Dr. Craig Venter
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
A Clone-Array Pooled Shotgun Strategy for Sequencing Large Genomes
Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Perspective A Clone-Array Pooled Shotgun Strategy for Sequencing Large Genomes Wei-Wen Cai,1,2 Rui Chen,1,2 Richard A. Gibbs,1,2,5 and Allan Bradley1,3,4 1Department of Molecular and Human Genetics, 2Human Genome Sequencing Center, and 3Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA A simplified strategy for sequencing large genomes is proposed. Clone-Array Pooled Shotgun Sequencing (CAPSS) is based on pooling rows and columns of arrayed genomic clones,for shotgun library construction. Random sequences are accumulated,and the data are processed by sequential comparison of rows and columns to assemble the sequence of clones at points of intersection. Compared with either a clone-by-clone approach or whole-genome shotgun sequencing,CAPSS requires relatively few library constructions and only minimal computational power for a complete genome assembly. The strategy is suitable for sequencing large genomes for which there are no sequence-ready maps,but for which relatively high resolution STS maps and highly redundant BAC libraries are available. It is immediately applicable to the sequencing of mouse,rat,zebrafish, and other important genomes,and can be managed in a cooperative fashion to take advantage of a distributed international DNA sequencing capacity. Advances in DNA sequencing technology in recent years have Drosophila genome, and the computational requirements to greatly increased the throughput and reduced the cost of ge- perform the necessary pairwise comparisons increase approxi- nome sequencing. Sequencing of a complex genome the size mately as a square of the size of the genome (see Appendix). -
Probabilities and Statistics in Shotgun Sequencing Shotgun Sequencing
Probabilities and Statistics in Shotgun Sequencing Shotgun Sequencing. Before any analysis of a DNA sequence can take place it is first necessary to determine the actual sequence itself, at least as accurately as is reasonably possible. Unfortunately, technical considerations make it impossible to sequence very long pieces of DNA all at once. Current sequencing technologies allow accurate reading of no more than 500 to 800bp of contiguous DNA sequence. This means that the sequence of an entire genome must be assembled from collections of comparatively short subsequences. This process is called DNA sequence “assembly ”. One approach of sequence assembly is to produce the sequence of a DNA segment (called as a “contig”, or perhaps a genome) from a large number of randomly chosen sequence reads (many overlapping small pieces, each on the order of 500-800 bases). One difficulty of this process is that the locations of the fragments within the genome and with respect to each other are not generally known. However, if enough fragments are sequenced so that there will be many overlaps between them, the fragments can be matched up and assembled. This method is called “ shotgun sequencing .” Shotgun sequencing approaches, including the whole-genome shotgun approach, are currently a central part of all genome-sequencing efforts. These methods require a high level of automation in sample preparation and analysis and are heavily reliant on the power of modern computers. There is an interplay between substrates to be sequenced (genomes and their representation in clone libraries), the analytical tools for generating a DNA sequence, the sequencing strategies, and the computational methods. -
Metagenomics Analysis of Microbiota by Next Generation Shotgun Sequencing
THE SWISS DNA COMPANY Application Note · Next Generation Sequencing Metagenomics Analysis of Microbiota by Next Generation Shotgun Sequencing Understand the genetic potential of your community samples Provides you with hypothesis-free taxonomic analysis Introduction Microbiome studies are often based on as the dependency on a single gene to microbiome analysis overcoming said the sequencing of specific marker genes analyze a whole community, the intro- limitations. Whole genomic DNA of as for instance the prokaryotic 16S rRNA duction of PCR bias and the restriction a sample is isolated, fragmented and gene. Such amplicon-based approaches to describe only the taxonomic compo- finally sequenced. This allows a detailed are well established and