologic cancer have dysregulated miRNA as well as mRNA expression. Identification of miRNA-mRNA regulatory modules may help in understanding the mechanism of altered gynecologic cancer pathways. In this regard, an existing robust mutual information-based Maximum-Relevance Maximum-Significance algorithm has been used for identification of miRNA-mRNA regulatory modules in gynecologic cancer. A set of miRNA-mRNA modules are identified first than their association with gynecologic cancer are studied exhaustively. The effectiveness of the proposed approach is compared with the existing methods. The proposed approach is found to generate more robust integrated networks of miRNA-mRNA in gynecologic cancer.
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Affiliation(s)
- Sushmita Paul
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India.
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14
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Adolfi A, Lycett GJ. Opening the toolkit for genetic analysis and control of Anopheles mosquito vectors. Curr Opin Insect Sci 2018; 30:8-18. [PMID: 30553490 DOI: 10.1016/j.cois.2018.07.014] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/24/2018] [Indexed: 06/09/2023]
Abstract
Anopheles is the only genus of mosquitoes that transmit human malaria and consequently the focus of large scale genome and transcriptome-wide association studies. Genetic tools to define the function of the candidate genes arising from these analyses are vital. Moreover, genome editing offers the potential to modify Anopheles population structure at local and global scale to provide complementary tools towards the ultimate goal of malaria elimination. Major breakthroughs in Anopheles genetic analysis came with the development of germline transformation and RNA interference technology. Yet, the field has been revolutionised again by precise genome editing now possible through site-specific nucleases. Here we review the components of the current genetic toolkit available to study Anopheles, focusing particularly on how these technical advances are used to gain insight into malaria transmission and the design of genetic methods to control Anopheles vectors.
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Affiliation(s)
- Adriana Adolfi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4500, USA
| | - Gareth John Lycett
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
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15
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Abstract
The genomics community has frequently compared advances in sequencing to advances in microelectronics. Lately there have been many claims, including by the National Human Genome Research Institute (NHGRI), that genomics is outpacing developments in computing as measured by Moore's law - the notion that computers double in processing capability per dollar spent every 18-24 months. Celebrations of the "$1000 genome" and other speed-related sequencing milestones might be dismissed as a distraction from genomics' slowness in delivering clinical breakthroughs, but the fact that such celebrations have been persistently encouraged by the NHGRI reveals a great deal about the priorities and expectations of the American general public, the intended audience of the genomics-computing comparison. By delving into the history of speculative thinking about sequencing and computing, this article demonstrates just how much more receptive to high-risk/high-payoff ventures the NIH and the general public have become. The article also provides access to some of the roots and consequences of the association of "innovation talk" with genomics, and the means to look past that association to the less glamorous (but arguably much more important) contributions of the NHGRI to building the field of genomics.
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Affiliation(s)
- Joseph November
- Department of History, University of South Carolina, Columbia, SC, USA.
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16
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Dungey HS, Dash JP, Pont D, Clinton PW, Watt MS, Telfer EJ. Phenotyping Whole Forests Will Help to Track Genetic Performance. Trends Plant Sci 2018; 23:854-864. [PMID: 30217472 DOI: 10.1016/j.tplants.2018.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Phenotyping is the accurate and precise physical description of organisms. Accurate and quantitative phenotyping underpins the delivery of benefits from genetic improvement programs in agriculture. In forest trees, phenotyping at an equivalent precision has been impossible because trees and forests are large, long-lived, and highly variable. These facts have restricted the delivery of genetic gains in forestry compared to other agricultural sectors. We describe a landscape-scale phenotyping platform that integrates remote sensing, spatial information systems, and genomics to facilitate the delivery of greater gains enabling forestry to catch up with other sectors. Combining remote sensing at a range of spatial and temporal scales with genomics will ultimately impact on tree breeding globally.
