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  • 1
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    A draft sequence of the Neandertal genome (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-08
    Description: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Richard E -- Krause, Johannes -- Briggs, Adrian W -- Maricic, Tomislav -- Stenzel, Udo -- Kircher, Martin -- Patterson, Nick -- Li, Heng -- Zhai, Weiwei -- Fritz, Markus Hsi-Yang -- Hansen, Nancy F -- Durand, Eric Y -- Malaspinas, Anna-Sapfo -- Jensen, Jeffrey D -- Marques-Bonet, Tomas -- Alkan, Can -- Prufer, Kay -- Meyer, Matthias -- Burbano, Hernan A -- Good, Jeffrey M -- Schultz, Rigo -- Aximu-Petri, Ayinuer -- Butthof, Anne -- Hober, Barbara -- Hoffner, Barbara -- Siegemund, Madlen -- Weihmann, Antje -- Nusbaum, Chad -- Lander, Eric S -- Russ, Carsten -- Novod, Nathaniel -- Affourtit, Jason -- Egholm, Michael -- Verna, Christine -- Rudan, Pavao -- Brajkovic, Dejana -- Kucan, Zeljko -- Gusic, Ivan -- Doronichev, Vladimir B -- Golovanova, Liubov V -- Lalueza-Fox, Carles -- de la Rasilla, Marco -- Fortea, Javier -- Rosas, Antonio -- Schmitz, Ralf W -- Johnson, Philip L F -- Eichler, Evan E -- Falush, Daniel -- Birney, Ewan -- Mullikin, James C -- Slatkin, Montgomery -- Nielsen, Rasmus -- Kelso, Janet -- Lachmann, Michael -- Reich, David -- Paabo, Svante -- GM40282/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):710-22. doi: 10.1126/science.1188021.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. green@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448178" target="_blank"〉PubMed〈/a〉
    Keywords: African Continental Ancestry Group/genetics ; Animals ; Asian Continental Ancestry Group/genetics ; Base Sequence ; Bone and Bones ; DNA, Mitochondrial/genetics ; European Continental Ancestry Group/genetics ; Evolution, Molecular ; Extinction, Biological ; Female ; *Fossils ; Gene Dosage ; Gene Flow ; Genetic Variation ; *Genome ; *Genome, Human ; Haplotypes ; Hominidae/*genetics ; Humans ; Pan troglodytes/genetics ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Alignment ; *Sequence Analysis, DNA ; Time
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Targeted investigation of the Neandertal genome by array-based sequence capture (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-08
    Description: It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of approximately 99.8% microbial DNA. Using this approach, we have sequenced approximately 14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140021/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140021/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burbano, Hernan A -- Hodges, Emily -- Green, Richard E -- Briggs, Adrian W -- Krause, Johannes -- Meyer, Matthias -- Good, Jeffrey M -- Maricic, Tomislav -- Johnson, Philip L F -- Xuan, Zhenyu -- Rooks, Michelle -- Bhattacharjee, Arindam -- Brizuela, Leonardo -- Albert, Frank W -- de la Rasilla, Marco -- Fortea, Javier -- Rosas, Antonio -- Lachmann, Michael -- Hannon, Gregory J -- Paabo, Svante -- P01 CA013106/CA/NCI NIH HHS/ -- P01 CA013106-38/CA/NCI NIH HHS/ -- P01 CA013106-39/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):723-5. doi: 10.1126/science.1188046.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448179" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Fossils ; Genes ; *Genome ; *Genome, Human ; Hominidae/*genetics ; Humans ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis/*methods ; Pan troglodytes/genetics ; Proteins/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    A high-coverage genome sequence from an archaic Denisovan individual (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-01
    Description: We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30x) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617501/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617501/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, Matthias -- Kircher, Martin -- Gansauge, Marie-Theres -- Li, Heng -- Racimo, Fernando -- Mallick, Swapan -- Schraiber, Joshua G -- Jay, Flora -- Prufer, Kay -- de Filippo, Cesare -- Sudmant, Peter H -- Alkan, Can -- Fu, Qiaomei -- Do, Ron -- Rohland, Nadin -- Tandon, Arti -- Siebauer, Michael -- Green, Richard E -- Bryc, Katarzyna -- Briggs, Adrian W -- Stenzel, Udo -- Dabney, Jesse -- Shendure, Jay -- Kitzman, Jacob -- Hammer, Michael F -- Shunkov, Michael V -- Derevianko, Anatoli P -- Patterson, Nick -- Andres, Aida M -- Eichler, Evan E -- Slatkin, Montgomery -- Reich, David -- Kelso, Janet -- Paabo, Svante -- GM100233/GM/NIGMS NIH HHS/ -- R01 GM040282/GM/NIGMS NIH HHS/ -- R01 GM100233/GM/NIGMS NIH HHS/ -- R01-GM40282/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. mmeyer@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22936568" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Base Sequence ; Fossils ; Gene Flow ; Gene Library ; *Genetic Variation ; Genome, Human/*genetics ; *Heterozygote ; Humans ; Molecular Sequence Data ; Neanderthals/*genetics ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Targeted retrieval and analysis of five Neandertal mtDNA genomes (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-07-18
    Description: Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Briggs, Adrian W -- Good, Jeffrey M -- Green, Richard E -- Krause, Johannes -- Maricic, Tomislav -- Stenzel, Udo -- Lalueza-Fox, Carles -- Rudan, Pavao -- Brajkovic, Dejana -- Kucan, Zeljko -- Gusic, Ivan -- Schmitz, Ralf -- Doronichev, Vladimir B -- Golovanova, Liubov V -- de la Rasilla, Marco -- Fortea, Javier -- Rosas, Antonio -- Paabo, Svante -- New York, N.Y. -- Science. 2009 Jul 17;325(5938):318-21. doi: 10.1126/science.1174462.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. briggs@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19608918" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bayes Theorem ; DNA Primers ; DNA, Mitochondrial/analysis/*genetics/isolation & purification ; Evolution, Molecular ; Female ; *Fossils ; Gene Library ; Genetic Variation ; Genome, Human ; *Genome, Mitochondrial ; Geography ; Hominidae/*genetics ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; Population Density ; *Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Genetic history of an archaic hominin group from Denisova Cave in Siberia (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-12-24