widely used. sition and diversity. Shotgun metage- analysis of the taxonomic and functional However, they have limitations such nomics is a cutting edge technique for composition of a microbial community. Microsynth Competences and Services Microsynth offers a full shotgun to your project requirements, thus pro- requirements to guarantee scientifically metagenomics service for taxonomic viding you with just the right amount of reliable results for your project. After and functional profiling of clinical, envi- data to answer your questions. quality processing the reads are aligned ronmental or engineered microbiomes. Bioinformatics: Taxonomic and func- against a protein reference database The service covers the entire process tional analysis of metagenomic data- (e.g. NCBI nr). Taxonomic and functional from experimental design, DNA isola- sets is challenging. Alignment, binning binning and annotation are performed. tion, tailored sequencing to detailed and annotation of the large amounts The analysis is not restricted to prokar- and customized bioinformatics analy- of sequencing reads require expertise yotes but also includes eukaryotes and sis. -
Randomness Versus Order
MILESTONES DOI: 10.1038/nrg2245 M iles Tone 1 0 Randomness versus order Whereas randomness is avoided used — in their opinion mistakenly The H. influenzae genome, in most experimental techniques, — direct sequencing strategies to however, was a mere DNA fragment it is fundamental to sequencing finish compared with the 1,500-fold longer approaches. In the race to sequence the last 10% of the bacteriophage λ ~3 billion base-pair human genome. the human genome, research groups sequence. In 1991, Al Edwards and In 1996, Craig Venter and colleagues had to choose between the random Thomas Caskey proposed a method proposed that the whole-genome whole-genome shotgun sequencing to maximize efficiency by minimiz- shotgun approach could be used to approach or the more ordered map- ing gap formation and redundancy: sequence the human genome owing based sequencing approach. sequence both ends (but not the to two factors: its past successes When Frederick Sanger and middle) of a long clone, rather than in assembling genomes and the colleagues sequenced the 48-kb the entirety of a short clone. development of bacterial artificial bacteriophage λ genome in 1982, Although the shotgun approach chromosomes (BAC) libraries, which the community was still undecided was now accepted for sequencing allowed large fragments of DNA to as to whether directed or random short stretches of DNA, map-based be cloned. sequencing strategies were better. techniques were still considered A showdown ensued, with the With directed strategies, DNA necessary for large genomes. Like biotechnology firm Celera Genomics sequences were broken down into the directed strategies, map-based wielding whole-genome shotgun ordered and overlapping fragments sequencing subdivided the genome sequencing and the International to build a map of the genome, and into ordered 40-kb fragments, which Human Genome Sequencing these fragments were then cloned were then sequenced using the Consortium wielding map-based and sequenced. -
Shotgun Metagenomics, from Sampling to Sequencing and Analysis Christopher Quince1,^, Alan W
Shotgun metagenomics, from sampling to sequencing and analysis Christopher Quince1,^, Alan W. Walker2,^, Jared T. Simpson3,4, Nicholas J. Loman5, Nicola Segata6,* 1 Warwick Medical School, University of Warwick, Warwick, UK. 2 Microbiology Group, The Rowett Institute, University of Aberdeen, Aberdeen, UK. 3 Ontario Institute for Cancer Research, Toronto, Canada 4 Department of Computer Science, University of Toronto, Toronto, Canada. 5 Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK. 6 Centre for Integrative Biology, University of Trento, Trento, Italy. ^ These authors contributed equally * Corresponding author: Nicola Segata ([email protected]) Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging members and understanding how communities function. Cheap, high-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples, or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offer biotechnological promise in therapeutic discovery, or innovative ways to synthesize products using microbial factories, but can also pinpoint the contributions of microorganisms to planetary, animal and human health. Introduction High throughput sequencing approaches enable genomic analyses of ideally all microbes in a sample, not just those that are more amenable to cultivation. One such method, shotgun metagenomics, is the untargeted (“shotgun”) sequencing of all (“meta”) of the microbial genomes (“genomics”) present in a sample. -