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Affiliation(s)
- Heidi S Dungey
- Scion, 49 Sala Street, Rotorua, 3020, New Zealand; www.scionresearch.com/about-us/about-scion/our-people/people/forest-science/heidi-dungey.
| | | | - David Pont
- Scion, 49 Sala Street, Rotorua, 3020, New Zealand
| | - Peter W Clinton
- Scion, 10 Kyle Street, Riccarton, Christchurch 8011, New Zealand
| | - Michael S Watt
- Scion, 10 Kyle Street, Riccarton, Christchurch 8011, New Zealand
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17
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Christensen KD, Phillips KA, Green RC, Dukhovny D. Cost Analyses of Genomic Sequencing: Lessons Learned from the MedSeq Project. Value Health 2018; 21:1054-1061. [PMID: 30224109 PMCID: PMC6444358 DOI: 10.1016/j.jval.2018.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/11/2018] [Indexed: 05/17/2023]
Abstract
OBJECTIVE To summarize lessons learned while analyzing the costs of integrating whole genome sequencing into the care of cardiology and primary care patients in the MedSeq Project by conducting the first randomized controlled trial of whole genome sequencing in general and specialty medicine. METHODS Case study that describes key methodological and data challenges that were encountered or are likely to emerge in future work, describes the pros and cons of approaches considered by the study team, and summarizes the solutions that were implemented. RESULTS Major methodological challenges included defining whole genome sequencing, structuring an appropriate comparator, measuring downstream costs, and examining clinical outcomes. Discussions about solutions addressed conceptual and practical issues that arose because of definitions and analyses around the cost of genomic sequencing in trial-based studies. CONCLUSIONS The MedSeq Project provides an instructive example of how to conduct a cost analysis of whole genome sequencing that feasibly incorporates best practices while being sensitive to the varied applications and diversity of results it may produce. Findings provide guidance for researchers to consider when conducting or analyzing economic analyses of whole genome sequencing and other next-generation sequencing tests, particularly regarding costs.
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Affiliation(s)
- Kurt D Christensen
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Kathryn A Phillips
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, CA, USA; Philip R. Lee Institute for Health Policy and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Partners HealthCare Personalized Medicine, Boston, MA, USA
| | - Dmitry Dukhovny
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
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18
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Michael TP, Jupe F, Bemm F, Motley ST, Sandoval JP, Lanz C, Loudet O, Weigel D, Ecker JR. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat Commun 2018; 9:541. [PMID: 29416032 PMCID: PMC5803254 DOI: 10.1038/s41467-018-03016-2] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [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: 06/23/2017] [Accepted: 01/11/2018] [Indexed: 12/17/2022] Open
Abstract
The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal.
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Affiliation(s)
| | - Florian Jupe
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Monsanto Company, Creve Coeur, MO, 63141, USA
| | - Felix Bemm
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | | | - Justin P Sandoval
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Christa Lanz
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
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19
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Abstract
Functional genomics is the study of the function of genes on a genome-wide level. Reporter gene assays can be utilized in this context to dissect signaling cascades, find new drug targets, or decipher the function of gene expression. The genome-wide scale of these experiments necessitates a different approach toward science than traditional single hypothesis driven research. High-throughput experimentation requires large project teams, automation, and discrete validation of each step in the automation and assay process. The purpose of this chapter is to provide a general outline of a standard functional genomics project with a reporter gene assay as readout, give an overview of the methodologies employed and familiarize the reader with the subsequent data analysis. The advantages of such high throughput experimentation are speed, quantitative results, and insights into biology on a genome-wide scale all of which enable a more rapid progress of science.
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Affiliation(s)
- Genevieve Welch
- Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
- Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Loren Miraglia
- Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
- Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
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20
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Cohen H, Szymanski J, Aharoni A, Dominguez E. Assimilation of 'omics' strategies to study the cuticle layer and suberin lamellae in plants. J Exp Bot 2017; 68:5389-5400. [PMID: 29040673 DOI: 10.1093/jxb/erx348] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The assembly of the lipophilic cuticle layer and suberin lamellae, approximately 450 million years ago, was a major evolutionary development that enabled plants to colonize terrestrial habitats. The cuticle layer is composed of cutin polyester and embedded cuticular waxes, whereas the suberin lamellae consist of very long chain fatty acid derivatives, glycerol, and phenolics cross-linked with alkyl ferulate-embedded waxes. Due to their substantial biological roles in plant life, the mechanisms underlying the assembly of these structures have been extensively investigated. In the last decade, the introduction of 'omics' approaches, including genomics, transcriptomics, proteomics, and metabolomics, have been key in the identification of novel genetic and chemical elements involved in the formation and function of the cuticle layer and suberin lamellae. This review summarizes contemporary studies that utilized various large-scale, 'omics' strategies in combination with novel technologies to unravel how building blocks and polymers of these lipophilic barriers are made, and moreover linking structure to function along developmental programs and stress responses. We anticipate that the studies discussed here will inspire scientists studying lipophilic barriers to integrate complementary 'omics' approaches in their efforts to tackle as yet unresolved questions and engage the main challenges of the field to date.
