Genome Project-Write

Last updated

Since the Human Genome Project first sequenced the human genome from 1987 to 2004 at a cost of US$3 billion, costs have fallen precipitously, outpacing even Moore's law, and were [?]US$1,000 in 2015. More widely available genome sequencing has led to more data on variants of uncertain significance. Cost per Genome.png
Since the Human Genome Project first sequenced the human genome from 1987 to 2004 at a cost of US$3 billion, costs have fallen precipitously, outpacing even Moore's law, and were ≈US$1,000 in 2015. More widely available genome sequencing has led to more data on variants of uncertain significance.

The Genome Project - Write (also known as GP-Write) is a large-scale collaborative research project (an extension of Genome Projects, aimed at reading genomes since 1984) that focuses on the development of technologies for the synthesis and testing of genomes of many different species of microbes, plants, and animals, including the human genome in a sub-project known as Human Genome Project-Write (HGP-Write). [1] [2] [3] [4] [5] [6] Formally announced on 2 June 2016, the project leverages two decades of work on synthetic biology and artificial gene synthesis.

Contents

The newly created GP-Write project will be managed by the Center of Excellence for Engineering Biology, [7] an American nonprofit organization. Researchers expect that the ability to artificially synthesize large portions of many genomes will result in many scientific and medical advances. [1] [2] [3] [4] [5] [6]

Science & development

In May 2021, GP-write and Twist Bioscience launched a new CAD platform for whole genome design. The GP-write CAD will automate workflows to enable collaborative efforts critical for scale-up from designing plasmids to megabases across entire genomes. [8]

Microbial Genome Projects - Write

Technologies for constructing and testing yeast artificial chromosomes (YACs), synthetic yeast genomes (Sc2.0), [9] and virus/phage-resistant bacterial genomes have industrial, agricultural, and medical applications. [2]

Human Genome Project-Write

A complete haploid copy of the human genome consists of at least three billion DNA nucleotide base pairs, which have been described in the Human Genome Project - Read program (95% completed as of 2004). Among the many goals of GP-Write are the making of cell lines resistant to all viruses and synthesis assembly lines to test variants of unknown significance that arise in research and diagnostic sequencing of human genomes (which has been exponentially improving in cost, quality, and interpretation). [2]

See also

Related Research Articles

<span class="mw-page-title-main">Craig Venter</span> American biotechnologist and businessman

John Craig Venter is an American biotechnologist and businessman. He is known for leading one of the first draft sequences of the human genome and assembled the first team to transfect a cell with a synthetic chromosome. Venter founded Celera Genomics, the Institute for Genomic Research (TIGR) and the J. Craig Venter Institute (JCVI). He was the co-founder of Human Longevity Inc. and Synthetic Genomics. He was listed on Time magazine's 2007 and 2008 Time 100 list of the most influential people in the world. In 2010, the British magazine New Statesman listed Craig Venter at 14th in the list of "The World's 50 Most Influential Figures 2010". In 2012, Venter was honored with Dan David Prize for his contribution to genome research. He was elected to the American Philosophical Society in 2013. He is a member of the USA Science and Engineering Festival's advisory board.

<span class="mw-page-title-main">Genetic engineering</span> Manipulation of an organisms genome

Genetic engineering, also called genetic modification or genetic manipulation, is the modification and manipulation of an organism's genes using technology. It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. New DNA is obtained by either isolating and copying the genetic material of interest using recombinant DNA methods or by artificially synthesising the DNA. A construct is usually created and used to insert this DNA into the host organism. The first recombinant DNA molecule was made by Paul Berg in 1972 by combining DNA from the monkey virus SV40 with the lambda virus. As well as inserting genes, the process can be used to remove, or "knock out", genes. The new DNA can be inserted randomly, or targeted to a specific part of the genome.

<span class="mw-page-title-main">Genomics</span> Discipline in genetics

Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

<span class="mw-page-title-main">Michael Smith (chemist)</span> British-born Canadian biochemist, businessman and Nobel Prize laureate (1932-2000)

Michael Smith was a British-born Canadian biochemist and businessman. He shared the 1993 Nobel Prize in Chemistry with Kary Mullis for his work in developing site-directed mutagenesis. Following a PhD in 1956 from the University of Manchester, he undertook postdoctoral research with Har Gobind Khorana at the British Columbia Research Council in Vancouver, British Columbia, Canada. Subsequently, Smith worked at the Fisheries Research Board of Canada Laboratory in Vancouver before being appointed a professor of biochemistry in the UBC Faculty of Medicine in 1966. Smith's career included roles as the founding director of the UBC Biotechnology Laboratory and the founding scientific leader of the Protein Engineering Network of Centres of Excellence (PENCE). In 1996 he was named Peter Wall Distinguished Professor of Biotechnology. Subsequently, he became the founding director of the Genome Sequencing Centre at the BC Cancer Research Centre.

