NGS Expert Blog

A recent article in Scientific American by Jennifer Ackerman entitled “The Ultimate Social Network”, highlights a particular problem when trying to sequence the genomes of eukaryotic organisms. The problem is that the organism in question, whether it is an ant, butterfly, a polar bear, frog or Blue whale is not a singular organism at all.

In fact the organism in question plays host to many millions of other prokaryotic organisms, mainly bacteria, viruses, fungi or parasites. In humans for example the genetic material from the microbiome outnumbers the human genome by at least 10 to 1. This is also expected to be true of all other eukaryotic species which harbour and maintain a symbiotic relationship with their microbiome.

The genes from the microbiome help process beneficial compounds and act to temper host immune defences for example. Therefore, when taking and extracting DNA from a eukaryotic organism it has to be considered what other genomes you may be preparing and sequencing alongside the desired genome of interest. For example it cannot be simply a case of freeze drying an insect crushing into a powder then extracting the DNA, as the resultant samples will contain a highly mixed and diverse set of genomes,  whereby the genome of interest may be present only in the lowest possible ratio. So, be warned! When assembling genomes be sure you know what your starting material actually contains.

Next Generation Sequencing (NGS) is transforming today’s genomic research and is used in numerous applied areas from clinical diagnostics to academic research. In Texas USA, Dr. Steven Phelps and his research team recently used NGS sequencing to discover a gene which allows mice to communicate by singing a song. I have to admit it sounds more like screaming than singing to me. But Phelps and his team found out that a gene called FOXP2 is responsible for this way of communication.

Phelps’ uses next-generation sequencing to decipher how FOXP2 interacts with DNA to regulate the function of other genes. The process involves reading tiny fragments of overlapping DNA so that the entire sequence can be deduced. It is a procedure that generates massive amount of data that only the processing power of a supercomputer can handle, said O’Connell (Source: www.tacc.utexas.edu). So data handling & storage is still one of the biggest challenges when performing Next Generation Sequencing projects. But now take the chance an listen to the song of this little mouse.

Illumina product experts discuss within 4 videos

1. what it takes to get a good genome out of a sequencing system,
2. what attributes of a sequencing system contribute to the quality of a sequencing data set,
3. the hidden costs of accuracy and
4. how next generation sequencing is moving into the clinic because of a better understanding of accuracy.

Please be tolerant, they’re from Marketing

Nacreous luster is held in high industrial value since ancient time. It is a jewelry which is generated in pearl oysters, so it is also called “biomineral”. Nacre consists of two kinds of layer structures: an “inorganic crystal layer by calcium carbonate” and a “protein layer”. The protein layer is made of a laminate structure, which comes up the characteristic luster by multilayer reflective. Recently, pearls are not only used as jewels but take on greater importance like as a new functional material for nano technology, as a CO2 fixation carrier for environmental science, and as a model of bone formation/bio-calcification for medical science.

However, molecular entity of the protein layer is not understood so much. To clarify it, Kinoshita et al. tried transcriptome analysis of the pearl oyster Pinctada fucata with 3’-fragment library and GS FLX sequencing. They could identify 29,682 novel genes, and clustering analysis of gene expression pattern with known nacreous genes revealed 20 candidates that most probably have an association with bio-mineralization. Furthermore, Takeuchi et al.　determined the 1.15 Gb draft genome sequence of P. fukata. They found 23 257 complete gene models that included the candidate genes reported in the study from Kinoshita et al.

The spinning process of nacreous luster will be clarified by harmony of gene expression in near future!

Earlier this year Oxford Nanopore Technologies presented their solution for Next Generation Sequencing: the MinIon & GridIon instruments outranges the current available techniques like Illumina or Roche systems by read length, hands on time and pricing. But since the technology is not launched yet, we don’t know if these specs are realistic.

This is why we asked you about your opinion in our latest poll (Nanopore sequencing from Oxford Nanopore Technologies sounds really fascinating. What is your opinion regarding this technology?). More than 50 voters took part in this survey and 42% share my opinon: “I prefer to wait and check out the real system before judging it”.

“Paper doesn’t blush” is what 15% think of this announcement – like every other company the first presentation needs to be spectacular, but let’s see what happens when the instrument is really on the market.

And still some of you are convinced that this will change a lot in the NGS market – and I agree it would be great if it turns out to be true.

Some of you haven’t heard about this technology – so if you are interested to learn more about it you might start by reading our recent blog post about it.

Thanks again to all you participated in our voting and please have a look at our new poll.

Last week The Smithsonian Institution’s National Museum of Natural History at Washington DC announced a new exhibit to celebrate the 10th anniversary of the completion of the human genome. The project is a collaboration between the museum and the National Human Genome Research Institute, with major funding coming from the Life Technologies Foundation. It will open in 2013 to the 7 million annual visitors of the museum.

“The goal of the exhibition is not just to celebrate but to look ahead and acknowledge that we are in the early stages of a very exciting genomic era, that we have learned a remarkable amount about how the genome works and how it contributes to health and disease, and that the pace of research is only accelerating and becoming increasingly relevant to people,” said NHGRI Director Eric Green.
Also announced last week was a new grant program by the NHGRI to study newborn genome sequencing. It will provide $25 million to study how whole genome or whole exome sequencing will benefit newborn care as well as its social implications.
“Genome”, “genomics” etc used to be terms understood by few outside of biology and bioinformatics. This is changing rapidly. It is exciting time ahead of us to witness the genomics revolution.

A documentary titled “Cracking Your Genetic Code” was recently released, and it offers a glimpse on how genomics is transforming medicine. Prominent scientists are featured, including Francis Collins from the National Institute of Health and Eric Lander from the Massachusetts Institute of Technology. In the documentary we are introduced to technologies for sequencing the entire genome; Illumina is being mentioned as one of the companies with such technology. We hear real-life stories where genome sequencing and genotyping led to diagnoses and successful treatments that would not happen otherwise.

The documentary does not only present the promises that personalized medicine is bringing, it also raises important questions concerning the readiness of the society in adopting this new form of medicine. There are always pros and cons with introducing new technologies to our daily lives. It is a matter of engaging and educating the public so the society as a whole can make some informed decisions during this healthcare revolution. Cracking your Genetic Code is a great introduction to the new role of sequencing in medicine, and I hope you will share it with your colleagues and friends!

Recently the Hollywood filmmaker James Cameron (director of “Titanic”) reached in a custom made submarine the deepest point of the Mariana Trench, breaking a world record for the deepest solo dive. Deep-sea trenches have lured explorers for decades, tantalizing them with glimpses of an ecosystem shrouded in darkness.

Although Cameron’s journey to the abyss yielded little new scientific data, it whetted the public appetite for information about life in the otherworldly environments of deep-sea trenches.

An international group of marine scientists may soon provide a feast of such data, from the first major systematic study of a deep-sea trench. If all goes well the team will start exploring the South sea of New Zealand in a depth between 6.000 and 11.000 meters. A team around Timothy Shank from the Woods Hole Institution (WHI) inMassachusetts will systematically explore this complete unknown biotope with robots. An article about this program is published in the recent issue of Science.

New forms of life and deep insight into evolution are to be expected.

As a scuba diver I am excited to learn more about this fascinating biotope and I am sure that Next Generation sequencing technologies will significantly contribute to new chapters of the book of life.

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!