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Affiliation(s)
- Hagai Cohen
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jedrzej Szymanski
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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21
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Picollet-D'hahan N, Dolega ME, Freida D, Martin DK, Gidrol X. Deciphering Cell Intrinsic Properties: A Key Issue for Robust Organoid Production. Trends Biotechnol 2017; 35:1035-1048. [PMID: 28927991 DOI: 10.1016/j.tibtech.2017.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 07/18/2017] [Accepted: 08/08/2017] [Indexed: 02/07/2023]
Abstract
We highlight the disposition of various cell types to self-organize into complex organ-like structures without necessarily the support of any stromal cells, provided they are placed into permissive 3D culture conditions. The goal of generating organoids reproducibly and efficiently has been hampered by poor understanding of the exact nature of the intrinsic cell properties at the origin of organoid generation, and of the signaling pathways governing their differentiation. Using microtechnologies like microfluidics to engineer organoids would create opportunities for single-cell genomics and high-throughput functional genomics to exhaustively characterize cell intrinsic properties. A more complete understanding of the development of organoids would enhance their relevance as models to study organ morphology, function, and disease and would open new avenues in drug development and regenerative medicine.
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Affiliation(s)
| | - Monika E Dolega
- Université Grenoble Alpes, INSERM, CEA, BIG, F-38000 Grenoble, France
| | - Delphine Freida
- Université Grenoble Alpes, INSERM, CEA, BIG, F-38000 Grenoble, France
| | - Donald K Martin
- Université Grenoble Alpes, F-38000 Grenoble, France; TIMC-IMAG/CNRS UMR 5525, F-38041 Grenoble, France
| | - Xavier Gidrol
- Université Grenoble Alpes, INSERM, CEA, BIG, F-38000 Grenoble, France.
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22
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Berry MD, White RS. Pharmaceuticals and Medical Devices: FDA Oversight. Issue Brief Health Policy Track Serv 2016; 2016:1-59. [PMID: 28252888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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23
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Abstract
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
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Affiliation(s)
- Miten Jain
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Hugh E Olsen
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.
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24
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Chen Z, Fu Y, Zhang F, Liu L, Zhang N, Zhou D, Yang J, Pang Y, Huang Y. Spinning micropipette liquid emulsion generator for single cell whole genome amplification. Lab Chip 2016; 16:4512-4516. [PMID: 27775138 DOI: 10.1039/c6lc01084a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Many on-chip approaches that use flow-focusing to pinch the continuous aqueous phase into droplets have become the most popular methods that provide monodisperse emulsion droplets. However, not every lab can easily adapt a microfluidic workflow into their familiar protocols. We develop an off-chip approach, spinning micro-pipette liquid emulsion (SiMPLE) generator, to produce highly stable monodisperse water-in-oil emulsions using a moving micropipette to disperse the aqueous phase in an oil-filled microcentrifuge tube. This method provides a simple way to produce picoliter-size droplets in situ with no dead volume during emulsification. With SiMPLE, single-cell emulsion whole genome amplification was performed to demonstrate that this novel method can seamlessly be integrated with experimental operations and supplies that most researchers are familiar with. The SiMPLE generator has effectively lowered the technical difficulties in applications relying on emulsion droplets.
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Affiliation(s)
- Zitian Chen
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and College of Engineering, Peking University, Beijing, China. and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Yusi Fu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and College of Engineering, Peking University, Beijing, China. and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Fangli Zhang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and College of Engineering, Peking University, Beijing, China. and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Lu Liu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and College of Engineering, Peking University, Beijing, China. and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Naiqing Zhang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and College of Engineering, Peking University, Beijing, China.
| | - Dong Zhou
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and College of Engineering, Peking University, Beijing, China.
