NGS Expert Blog

Is sequencing your personal genome a curse or a blessing? A recent radio broadcast from NPR news summarises two scientist’s opinions and their practical experiences with genome sequencing  (listen to the radio broadcast below).

World renowned scientist James Watson, from the famous Watson & Crick team that discovered the DNA structure, recently sequenced his own genome. His discovery didn’t earn him the next Nobel prize for science, but he found out that he belongs to the elite few people whose body is more sensitive to ß-blockers. Now James Watson finally realized why it was so difficult for him to balance his blood pressure. It definitely paid off for Watson to sequence his own genome since he could significantly reduce his weekly ß -blocker intake. But despite this “health-changing” experience, he forbid his colleagues to reveal any information about his likelihood to develop Alzheimer. He said, “since you cannot cure it why would you like to know about it?”

The second candidate to share his experience after he personally sequenced his genome is Stanford geneticist Michale Snyder. His genome sequencing revealed that he was at high risk to develop Type 2 diabetes. A few months after his discovery, Synder got the disease that his genome anticipated. Was this a coincidence or fate? For Snyder, knowledge about his genome gave him a head start against the disease.  By completely transforming his diet and participating in various sport activities,  he overcame his Type 2 diabetes.

From my perspective, both examples show that knowledge about our genetic information can be useful in preventing and treating diseases. It boils down to how much experience exist to reliably interpret the data.

16S rRNA sequencing of samples from 54 office-common surfaces in 3 different cities (New York, San Franscisco, Tuscon) revealed that offices of men are dirtier than these of women and the offices in San Francisco are the cleanest among the three cities. This is part of the results from Hewitt et al. published in PLoS ONE just recently. Overall they found “more than 500 bacterial genera from 20 different divisions” (Hewitt et al.) whereas most could be found on chairs and phones (see graph). But interestingly the bacterial population from Tuscon was significant different to the one from San Francisco and NewYork although the distance between Tuscon and San Francisco is smaller. From my point of view this is a great study showing that distribution is not as obvious as we think and that we haven’t revealed every secret on earth yet.

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!

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”?

John Lauerman, reporter with Bloomberg News got his genome sequenced. He is part of the Human Genome Project of the harvard medical school, where 10 genomes have been sequenced and analysed so far (Bloomberg).

After receiving his result he was first relieved to find no hint to have the APOE4 gene variant that raises the risk of Alzheimer’s disease. But what he learned then is that “No news wasn’t always good news; it just wasn’t bad news”. (Bloomberg) The researchs told him that the sequencing simply didn’t reveal information about APOE4. A study update however revealed later that the APOE4 gene variant indeed is present in his genome. This variant means an approx. 3 percent increased risk of developing the disease by age 80. But what does that mean in any single individual’s genome? At least Lauerman was less worried being his parents in the late 70s and 80s and having not developed Alzheimer’s disease.

But the researches have found in addition the rare JAK2 variant in Lauerman’s genome that is linked to a cancer-like blood disorder.  Knowing the risk, he now has the chance with increased vigilance to evaluate a potential disease early and to react accordingly.

And in that context Lauerman pointed out an even more important point: as a reporter working on a story about genomics, he had access to experts and genetic counselors that many people wouldn’t. What will happen as more people get results from broad genome sequencing? (Bloomberg) The question is if people can even handle the reports.

So as a personal conclusion I suppose I would be worried to hell when I would get to know my genome disorders. But it might be also a good thing, like in John Lauerman’s case. You would have the chance to detect a potential disease in an very early stage. You never know…

Great retro webcast: Nobel laureate James Watson and former NHGRI Director Francis Collins discuss the history and future of human genetics. It was created in 2003 when the human genome was sequenced the first time. In 2003 the 50th anniversary of James Watson and Francis Crick’s Nobel Prize winning description of the DNA double helix was also celebrated.