The Genome Project-Write

@article{Boeke2016TheGP,
  title={The Genome Project-Write},
  author={Jef D. Boeke and George M. Church and Andrew Hessel and Nancy J. Kelley and Adam Paul Arkin and Yizhi Cai and Rob Carlson and Aravinda Chakravarti and Virginia W. Cornish and Liam J. Holt and Farren J. Isaacs and Todd Kuiken and Marc J. Lajoie and Tracy Lessor and Jeantine E. Lunshof and Matthew T. Maurano and Leslie A. Mitchell and Jasper Rine and Susan J. Rosser and Neville E. Sanjana and Pamela A. Silver and David Valle and Harris H. Wang and Jeffrey C. Way and Luhan Yang},
  journal={Science},
  year={2016},
  volume={353},
  pages={126 - 127}
}
We need technology and an ethical framework for genome-scale engineering The Human Genome Project (“HGP-read”), nominally completed in 2004, aimed to sequence the human genome and to improve the technology, cost, and quality of DNA sequencing (1, 2). It was biology's first genome-scale project and at the time was considered controversial by some. Now, it is recognized as one of the great feats of exploration, one that has revolutionized science and medicine. 
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References

SHOWING 1-10 OF 34 REFERENCES
Genomes by design
TLDR
In this Review, techniques and applications in genome engineering are explored, outlining key advances and defining challenges.
A prudent path forward for genomic engineering and germline gene modification
TLDR
The meeting identified immediate steps to take toward ensuring that the application of genome engineering technology is performed safely and ethically, and identified those areas where action is essential to prepare for future developments.
Finishing the euchromatic sequence of the human genome
TLDR
The near-complete sequence reported here should serve as a firm foundation for biomedical research in the decades ahead and greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death.
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
TLDR
H hierarchical conjugative assembly genome engineering (CAGE) was developed to merge these sets of codon modifications into genomes with 80 precise changes, which demonstrate that these synonymous codon substitutions can be combined into higher-order strains without synthetic lethal effects.
Synthetic chromosome arms function in yeast and generate phenotypic diversity by design
TLDR
This work describes a synthetic yeast genome project, Sc2.0, and the first partially synthetic eukaryotic chromosomes, Saccharomyces cerevisiae chromosome synIXR, and semi-synVIL, and shows the utility of SCRaMbLE as a novel method of combinatorial mutagenesis, capable of generating complex genotypes and a broad variety of phenotypes.
The challenges of sequencing by synthesis
TLDR
This work frames the challenges of DNA sequencing-by-synthesis in a manner accessible to a broad community of scientists and engineers, and hopes to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
TLDR
The design, synthesis, and assembly of the 1.08–mega–base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new cells that are controlled only by the synthetic chromosome are reported.
Total Synthesis of a Functional Designer Eukaryotic Chromosome
TLDR
The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology, and includes TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling.
Multiplex Genome Engineering Using CRISPR/Cas Systems
TLDR
Two different type II CRISPR/Cas systems are engineered and it is demonstrated that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
RNA-Guided Human Genome Engineering via Cas9
TLDR
The type II bacterial CRISPR system is engineer to function with custom guide RNA (gRNA) in human cells to establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
...
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