| | - Junrui Yang
- School of Electronics Engineering and Computer Science, Peking University, Beijing, China
| | - Yuhong Pang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and College of Engineering, Peking University, Beijing, China. and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Yanyi Huang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and College of Engineering, Peking University, Beijing, China. and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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25
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Louro B, Marques JP, Power DM, Canário AVM. Having a BLAST: Searchable transcriptome resources for the gilthead sea bream and the European sea bass. Mar Genomics 2016; 30:67-71. [PMID: 27742405 DOI: 10.1016/j.margen.2016.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 09/09/2016] [Accepted: 10/06/2016] [Indexed: 11/16/2022]
Abstract
The gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax) are the most important aquaculture species in the Mediterranean Sea and since the last decade it has been seen an exponential increase in their available molecular resources. In order to improve accessibility to transcriptome resources, Expressed Sequence Tags (ESTs), mRNA sequences and raw read sequences were assembled and deposited in BLAST queryable databases. The publicly available sea bream and sea bass sequences (6.4 and 247.5 million) generated 45,094 and 68,117 assembled sequences, with, respectively, arithmetic mean size of 998 and 2125bp and N50 of 1302 and 2966bp. The assemblies will be regularly updated and new analytical tools added to the web server at http://sea.ccmar.ualg.pt.
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Affiliation(s)
- Bruno Louro
- Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - João Pedro Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto. Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Deborah M Power
- Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Adelino V M Canário
- Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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26
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Zahid OK, Zhao BS, He C, Hall AR. Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores. Sci Rep 2016; 6:29565. [PMID: 27383905 PMCID: PMC4935868 DOI: 10.1038/srep29565] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 04/05/2016] [Accepted: 06/17/2016] [Indexed: 12/12/2022] Open
Abstract
5-hydroxymethylcytosine (5 hmC), the oxidized form of 5-methylcytosine (5 mC), is a base modification with emerging importance in biology and disease. However, like most epigenetic elements, it is transparent to many conventional genetic techniques and is thus challenging to probe. Here, we report a rapid solid-state nanopore assay that is capable of resolving 5 hmC with high specificity and sensitivity and demonstrate its utility in assessing global modification abundance in genomic DNA.
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Affiliation(s)
- Osama K. Zahid
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
| | - Boxuan Simen Zhao
- Department of Chemistry, Department of Biochemistry and Molecule Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecule Biology, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Adam R. Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
- Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
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27
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Wen N, Zhao Z, Fan B, Chen D, Men D, Wang J, Chen J. Development of Droplet Microfluidics Enabling High-Throughput Single-Cell Analysis. Molecules 2016; 21:E881. [PMID: 27399651 PMCID: PMC6272933 DOI: 10.3390/molecules21070881] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
This article reviews recent developments in droplet microfluidics enabling high-throughput single-cell analysis. Five key aspects in this field are included in this review: (1) prototype demonstration of single-cell encapsulation in microfluidic droplets; (2) technical improvements of single-cell encapsulation in microfluidic droplets; (3) microfluidic droplets enabling single-cell proteomic analysis; (4) microfluidic droplets enabling single-cell genomic analysis; and (5) integrated microfluidic droplet systems enabling single-cell screening. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on key performances of throughput, multifunctionality, and absolute quantification.
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Affiliation(s)
- Na Wen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zhan Zhao
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Beiyuan Fan
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Deyong Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Dong Men
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Junbo Wang
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jian Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing 100190, China.
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28
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Koshiba S. [Jananese Multi Omics Reference Panel]. Seikagaku 2016; 88:25-30. [PMID: 27025004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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29
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Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS Nano 2016; 10:6-37. [PMID: 26695070 DOI: 10.1021/acsnano.5b07826] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
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Affiliation(s)
- Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States
| | - Miyoung Chun
- The Kavli Foundation , Oxnard, California 93030, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | | | - Scott E Fraser
- Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States
| | - Jack A Gilbert
- Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States
- Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States
| | - Janet K Jansson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | - Sharif Taha
- The Kavli Foundation , Oxnard, California 93030, United States
| | - Ger van den Engh
- Center for Marine Cytometry , Concrete, Washington 98237, United States
- Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile
| | | | | | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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Chaitanya L, Ralf A, van Oven M, Kupiec T, Chang J, Lagacé R, Kayser M. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine. Hum Mutat 2015; 36:1236-47. [PMID: 26387877 PMCID: PMC5057296 DOI: 10.1002/humu.22905] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/01/2015] [Indexed: 11/13/2022]
Abstract
Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.