<span class="mw-page-title-main">Leroy Hood</span> American biologist (born 1938)

Leroy "Lee" Edward Hood is an American biologist who has served on the faculties at the California Institute of Technology (Caltech) and the University of Washington. Hood has developed ground-breaking scientific instruments which made possible major advances in the biological sciences and the medical sciences. These include the first gas phase protein sequencer (1982), for determining the sequence of amino acids in a given protein; a DNA synthesizer (1983), to synthesize short sections of DNA; a peptide synthesizer (1984), to combine amino acids into longer peptides and short proteins; the first automated DNA sequencer (1986), to identify the order of nucleotides in DNA; ink-jet oligonucleotide technology for synthesizing DNA and nanostring technology for analyzing single molecules of DNA and RNA.

<span class="mw-page-title-main">Yeast artificial chromosome</span> Genetically engineered chromosome derived from the DNA of yeast

Yeast artificial chromosomes (YACs) are genetically engineered chromosomes derived from the DNA of the yeast, Saccharomyces cerevisiae, which is then ligated into a bacterial plasmid. By inserting large fragments of DNA, from 100–1000 kb, the inserted sequences can be cloned and physically mapped using a process called chromosome walking. This is the process that was initially used for the Human Genome Project, however due to stability issues, YACs were abandoned for the use of Bacterial artificial chromosome

<span class="mw-page-title-main">Synthetic biology</span> Interdisciplinary branch of biology and engineering

Synthetic biology (SynBio) is a multidisciplinary field of science that focuses on living systems and organisms, and it applies engineering principles to develop new biological parts, devices, and systems or to redesign existing systems found in nature.

<span class="mw-page-title-main">National Human Genome Research Institute</span> Institute of the National Institutes of Health, located in Bethesda, Maryland, US

The National Human Genome Research Institute (NHGRI) is an institute of the National Institutes of Health, located in Bethesda, Maryland.

<span class="mw-page-title-main">ENCODE</span> Research consortium investigating functional elements in human and model organism DNA

The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims "to build a comprehensive parts list of functional elements in the human genome."

<span class="mw-page-title-main">George Church (geneticist)</span> American geneticist

George McDonald Church is an American geneticist, molecular engineer, chemist, serial entrepreneur, and pioneer in personal genomics and synthetic biology. He is the Robert Winthrop Professor of Genetics at Harvard Medical School, Professor of Health Sciences and Technology at Harvard University and Massachusetts Institute of Technology, and a founding member of the Wyss Institute for Biologically Inspired Engineering at Harvard. Through his Harvard lab Church has co-founded around 50 biotech companies pushing the boundaries of innovation in the world of life sciences and making his lab as a hotbed of biotech startup activity in Boston. In 2018, the Church lab at Harvard made a record by spinning off 16 biotech companies in one year. The Church lab works on research projects that are distributed in diverse areas of modern biology like developmental biology, neurobiology, info processing, medical genetics, genomics, gene therapy, diagnostics, chemistry & bioengineering, space biology & space genetics, and ecosystem. Research and technology developments at the Church lab have impacted or made direct contributions to nearly all "next-generation sequencing (NGS)" methods and companies. In 2017, Time magazine listed him in Time 100, the list of 100 most influential people in the world. In 2022, he was featured among the most influential people in biopharma by Fierce Pharma, and was listed among the top 8 famous geneticists of all time in human history. As of January 2023, Church serves as a member of the Bulletin of the Atomic Scientists' Board of Sponsors, established by Albert Einstein.

Steven Albert Benner has been a professor at Harvard University, ETH Zurich, and the University of Florida where he was the V.T. & Louise Jackson Distinguished Professor of Chemistry. In 2005, he founded The Westheimer Institute of Science and Technology (TWIST) and the Foundation For Applied Molecular Evolution. Benner has also founded the companies EraGen Biosciences and Firebird BioMolecular Sciences LLC.

