Saturday, April 13, 2013

Next-generation sequencing on Egyptian mummies

Nature has a news article out on a paper supposedly published last week in the Journal of Applied Genetics by Khairat, R. et al. which carried out next-generation sequencing on five Egyptian mummified heads, the paper is not accessible, some excerpts from the news article:

The ancient Egyptians could soon be getting their genomes sequenced as a matter of routine. That’s the view, at least, of the first researchers to use next-generation techniques to analyse DNA from Egyptian mummies.....

....Now, Pusch and his colleagues, including Rabab Khairat, have carried out next-generation sequencing on five Egyptian mummified heads held at the University of Tübingen. The heads date from relatively late in ancient Egyptian history — between 806 bc and 124 ad....

....they show that human DNA survives in the mummies and that it is amenable to sequencing...

....The researchers determined that one of the mummified individuals belongs to an ancestral group, or haplogroup, called I2, believed to have originated in Western Asia. They also retrieved genetic material from the pathogens that cause malaria and toxoplasmosis, and from a range of plants that includes fir and pine — both thought to be components of embalming resins — as well as castor, linseed, olive, almond and lotus....

....In mummies, “DNA preservation appears to be independent of temperature,” he says.....

.....Now that Pusch and his colleagues have demonstrated next-generation sequencing in Egyptian mummies, however, moving on to entire genomes “isn’t rocket science”, Gilbert says. “What limits you is the size of a sample. For Denisova Man they had just a finger bone. Here they have the whole mummy.”....

....“entire-genome sequencing of ancient Egyptian individuals is likely to become standard in the not-too-distant future”.....

http://www.nature.com/news/egyptian-mummies-yield-genetic-secrets-1.12793#/b1

Edit: Found link to the Abstract here: Khairat, R. et al.

We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC–124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a “bacterial fingerprint”, discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals.

3 comments:

  1. Ydna I2 or Mtdna I2 is now the question.

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  2. This comment has been removed by the author.

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