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Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Arwin Ralf
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Mannis van Oven
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Tomasz Kupiec
- Institute of Forensic ResearchSection of Forensic GeneticsKrakówPoland
| | - Joseph Chang
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Robert Lagacé
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
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Gomez-Pulido JA, Schmidt B, Feng WC. Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems. IEEE/ACM Trans Comput Biol Bioinform 2015; 12:971-972. [PMID: 26734702 DOI: 10.1109/tcbb.2015.2457736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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32
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You Q, Zhang L, Yi X, Zhang Z, Xu W, Su Z. SIFGD: Setaria italica Functional Genomics Database. Mol Plant 2015; 8:967-70. [PMID: 25676456 DOI: 10.1016/j.molp.2015.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/26/2014] [Accepted: 02/01/2015] [Indexed: 05/12/2023]
Affiliation(s)
- Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Liwei Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhenghai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wengying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Colmsee C, Beier S, Himmelbach A, Schmutzer T, Stein N, Scholz U, Mascher M. BARLEX - the Barley Draft Genome Explorer. Mol Plant 2015; 8:964-6. [PMID: 25804976 DOI: 10.1016/j.molp.2015.03.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/11/2015] [Accepted: 03/18/2015] [Indexed: 05/03/2023]
Affiliation(s)
- Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany.
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Krouk G, Carré C, Fizames C, Gojon A, Ruffel S, Lacombe B. GeneCloud Reveals Semantic Enrichment in Lists of Gene Descriptions. Mol Plant 2015; 8:971-973. [PMID: 25707756 DOI: 10.1016/j.molp.2015.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France.
| | - Clément Carré
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France; Institut de Modélisation Mathématique de Montpellier, CNRS UMR 5149, Université de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Cecile Fizames
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France
| | - Alain Gojon
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France
| | - Sandrine Ruffel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France
| | - Benoit Lacombe
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France.
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Fernandez-Pozo N, Rosli HG, Martin GB, Mueller LA. The SGN VIGS tool: user-friendly software to design virus-induced gene silencing (VIGS) constructs for functional genomics. Mol Plant 2015; 8:486-8. [PMID: 25667001 DOI: 10.1016/j.molp.2014.11.024] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/21/2014] [Accepted: 11/30/2014] [Indexed: 05/13/2023]
Affiliation(s)
| | - Hernan G Rosli
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús (IIB-INTECH), UNSAM-CONICET, Chascomús, B7130IWA Buenos Aires, Argentina
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
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Chen P, Wang C, Li X, Zhou X. Accelerating the Next Generation Long Read Mapping with the FPGA-Based System. IEEE/ACM Trans Comput Biol Bioinform 2014; 11:840-852. [PMID: 26356857 DOI: 10.1109/tcbb.2014.2326876] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To compare the newly determined sequences against the subject sequences stored in the databases is a critical job in the bioinformatics. Fortunately, recent survey reports that the state-of-the-art aligners are already fast enough to handle the ultra amount of short sequence reads in the reasonable time. However, for aligning the long sequence reads (>400 bp) generated by the next generation sequencing (NGS) technology, it is still quite inefficient with present aligners. Furthermore, the challenge becomes more and more serious as the lengths and the amounts of the sequence reads are both keeping increasing with the improvement of the sequencing technology. Thus, it is extremely urgent for the researchers to enhance the performance of the long read alignment. In this paper, we propose a novel FPGA-based system to improve the efficiency of the long read mapping. Compared to the state-of-the-art long read aligner BWA-SW, our accelerating platform could achieve a high performance with almost the same sensitivity. Experiments demonstrate that, for reads with lengths ranging from 512 up to 4,096 base pairs, the described system obtains a 10x -48x speedup for the bottleneck of the software. As to the whole mapping procedure, the FPGA-based platform could achieve a 1.8x -3:3x speedup versus the BWA-SW aligner, reducing the alignment cycles from weeks to days.
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Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, Kojima K, Nariai N, Sato Y, Yamaguchi-Kabata Y, Ito S, Kudo H, Nishijima I, Nishikawa S, Pan X, Saito R, Saito S, Saito T, Shirota M, Tsuda K, Yokozawa J, Igarashi K, Minegishi N, Tanabe O, Fuse N, Nagasaki M, Kinoshita K, Yasuda J, Yamamoto M. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population. BMC Genomics 2014; 15:673. [PMID: 25109789 PMCID: PMC4138778 DOI: 10.1186/1471-2164-15-673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 08/01/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. RESULTS Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. CONCLUSIONS Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.
