Category: Genetics

BioTech’s New Hot Shot

Genetics, Sequencing

There was an interesting article in the New York Times today (yes, I was magically granted access to their website again, not sure why but I’m glad) by Andrew Pollack. Taking DNA Sequencing to the Masses takes an in-depth look at the work of Jonathan M. Rothberg.

Dr. Rothberg is the founder of the genome sequencing company Ion Torrent. The article looks at Ion Torrent’s role in providing cheap (under $50,000) sequencing technology with the launch of their Personal Genome Machine. The technology isn’t intended for the general public, but will make obtaining a sequencing system more feasible for smaller universities and clinics that can’t afford larger machines.

The article draws a parallel between Rothberg and Apple founder Steve Jobs on several occasions. Pollack paints Rothberg as a bit of a rebellious nerd, who certainly has high hopes for his company and the technology they are developing.

Pollack ends the article with Rothberg saying that he believes that genome sequencing will become as useful for medical applications as imaging (like X-rays, CAT Scans, etc.) I like this article because statements like that aren’t blown out of proportion. I think that for an article that is focused on what can be achieved in the future the ideas all stay grounded in what is really feasible, which can sometimes be difficult in a science technology article.

Elephant Species

Genetics, New Research, Sequencing
Source: Wikimedia Commons.
Photographer: Johnny Liunggren.

Researchers have put an end to debate about whether the African Elephant is one species, or two. New findings published in the journal Public Library of Science Biology show that the African Elephants that dwell in the savannah are a distinct species from those that dwell in the forests.

Loxodonta africana, the savannah dwellers, are much larger and in some cases twice as heavy as Loxodonta cyclotis, the forest dwellers. The debate about whether the elephants were separate species has been going on for at least a decade. The research shows that the two species diverged from their common ancestor around the same time that humans and chimpanzees evolved. How long ago the species split was a surprise for the researchers.

1000 Genomes Project

Genetics, New Research, Sequencing

For as long as I can remember my parents have been telling me that I’m special (in a good way, not in the derogatory way the kids are using the term these days). Most of us start life out thinking that we’re unique and the more we learn about life, and the more it kicks out asses we become so disillusioned that we cease believing we’re really all that special.

But, new data generated by the 1000 Genomes Project recently confirmed that our parents have been right all along. The 1000 Genomes Project is an effort to sequence the genes of 2,500 people from around the world in an attempt to fill the gaps in the draft sequence of the human genome left by genetic variation. 
The draft sequence was established in 2000 by teams led by J. Craig Venter and Francis Collins. While that was a breakthrough moment in the field of genetics because it enabled the study of diseases caused by changes in our DNA, it only took us so far. 
Genetic variation refers to the differences in the human genome between individuals (ie: if my code is AGTCAGTC, yours might be AGCCAGTC). That kind of a difference can have a huge impact on how disease manifests itself, therefore studies looking for treatments for genetic-based disorders (Alzheimer’s, Parkinson’s Disease, Cancer, etc.) are hindered by these variations. 
The new data obtained by the 1000 Genomes Project, is a 95% map of human genetic variation. The results of the study show that each individual person has an average of 75 variations (single nucleotide polymorphisms, or SNPs, which are changes in the code like I described above). These variations are essentially what makes each of us different from everyone around us. My parents were right, I am special, but something tells me they weren’t referring to my genes. 
This is exciting for a few reasons:
1. Millions of dollars have been invested in this project, it is good to see something actually come of it. 
2. A better understanding of variation can enable more progressive research on genetic disease, from causes to treatments. 
3. Genome sequencing technology is advancing quickly, and making interesting research like this a reality. Expect more projects like 1000 Genomes, it’s definitely about to get ambitious in here. 
4. A project like this sets important standards for open access information and data sharing among researchers for genetic studies at this scale. 
Read more: 

Rare Variants

BioTechnology, Genetics, Sequencing

My article from the October issue of BioTechniques is out! I reported this one back in August right as I was moving to Madison. It is exciting to finally be able to see it in print. It is also available online, which means you should be reading it right now.

Many thanks to the scientists who spent so much time talking to me about rare variants, and to the editorial staff at BioTechniques for editing, and editing, and editing some more. 
Posing with the October issue!

Before you dive into the article, I’m sure you are asking yourself what is a rare variant, and why do I care? Well – rare variants are specific mutations in the genome that only happen in a few individuals, in some cases even just a single person. These variants are important because any time that something is amiss in your genome, it has an effect on you. At times these effects include causing disease. So, studying rare variants can tell doctors important things about disease and possibly help come up with new treatments. But, studying these rare variants is extremely difficult. To learn why, read the article!

Historical Documents

Genetics, Science History

I consider letters historical documents. I think that when you put words down on paper, even in the casual form of a personal letter it becomes a piece of history. It records what you were thinking at a specific time and place, sealing a bit of history onto paper. I love seeing an envelope in my mailbox, so in the age of email I am lucky to have a few friends that love mail as much as I do, and so write me letters in exchange for me filling their mailboxes.

I just got a letter today from my friend Cassi, and have been wanting to write a reply all day, but have been tremendously distracted by my paper on the American Red Cross, among other things. The paper is for J620 my International Communication class — we are studying the media of humanitarian movements, which has nothing to do with science writing but as far as electives go I’m learning a lot. It is due tomorrow and my brain is totally tapped out so I’m taking a break from editing to blog (although blogging isn’t exactly relaxing for my brain.)

Anyway, I was already thinking about letters and how much I love and appreciate all of my letters, when I saw the article “Rivalry Among DNA Sleuths Comes Alive In Letters,” by Nicholas Wade for the New York Times. I am very tempted by the field of science history, if I were ever to turn academic instead of professional I would definitely be interested in exploring the history of science journalism, which in my opinion would include correspondence between scientists (if it becomes part of public record of course.)

The authors of biographies of Watson and Crick (the scientists credited with discovering the double helix structure of DNA) told Wade that the newly found letters from Crick’s personal documents don’t really add anything new to the historical record of the research that led up to the double helix discovery, but do add personal anecdotes to the rivalry that existed between the researchers at the time.

The correspondence also added a bit to the sympathy that I feel for Rosalind Franklin. She is a researcher who was working on finding the structure of DNA, and she had done all the research and documented everything that she needed to unravel the structure — she just didn’t realize the significance. Watson and Crick are the ones that took Franklin’s basic research and realized that DNA has a double helix structure. I’ve always felt that Franklin got gypped when they were giving out the Nobel Prizes, so I feel for her, she was so close! The snippets from the letters in Wade’s article just reminded me of that.