PA00XCSB.Pdf
Leidos Proprietary 1. EXECUTIVE SUMMARY A summary of efforts for the planned, ongoing, and completed projects for the Malaria Vaccine Development Program (MVDP) contract for this reporting period are herein detailed. A compiled Gantt chart including activities associated with each of the projects has been created and included as an attachment to this report. Ongoing projects that will continue through FY2019 include two vaccine development projects, the CSP vaccine development project (CSP Vaccine) and liver stage vaccine development project (Liver Stage Vaccine), as well as the clinical study with RH5 (RH5.1 Clinical Study), the latter to assess long-term immunogenicity in RH5.1/AS01 vaccinees. Of note is that while both the CSP and the liver stage vaccine development projects were initiated as epitope-based projects, these have since been realigned to target whole proteins; therefore, the project names have also been realigned to remove “epitope-based.” Expansion of work on the RCR complex into a vaccine development project (RCR Complex) occurred in early FY2019 and this project will continue until the end date of the contract. Lastly, a new project, the RH5.1 human monoclonal antibody identification and development project (RH5.1 Human mAb), was initiated in early FY2019 and will continue until the end date of the contract. Two projects were completed in FY2019, the blood stage epitope-based vaccine development project and the PD1 blockade inhibitor project (PD1 Block Inh). Leidos continues to seek collaborators for information exchange under NDA, reagent exchange under MTA, and collaboration under CRADA, to expand our body of knowledge and access to reagents with minimal cost to the program. -
Synthetic Genomics and Synthetic Biology Applications Between Hopes and Concerns
Send Orders of Reprints at [email protected] Current Genomics, 2013, 14, 11-24 11 Synthetic Genomics and Synthetic Biology Applications Between Hopes and Concerns 1,2, 1 1 1 Harald König *, Daniel Frank , Reinhard Heil and Christopher Coenen 1Institute for Technology Assessment and Systems Analysis (ITAS); 2Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, PO box 3640, 76021 Karlsruhe, Germany Abstract: New organisms and biological systems designed to satisfy human needs are among the aims of synthetic ge- nomics and synthetic biology. Synthetic biology seeks to model and construct biological components, functions and or- ganisms that do not exist in nature or to redesign existing biological systems to perform new functions. Synthetic genom- ics, on the other hand, encompasses technologies for the generation of chemically-synthesized whole genomes or larger parts of genomes, allowing to simultaneously engineer a myriad of changes to the genetic material of organisms. Engi- neering complex functions or new organisms in synthetic biology are thus progressively becoming dependent on and con- verging with synthetic genomics. While applications from both areas have been predicted to offer great benefits by mak- ing possible new drugs, renewable chemicals or clean energy, they have also given rise to concerns about new safety, en- vironmental and socio-economic risks – stirring an increasingly polarizing debate. Here we intend to provide an overview on recent progress in biomedical and biotechnological applications of synthetic genomics and synthetic biology as well as on arguments and evidence related to their possible benefits, risks and governance implications. Received on: May 22, 2012- Revised on: October 11, 2012- Accepted on: October 12, 2012 Keywords: Applications, Benefits, Biofuels, Biomedicine, Environment, Risks, Synthetic genomics, Synthetic biology. -
Commissioned Papers Synthetic Genomics: Risks and Benefits For
