Ancient human genome sequence of an extinct Palaeo-Eskimo

@article{Rasmussen2010AncientHG,
  title={Ancient human genome sequence of an extinct Palaeo-Eskimo},
  author={Morten Rasmussen and Yingrui Li and Stinus Lindgreen and Jakob Skou Pedersen and Anders Albrechtsen and Ida Moltke and Mait Metspalu and Ene Metspalu and Toomas Kivisild and Ramneek Gupta and Marcelo Bertalan and Kasper Nielsen and M. Thomas P. Gilbert and Yong Wang and Maanasa Raghavan and Paula F. Campos and Hanne Munkholm Kamp and Andrew S. Wilson and Andrew Gledhill and Silvana R. Tridico and Michael Bunce and Eline D. Lorenzen and Jonas Binladen and Xiaosen Guo and Jing Zhao and Xiuqing Zhang and Hao Zhang and Zhuo Li and Minfeng Chen and Ludovic Orlando and Karsten Kristiansen and Mads Bak and Niels Tommerup and Christian Bendixen and Tracey L. Pierre and Bjarne Gr{\o}nnow and Morten Meldgaard and Claus Bo Andreasen and Sardana A. Fedorova and L. P. Osipova and Thomas F.G. Higham and Christopher Bronk Ramsey and Thomas v. O. Hansen and Finn Cilius Nielsen and Michael H. Crawford and S{\o}ren Brunak and Thomas Sicheritz-Pont{\'e}n and Richard Villems and Rasmus Nielsen and Anders Krogh and Jun Wang and Eske Willerslev},
  journal={Nature},
  year={2010},
  volume={463},
  pages={757-762}
}
We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw… 
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References

SHOWING 1-10 OF 55 REFERENCES
Sequencing and Analysis of Neanderthal Genomic DNA
TLDR
The characterization of Neanderthals from a new perspective is described, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis, and the finding that the Neanderthal and human genomes are at least 99.5% identical is found.
Analysis of one million base pairs of Neanderthal DNA
TLDR
A 38,000-year-old Neanderthal fossil that is exceptionally free of contamination from modern human DNA is identified and it is revealed that modern human and Neanderthal DNA sequences diverged on average about 500,000 years ago.
Sequencing the nuclear genome of the extinct woolly mammoth
TLDR
This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction.
The Neandertal genome and ancient DNA authenticity
TLDR
It is argued that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination, and a similar ‘boot‐strap’ approach is suggested in which interim approaches are applied until sufficient data for more definitive directAssays are acquired.
Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland
TLDR
A mitochondrial genome from a Paleo-Eskimo human sequenced by using 3400-to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement suggests that the earliest migrants into the New World's northern extremes derived from populations in the Bering Sea area and were not directly related to Native Americans or the later Neo-ESkimos that replaced them.
Review Paper. Ancient DNA
TLDR
Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past.
The diploid genome sequence of an Asian individual
TLDR
Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly, and the potential usefulness of next-generation sequencing technologies for personal genomics.
Ancient DNA
TLDR
Ancient DNA has benefited in particular from recent advances in high-throughput sequencing technologies and from the development of analytical techniques that take advantage of the evolutionary information gained by sampling genetic data over both space and time.
A highly annotated whole-genome sequence of a Korean individual
TLDR
The genome of AK1 was determined by an exacting, combined approach that included whole-genome shotgun sequencing, targeted bacterial artificial chromosome sequencing, and high-resolution comparative genomic hybridization using custom microarrays featuring more than 24 million probes.
The Diploid Genome Sequence of an Individual Human
TLDR
A modified version of the Celera assembler is developed to facilitate the identification and comparison of alternate alleles within this individual diploid genome, and a novel haplotype assembly strategy is used, able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploids nature of the genome.
...
1
2
3
4
5
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