NGS Expert Blog

Dear Blog Reader,

In our last NGS poll we asked you about your opinion, which of the product launches from 2011 would have the most impact on your research. We are delighted that more than 50 NGS blog readers gave us their vote.

More than half of you rated the launch of the benchtop sequencer MiSeq as the most important event in 2011. 15% voted for the Roche GS FLX+ technology and 15% voted for the increased data output with Illumina chemistry v3.0. PacBio RS sequencing and the new exomes on the market have the least importance for you (10% and 8%, respectively).

I also see the MiSeq benchtop sequencer as a door opener for many groups towards inhouse access to Illumina sequencing data. The investment for the technology is considerably lower than for the Illumina HiSeq 2000 or HiSeq 2500 and when having not too many projects the higher consumable cost per basepair may be acceptable. Furthermore the MiSeq stands out by its short run time of only several hours.

For a Service Provider using several Illumina HiSeq 2000 sequencer the MiSeq is very interesting, too. It can be used for resequencing and scaffolding of small genomes, for quality control of sequencing libraries and especially for developping new protocols and services.

Did you perform already first sequencing runs on the MiSeq and for what kind of projects do you think is the sequencer most suitable for? I am very much looking forward to hearing about your experiences.

The Neandertals lived around 30.000 years ago. The Oetzi died around 5.000 years ago. For both human ancestors researchers were able to fully sequence the genome now. Prof. Pääbo and his group from the MPI in Leipzig published around ~60% of the Neandertal genome in Science (2010). And quite impressively from my point of view is that they give full access to the genome to everyone: they simply put all data on their website. What also fascinated me is that it is quite difficult to study the resemblance between the Neandertal and modern humans since most of the bones found from the Neandertal are “contaminated” with modern human genes. And of course this is obvious since no anthropologist is wearing gloves by default and therefore all people touching the bones to do studies about age and the lifestile of our ancestors will leave their genes on the bones.

An eye opener for me is also that the most obvious thing we discover in the genome is always the impairment of a species. A good example is the recent publication of the complete genome of the Iceman (Oetzi). 96% of the Iceman’s genome has been sequenced and what did we learn: he belonged to blood group O, was lactose intolerant, had probably a genetic tendency towards coronary heart disease, and was carrying Lyme disease.

But researchers also found interesting information about the linkage of both Oetzi and Neandertal to modern humans:

The genome of Oetzi has been compared to 1300 Europeans, 125 North Africans and 20 people from the Arab peninsula. The study revealed that his closest living kin are found on Sardinia and Corsica.

For the Neandertal five modern humans from different populations were used for comparison studies. The stunning result is that some Neandertals and early modern humans interbred since 1 to 4% of the DNA of many humans who live outside of Africa originate from the Neandertal.

In all the discussions about our ancestors and close relatives I sometimes come to think if we will be close relatives in let’s say 1 million years? Wouldn’t it be possible that a new population or species of humans develop? It sounds absurd or science fiction-like but who are we that we think there is nothing “after us”?

photography: Doris Lauscher

After the Humans, chimpanzees and orangutans genome, last week another great ape genome was reported as being sequenced and assembled in Nature: The Gorilla genome.

Gorillas that are in immediate danger of extinction are humans’ closest living relatives after chimpanzees, followed by orangutans. Therefore the genome of the gorilla represents the missing piece of the puzzle, to study the origin and evolution of the humans in much more detail. 

The comparison had indeed some surprises in store: It revealed that the gorilla and humans are more closely related to each other than assumed previously. The separation of both species took place approx. 10 million years ago. Approx.  4 million years after that the chimpanzees separated from the humans.

To gain a genome assembly with contigs and scaffolds long enough to allow those comparisons, the international research team, not only sequenced the genome with Illumina short read technology (167 Gbp) but included 5.4 Gbp of long read technology sequencing data in addition. Based on a genome size of approx. 3 Gbp the Sanger reads referred to a coverage of 1.8-fold. The initial assembly was produced with a de novo strategy but in later phases of the assembly the researchers made use of the human reference genome to improve the assembly.

For me personally, the assembly and scaffolding approach described is really impressive. A variety of software tools was used to integrate sequence data and paired-end information from different technologies as well as the similarity to the human genome to best use all the information available. Have a look at it!

Dear Blog readers,
today I am really delighted to announce the launch of the NGS Favourites.

NGS Favourites are the straightforward solution for your Next Generation Sequencing project. They are based on the wealth of knowledge that we have accumulated from over 5 years of servicing the NGS community and represent optimised packages for common NGS applications.

The NGS Favourites stand out due to:

• Project-oriented solutions
• Economic costs
• Easy ordering

The NGS Favourites are available for different fields of applications:

• Genome Sequencing Favourites - using shotgun (SG) libraries only or a combination of SG and LPE libraries
• Transcriptome Sequencing Favourites – receive comprehensive data you can really build on
• Exome Sequencing Favourites – sequence 6 human Exomes with the Illumina TruSeq Kit
• Library Service Favourites – get your libraries for GS FLX sequencing prepared from us

Find your suitable Favourite and explore the easy way of sequencing with us as your professional project partner.