Commissioned Papers Synthetic Genomics: Risks and Benefits for Science and Society This volume of papers accompanies the report Synthetic Genomics: Options for Governance Synthetic Genomics: Risks and Benefits for Science and Society (this page blank) Synthetic Genomics: Risks and Benefits for Science and Society COMMISSIONED PAPERS TABLE OF CONTENTS Robert Jones Sequence Screening……………………………………………………………...……1-16 Yogesh Sanghvi A Roadmap to the Assembly of Synthetic DNA from Raw Materials……..………….17-33 Ralph S. Baric Synthetic Viral Genomics…………………………………………………………….35-81 Marc S. Collett Impact of Synthetic Genomics on the Threat of Bioterrorism with Viral Agents..………………………………………………………………………..83-103 Diane O. Fleming Risk Assessment of Synthetic Genomics: A Biosafety and Biosecurity Perspective………………………...………………………………….105-164 Franco Furger From Genetically Modified Organisms to Synthetic Biology: Legislation in the European Union, in Six Member Countries, and in Switzerland…………………………………………………………..……..165-184 Synthetic Genomics: Risks and Benefits for Science and Society (this page blank) Synthetic Genomics: Risks and Benefits for Science and Society The following papers were commissioned for the project Synthetic Genomics: Risks and Benefits for Science and Society. These papers formed the basis of many discussions at project workshops and at a large invitational meeting. The information elicited from these meetings, and from the commissioned papers themselves, formed the basis of our report Synthetic Genomics: Options for Governance (http://dspace.mit.edu/handle/1721.1/39141). The views and opinions expressed in these commissioned papers are those of the authors of the papers and not necessarily those of the authors of the report, or of the institutions at which the authors work. Citation: Working Papers for Synthetic Genomics: Risks and Benefits for Science and Society. -
Xenobiology: a New Form of Life As the Ultimate Biosafety Tool Markus Schmidt* Organisation for International Dialogue and Conflict Management, Kaiserstr
Review article DOI 10.1002/bies.200900147 Xenobiology: A new form of life as the ultimate biosafety tool Markus Schmidt* Organisation for International Dialogue and Conflict Management, Kaiserstr. 50/6, 1070 Vienna, Austria Synthetic biologists try to engineer useful biological search for alternatives. They belong to apparently very systems that do not exist in nature. One of their goals different science fields and their quest for biochemical is to design an orthogonal chromosome different from diversity is driven by different motivations.(1–3) The science DNA and RNA, termed XNA for xeno nucleic acids. XNA exhibits a variety of structural chemical changes relative fields in question include four areas: origin of life, exobiology, to its natural counterparts. These changes make this systems chemistry, and synthetic biology (SB). The ancient novel information-storing biopolymer ‘‘invisible’’ to nat- Greeks, including Aristotle, believed in Generatio spontanea, ural biological systems. The lack of cognition to the the idea that life could suddenly come into being from non- natural world, however, is seen as an opportunity to living matter on an every day basis. Spontaneous generation implement a genetic firewall that impedes exchange of genetic information with the natural world, which means of life, however, was finally discarded by the scientific it could be the ultimate biosafety tool. Here I discuss, why experiments of Pasteur, whose empirical results showed that it is necessary to go ahead designing xenobiological modern organisms do not spontaneously arise in nature from systems like XNA and its XNA binding proteins; what non-living matter. On the sterile earth 4 billion years ago, the biosafety specifications should look like for this however, abiogenesis must have happened at least once, genetic enclave; which steps should be carried out to boot up the first XNA life form; and what it means for the eventually leading to the last universal common ancestor society at large. -
Random Shotgun Fire
Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press EDITORIAL Random Shotgun Fire Craig Venter’s and Perkin-Elmer’s May 9th announce- lengths. The sequencing machine will be accompanied ment of a new joint venture to complete the sequence by an automated workstation that does colony picking, of the human genome in just 3 years set off a furor extraction, PCR, and sequencing reactions. The com- among the scientific community. The uproar, how- pany is committed to publicly releasing data on a quar- ever, was unsurprising given that the earliest newspa- terly basis on contigs greater than 2 kb, though the per articles presented the plan as if it were a fait accom- exact details for this release are