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Affiliation(s)
- Ikuko N Motoike
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Mitsuyo Matsumoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Fumiki Katsuoka
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaname Kojima
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Naoki Nariai
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yukuto Sato
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yumi Yamaguchi-Kabata
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Shin Ito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hisaaki Kudo
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Ichiko Nishijima
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Satoshi Nishikawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Xiaoqing Pan
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Rumiko Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sakae Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Tomo Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Matsuyuki Shirota
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaoru Tsuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junji Yokozawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kazuhiko Igarashi
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Osamu Tanabe
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Nobuo Fuse
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masao Nagasaki
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kengo Kinoshita
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, Sendai, 980-8575 Japan
| | - Jun Yasuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masayuki Yamamoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
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Abstract
Genome-wide association studies (GWAS) revealed genomic risk loci that potentially have an impact on disease and phenotypic traits. This extensive resource holds great promise in providing novel directions for personalized medicine, including disease risk prediction, prevention and targeted medication. One of the major challenges that researchers face on the path between the initial identification of an association and precision treatment of patients is the comprehension of the biological mechanisms that underlie these associations. Currently, the focus to solve these questions lies on the integrative analysis of system-wide data on global genome variation, gene expression, transcription factor binding, epigenetic profiles and chromatin conformation. The generation of this data mainly relies on next-generation sequencing. However, due to multiple recent developments, mass spectrometry-based proteomics now offers additional, by the GWAS field so far hardly recognized possibilities for the identification of functional genome variants and, in particular, for the identification and characterization of (differentially) bound protein complexes as well as physiological target genes. In this review, we introduce these proteomics advances and suggest how they might be integrated in post-GWAS workflows. We argue that the combination of highly complementary techniques is powerful and can provide an unbiased, detailed picture of GWAS loci and their mechanistic involvement in disease.
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Affiliation(s)
- Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Nina C. Hubner
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
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McBride D. Smartphone gamers decode six months of cancer DNA data in one month. ONS Connect 2014; 29:40. [PMID: 24961043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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Abstract
The recent revolution of genomics techniques has allowed the detection of various sequence features and biological variations on whole-genome scale. However, these high-resolution data present significant challenges for experimental biologists to understand and analyze. The conventional way is to use genome browsers to locate and visualize regions of interest. But it lacks user-friendly data mining functionality. Here we present a protocol that allows rapid annotation of genomic coordinate data by using TileMapper. Interesting biological annotations from large-scale genomic data, such as transcriptome analysis, chromatin immunoprecipitation on chip, or methyl-DNA immunoprecipitation (MeDIP) studies generated from the tiling microarrays and other platforms, could be analyzed without requiring computational skills. The outputs are saved in tabulated format, which permit flexible and simple processing in spreadsheet software, or to be exported to other pipelines for subsequent analysis.
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Affiliation(s)
- Hoi-Hung Cheung
- Laboratory of Clinical and Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Glorikian H. Genomics: gearing up for the laboratory of the future. MLO Med Lab Obs 2014; 46:8-11. [PMID: 24672844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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Abstract
PINK1/PARK6 and Parkin/PARK2 are amongst the most commonly mutated genes associated with recessive forms of familial Parkinson's disease. Recent evidence indicates that the proteins they encode, PINK1 and Parkin, function in the same pathway to mediate the selective autophagic clearance of dysfunctional mitochondria. Upon mitochondrial damage, PINK1 is stabilized on the outer mitochondrial membrane where it phosphorylates ubiquitin, generating a signal for the recruitment and activation of Parkin. However, key mechanistic questions still exist regarding Parkin recruitment, including whether or not other factors are required for the PINK1 and Parkin pathway. We describe a method below using high-throughput RNA interference technology to interrogate the genome for novel components of the PINK1 and Parkin pathway.
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Affiliation(s)
- Andy Cheuk-Him Ng
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Stephen D Baird
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Robert A Screaton
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada.