    Description: Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306417/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306417/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, David -- Green, Richard E -- Kircher, Martin -- Krause, Johannes -- Patterson, Nick -- Durand, Eric Y -- Viola, Bence -- Briggs, Adrian W -- Stenzel, Udo -- Johnson, Philip L F -- Maricic, Tomislav -- Good, Jeffrey M -- Marques-Bonet, Tomas -- Alkan, Can -- Fu, Qiaomei -- Mallick, Swapan -- Li, Heng -- Meyer, Matthias -- Eichler, Evan E -- Stoneking, Mark -- Richards, Michael -- Talamo, Sahra -- Shunkov, Michael V -- Derevianko, Anatoli P -- Hublin, Jean-Jacques -- Kelso, Janet -- Slatkin, Montgomery -- Paabo, Svante -- R01 GM040282/GM/NIGMS NIH HHS/ -- R01-GM40282/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Dec 23;468(7327):1053-60. doi: 10.1038/nature09710.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. reich@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21179161" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Asia ; DNA, Mitochondrial/genetics ; Europe ; Finger Phalanges/chemistry ; *Fossils ; *Gene Flow ; Genome/*genetics ; Hominidae/*classification/*genetics ; Humans ; Melanesia ; Molecular Sequence Data ; Phylogeny ; Siberia ; Tooth/anatomy & histology/chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Patterns of damage in genomic DNA sequences from a Neandertal (2007)
    National Academy of Sciences
    Details
    Publication Date: 2007-08-21
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    Optimization of scarless human stem cell genome editing (2013)
    Oxford University Press
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    Publication Date: 2013-10-19
    Description: Efficient strategies for precise genome editing in human-induced pluripotent cells (hiPSCs) will enable sophisticated genome engineering for research and clinical purposes. The development of programmable sequence-specific nucleases such as Transcription Activator-Like Effectors Nucleases (TALENs) and Cas9-gRNA allows genetic modifications to be made more efficiently at targeted sites of interest. However, many opportunities remain to optimize these tools and to enlarge their spheres of application. We present several improvements: First, we developed functional re-coded TALEs (reTALEs), which not only enable simple one-pot TALE synthesis but also allow TALE-based applications to be performed using lentiviral vectors. We then compared genome-editing efficiencies in hiPSCs mediated by 15 pairs of reTALENs and Cas9-gRNA targeting CCR5 and optimized ssODN design in conjunction with both methods for introducing specific mutations. We found Cas9-gRNA achieved 7–8 x higher non-homologous end joining efficiencies (3%) than reTALENs (0.4%) and moderately superior homology-directed repair efficiencies (1.0 versus 0.6%) when combined with ssODN donors in hiPSCs. Using the optimal design, we demonstrated a streamlined process to generated seamlessly genome corrected hiPSCs within 3 weeks.
    Keywords: Synthetic Biology and Assembly Cloning, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Genetic Evidence of Human Adaptation to a Cooked Diet (2016)
    Oxford University Press
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    Publication Date: 2016-04-15
    Description: Humans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. Here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. Liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not by caloric intake or consumer energy balance. Genes affected by cooking were highly correlated with genes known to be differentially expressed in liver between humans and other primates, and more genes in this overlap set show signals of positive selection in humans than would be expected by chance. Sequence changes in the genes under selection appear before the split between modern humans and two archaic human groups, Neandertals and Denisovans, supporting the idea that human adaptation to a cooked diet had begun by at least 275,000 years ago.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-23
    Description: DNA built from modular repeats presents a challenge for gene synthesis. We present a solid surface-based sequential ligation approach, which we refer to as iterative capped assembly (ICA), that adds DNA repeat monomers individually to a growing chain while using hairpin ‘capping’ oligonucleotides to block incompletely extended chains, greatly increasing the frequency of full-length final products. Applying ICA to a model problem, construction of custom transcription activator-like effector nucleases (TALENs) for genome engineering, we demonstrate efficient synthesis of TALE DNA-binding domains up to 21 monomers long and their ligation into a nuclease-carrying backbone vector all within 3 h. We used ICA to synthesize 20 TALENs of varying DNA target site length and tested their ability to stimulate gene editing by a donor oligonucleotide in human cells. All the TALENS show activity, with the ones 〉15 monomers long tending to work best. Since ICA builds full-length constructs from individual monomers rather than large exhaustive libraries of pre-fabricated oligomers, it will be trivial to incorporate future modified TALE monomers with improved or expanded function or to synthesize other types of repeat-modular DNA where the diversity of possible monomers makes exhaustive oligomer libraries impractical.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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