still under discussion. pli and accused the publicly funded Human Genome The general business plan of the company includes the Project of being a ‘‘waste’’ of money. The announce- intention to patent between 100 and 300 interesting ment, made just prior to the Genome Mapping, Se- gene systems. Additionally, they plan to position quencing, and Biology Meeting, held May 13–17 at themselves as a supplier of a sequence database and Cold Spring Harbor Laboratory, was discussed, at least analysis tools. Finally, they intend to exploit the dis- briefly, at the sequencing center director’s meeting covered single nucleotide polymorphisms (SNPs), that preceded the CSHL meeting, in a very well- probably through a new genotyping service. With attended session during the CSHL meeting, and in nu- their approach, they claim they can sequence the hu- merous speculative debates over meals and beers man genome in just 3 years at a cost of roughly $200 among attending scientists. -
IGF-II) Gene in Villus During 610 Gestational Weeks, Jianhong Chen, Qun Fang, Baojiang Chen, Yi Zhou, and Yanmin Luo Volume 2010, Article ID 965905, 4 Pages
Obstetrics and Gynecology International Epigenetic Regulation in Reproductive Medicine and Gynecologic Cancers Guest Editors: Shi-Wen Jiang, Brian Brost, Sean Dowdy, Xing Xie, and Fan Jin Epigenetic Regulation in Reproductive Medicine and Gynecologic Cancers Obstetrics and Gynecology International Epigenetic Regulation in Reproductive Medicine and Gynecologic Cancers Guest Editors: Shi-Wen Jiang, Brian Brost, Sean Dowdy, Xing Xie, and Fan Jin Copyright © 2010 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in volume 2010 of “Obstetrics and Gynecology International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Obstetrics and Gynecology International Editorial Board Sean Blackwell, USA Howard D. Homesley, USA Faustino R. Perez-L´ opez,´ Spain Diane C. Bodurka, USA Shi-Wen Jiang, USA Tonse N.K. Raju, USA Curt W. Burger, The Netherlands Marc J. N. C. Keirse, Australia Neal S. Rote, USA Linda D. Cardozo, UK Russell K. Laros Jr., USA Giovanni Scambia, Italy Nancy Chescheir, USA Jonathan Ledermann, UK Peter E. Schwartz, USA Robert Coleman, USA Kimberly K. Leslie, USA John J. Sciarra, USA W. T. Creasman, USA Lawrence D. Longo, USA J. L. Simpson, USA Mary E. D’Alton, USA G. A. Macones, USA Anil Sood, USA Gian Carlo Di Renzo, Italy Everett Magann, USA Wiebren A. A. Tjalma, Belgium Keith A. Eddleman, USA James A. McGregor, USA J. R. Van Nagell, USA Edmund F. Funai, USA Liselotte Mettler, Germany John M. G. van Vugt, The Netherlands Norbert Gleicher, USA Daniel R. -
Whole Genome Shotgun Sequencing
Whole Genome Shotgun Sequencing Before we begin, some thought experiments: Thought experiment: How big are genomes of phages, Bacteria, Archaea, Eu- karya?1 Thought experiment: Suppose that you want to sequence the genome of a bac- teria that is 1,000,000 bp and you are using a sequencing technology that reads 1,000 bp at a time. What is the least number of reads you could use to sequence that genome?2 Thought experiment: The human genome was “finished” in 2000 — to put that in perspective President Bill Clinton and Prime Minister Tony Blair made the announcement! — How many gaps remain in the human genome?3 A long time ago, when sequencing was expensive, these questions kept people awake. For example, Lander and Waterman published a paper describing the number of clones that need to be mapped (sequenced) to achieve representative coverage of the genome. Part of this theoretical paper is to discuss how many clones would be needed to cover the whole genome. In those days, the clones were broken down into smaller fragments, and so on and so on, and then the fewest possible fragments sequenced. Because the order of those clones was known (from genetics and restriction mapping), it was easy to put them back together. In 1995, a breakthrough paper was published in Science which the whole genome was just randomly sheared, lots and lots of fragments sequenced, and then big (or big for the time — your cell phone is probably computationally more powerful!) computers used to assemble the genome. This breakthrough really unleashed the genomics era, and opened the door for genome sequencing including the data that we are going to discuss here! As we discussed in the databases class, the NCBI GenBank database is a central repository for all the microbial genomes.