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De Coninck A, Fostier J, Maenhout S, De Baets B. A high performance computing approach for genomic prediction. Commun Agric Appl Biol Sci 2014; 79:115-119. [PMID: 25864324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Kim HS, Sung JS, Yang SJ, Kwon NJ, Jin L, Kim ST, Park KH, Shin SW, Kim HK, Kang JH, Kim JO, Park JY, Choi JE, Yoon H, Park CK, Yang KS, Seo JS, Kim YH. Predictive efficacy of low burden EGFR mutation detected by next-generation sequencing on response to EGFR tyrosine kinase inhibitors in non-small-cell lung carcinoma. PLoS One 2013; 8:e81975. [PMID: 24376508 PMCID: PMC3869671 DOI: 10.1371/journal.pone.0081975] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/18/2013] [Indexed: 11/21/2022] Open
Abstract
Direct sequencing remains the most widely used method for the detection of epidermal growth factor receptor (EGFR) mutations in lung cancer; however, its relatively low sensitivity limits its clinical use. The objective of this study was to investigate the sensitivity of detecting an epidermal growth factor receptor (EGFR) mutation from peptide nucleic acid-locked nucleic acid polymerase chain reaction (PNA-LNA PCR) clamp and Ion Torrent Personal Genome Machine (PGM) techniques compared to that by direct sequencing. Furthermore, the predictive efficacy of EGFR mutations detected by PNA-LNA PCR clamp was evaluated. EGFR mutational status was assessed by direct sequencing, PNA-LNA PCR clamp, and Ion Torrent PGM in 57 patients with non-small cell lung cancer (NSCLC). We evaluated the predictive efficacy of PNA-LNA PCR clamp on the EGFR-TKI treatment in 36 patients with advanced NSCLC retrospectively. Compared to direct sequencing (16/57, 28.1%), PNA-LNA PCR clamp (27/57, 47.4%) and Ion Torrent PGM (26/57, 45.6%) detected more EGFR mutations. EGFR mutant patients had significantly longer progressive free survival (14.31 vs. 21.61 months, P = 0.003) than that of EGFR wild patients when tested with PNA-LNA PCR clamp. However, no difference in response rate to EGFR TKIs (75.0% vs. 82.4%, P = 0.195) or overall survival (34.39 vs. 44.10 months, P = 0.422) was observed between the EGFR mutations by direct sequencing or PNA-LNA PCR clamp. Our results demonstrate firstly that patients with EGFR mutations were detected more frequently by PNA-LNA PCR clamp and Ion Torrent PGM than those by direct sequencing. EGFR mutations detected by PNA-LNA PCR clamp may be as a predicative factor for EGFR TKI response in patients with NSCLC.
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Affiliation(s)
- Hye Sook Kim
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Jae Sook Sung
- Cancer Research Institute, Korea University, Seoul, Korea
| | | | | | - LiHua Jin
- Cancer Research Institute, Korea University, Seoul, Korea
| | - Seung Tae Kim
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Kyong Hwa Park
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Sang Won Shin
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Han Kyeom Kim
- Department of Pathology, College of Medicine, Korea University, Seoul, Korea
| | - Jin-Hyoung Kang
- Division of Medical Oncology, Seoul Saint Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Jeong-Oh Kim
- Laboratory of Medical Oncology, Research Institutes of Medical Science, The Catholic University of Korea, Korea
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Korea
| | - Jin Eun Choi
- Department of Biochemistry, School of Medicine, Kyungpook National University, Daegu, Korea
| | - HyoungKyu Yoon
- Division of Pulmonology, Department of Internal Medicine, Saint Mary's Hospital, College of Medicine, The Catholic University of Korea, Korea
| | - Chan Kwon Park
- Division of Pulmonology, Department of Internal Medicine, Saint Mary's Hospital, College of Medicine, The Catholic University of Korea, Korea
| | | | - Jeong-Sun Seo
- Macroge Inc., Seoul, Korea
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
- Department of Biochemistry, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- * E-mail: (YHK); (J. Seo)
| | - Yeul Hong Kim
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
- Cancer Research Institute, Korea University, Seoul, Korea
- * E-mail: (YHK); (J. Seo)
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Esfandyarpour R, Esfandyarpour H, Harris JS, Davis RW. Simulation and fabrication of a new novel 3D injectable biosensor for high throughput genomics and proteomics in a lab-on-a-chip device. Nanotechnology 2013; 24:465301. [PMID: 24149048 PMCID: PMC3878440 DOI: 10.1088/0957-4484/24/46/465301] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Biosensors are used for the detection of biochemical molecules such as proteins and nucleic acids. Traditional techniques, such as enzyme-linked immuno-sorbent assay (ELISA), are sensitive but require several hours to yield a result and usually require the attachment of a fluorophore molecule to the target molecule. Micromachined biosensors that employ electrical detection are now being developed. Here we describe one such device, which is ultrasensitive, real-time, label free and localized. It is called the