<span class="mw-page-title-main">Human Genome Project</span> Human genome sequencing programme

The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a physical and a functional standpoint. It started in 1990 and was completed in 2003. It remains the world's largest collaborative biological project. Planning for the project started after it was adopted in 1984 by the US government, and it officially launched in 1990. It was declared complete on April 14, 2003, and included about 92% of the genome. Level "complete genome" was achieved in May 2021, with a remaining only 0.3% bases covered by potential issues. The final gapless assembly was finished in January 2022.

Synthetic genomics is a nascent field of synthetic biology that uses aspects of genetic modification on pre-existing life forms, or artificial gene synthesis to create new DNA or entire lifeforms.

<span class="mw-page-title-main">Artificial gene synthesis</span> Group of methods in synthetic biology

Artificial gene synthesis, or simply gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides de novo. Unlike DNA synthesis in living cells, artificial gene synthesis does not require template DNA, allowing virtually any DNA sequence to be synthesized in the laboratory. It comprises two main steps, the first of which is solid-phase DNA synthesis, sometimes known as DNA printing. This produces oligonucleotide fragments that are generally under 200 base pairs. The second step then involves connecting these oligonucleotide fragments using various DNA assembly methods. Because artificial gene synthesis does not require template DNA, it is theoretically possible to make a completely synthetic DNA molecule with no limits on the nucleotide sequence or size.

Mycoplasma laboratorium or Synthia refers to a synthetic strain of bacterium. The project to build the new bacterium has evolved since its inception. Initially the goal was to identify a minimal set of genes that are required to sustain life from the genome of Mycoplasma genitalium, and rebuild these genes synthetically to create a "new" organism. Mycoplasma genitalium was originally chosen as the basis for this project because at the time it had the smallest number of genes of all organisms analyzed. Later, the focus switched to Mycoplasma mycoides and took a more trial-and-error approach.

The following outline is provided as an overview of and topical guide to genetics:

A P1-derived artificial chromosome, or PAC, is a DNA construct derived from the DNA of P1 bacteriophages and Bacterial artificial chromosome. It can carry large amounts of other sequences for a variety of bioengineering purposes in bacteria. It is one type of the efficient cloning vector used to clone DNA fragments in Escherichia coli cells.

Synthetic virology is a branch of virology engaged in the study and engineering of synthetic man-made viruses. It is a multidisciplinary research field at the intersection of virology, synthetic biology, computational biology, and DNA nanotechnology, from which it borrows and integrates its concepts and methodologies. There is a wide range of applications for synthetic viral technology such as medical treatments, investigative tools, and reviving organisms.

Synthetic genome is a synthetically built genome whose formation involves either genetic modification on pre-existing life forms or artificial gene synthesis to create new DNA or entire lifeforms. The field that studies synthetic genomes is called synthetic genomics.

References

  1. 1 2 Pollack, Andrew (2 June 2016). "Scientists Announce HGP-Write, Project to Synthesize the Human Genome". The New York Times . Retrieved 2 June 2016.
  2. 1 2 3 4 Boeke, JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L; et al. (2 June 2016). "The Genome Project–Write". Science . 353 (6295): 126–127. Bibcode:2016Sci...353..126B. doi:10.1126/science.aaf6850. PMID   27256881. S2CID   206649424 . Retrieved 2 June 2016.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. 1 2 Callaway, Ewen (2 June 2016). "Plan to Synthesize Human Genome Triggers a Mixed Response". Scientific American . Retrieved 2 June 2016.
  4. 1 2 Regalado, Antonio (2 June 2016). "Plan to Fabricate a Genome Raises Questions on Designer Humans". MIT Technology Review . Retrieved 2 June 2016.
  5. 1 2 Akst, Jef (2 June 2016). ""Human Genome Project-Write" Unveiled". The Scientist . Retrieved 2 June 2016.
  6. 1 2 Opal, Puneet; Kini, Ameet (3 June 2016). "The Brave New World of the Synthetic Human Genome". Time . Retrieved 12 June 2016.
  7. "Center of Excellence for Engineering Biology" . Retrieved 2 March 2017.
  8. "CAD Platform Developed by GP-Write and Twist to Launch Large Genome Projects". Genetic Engineering & Technology News. 12 May 2021.
  9. "Synthetic yeast genomes (Sc2.0)" . Retrieved 2 March 2017.

Further reading