nanoneedle biosensor and shows promise to overcome some of the current limitations of biosensors. The key element of this device is a 10 nm wide annular gap at the end of the needle, which is the sensitive part of the sensor. The total diameter of the sensor is about 100 nm. Any change in the population of molecules in this gap results in a change of impedance across the gap. Single molecule detection should be possible because the sensory part of the sensor is in the range of bio-molecules of interest. To increase throughput we can flow the solution containing the target molecules over an array of such structures, each with its own integrated read-out circuitry to allow 'real-time' detection (i.e. several minutes) of label free molecules without sacrificing sensitivity. To fabricate the arrays we used electron beam lithography together with associated pattern transfer techniques. Preliminary measurements on individual needle structures in water are consistent with the design. Since the proposed sensor has a rigid nano-structure, this technology, once fully developed, could ultimately be used to directly monitor protein quantities within a single living cell, an application that would have significant utility for drug screening and studying various intracellular signaling pathways.
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Affiliation(s)
- Rahim Esfandyarpour
- Center for Integrated Systems, Department of Electrical Engineering, Stanford University, USA. Stanford Genome Technology Center, 855 California Avenue, Palo Alto, CA 94304, USA
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Abstract
The rapid detection and identification of infectious disease pathogens is a critical need for healthcare in both developed and developing countries. As we gain more insight into the genomic basis of pathogen infectivity and drug resistance, point-of-care nucleic acid testing will likely become an important tool for global health. In this paper, we present an inexpensive, handheld, battery-powered instrument designed to enable pathogen genotyping in the developing world. Our Microfluidic Biomolecular Amplification Reader (µBAR) represents the convergence of molecular biology, microfluidics, optics, and electronics technology. The µBAR is capable of carrying out isothermal nucleic acid amplification assays with real-time fluorescence readout at a fraction of the cost of conventional benchtop thermocyclers. Additionally, the µBAR features cell phone data connectivity and GPS sample geotagging which can enable epidemiological surveying and remote healthcare delivery. The µBAR controls assay temperature through an integrated resistive heater and monitors real-time fluorescence signals from 60 individual reaction chambers using LEDs and phototransistors. Assays are carried out on PDMS disposable microfluidic cartridges which require no external power for sample loading. We characterize the fluorescence detection limits, heater uniformity, and battery life of the instrument. As a proof-of-principle, we demonstrate the detection of the HIV-1 integrase gene with the µBAR using the Loop-Mediated Isothermal Amplification (LAMP) assay. Although we focus on the detection of purified DNA here, LAMP has previously been demonstrated with a range of clinical samples, and our eventual goal is to develop a microfluidic device which includes on-chip sample preparation from raw samples. The µBAR is based entirely around open source hardware and software, and in the accompanying online supplement we present a full set of schematics, bill of materials, PCB layouts, CAD drawings, and source code for the µBAR instrument with the goal of spurring further innovation toward low-cost genetic diagnostics.
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Affiliation(s)
- Frank B. Myers
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Berkeley Sensor and Actuator Center, University of California, Berkeley, California, United States of America
| | - Richard H. Henrikson
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Berkeley Sensor and Actuator Center, University of California, Berkeley, California, United States of America
| | - Jennifer Bone
- Department of Physics, University of California, Berkeley, California, United States of America
| | - Luke P. Lee
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Berkeley Sensor and Actuator Center, University of California, Berkeley, California, United States of America
- * E-mail:
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Bootman JL. The convergence of new technology with the delivery of health care services. Am J Pharm Educ 2013; 77:1. [PMID: 23460753 PMCID: PMC3578322 DOI: 10.5688/ajpe7711] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 12/09/2012] [Indexed: 05/16/2023]
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Abstract
Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.
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Affiliation(s)
- Elaine R Mardis
- The Genome Institute at Washington University School of Medicine, St. Louis, Missouri 63108, USA.
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