Thursday, October 30, 2008

The DNA Network

The DNA Network

Genes are at the heart of a new journal [The Navigator - Navigenics Blog]

Posted: 31 Oct 2008 12:08 AM CDT

Michael Nierenberg, M.D.

imageSitting in my mailbox last week was a sign of the times.

No, it wasn't a political brochure or a notice about homes for sale in my neighborhood. It was a scientific journal, tightly wrapped in plastic, attesting to the evolving importance of genetics in the delivery of medical care.

"Circulation: Cardiovascular Genetics," a journal of the American Heart Association, was launched this month to much fanfare, and has started arriving in the offices of physicians and the labs of researchers.

As the title suggests, the new publication will focus on the genetics of the cardiovascular system, exploring population genetics and biomarkers, pharmacogenetics, molecular genetics, genomics, proteomics, metabolomics and systems biology, among other pertinent topics.

In short, it delves into what those of us already firmly entrenched in the genetic testing industry have long known is the future of healthcare:  genomics and personalized medicine.

The Full mtDNA Genome of Ötzi is Sequenced (Twice?) [The Genetic Genealogist]

Posted: 30 Oct 2008 07:25 PM CDT

Großglockner seen from the southwest. The Groß...

Image via Wikipedia

Ötzi the Iceman is the popular name for a 5,000 year-old mummy discovered frozen in the ice of the Alps in 1991.  Studies of the Iceman has revealed an immense amount of information about him, including details of his life, his death, and his culture. 

Although Ötzi’s mtDNA has previously been studied, researchers had only examined short segments which suggested that his mtDNA belonged to Haplogroup K.  A new paper in Current Biology (subscription only darn it) details Ötzi’s full mtDNA genome for the first time:

"Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations."

The full sequence (which has been deposited in GenBank with accession number EU810403) was then compared to 115 published full mtDNA Haplogroup K sequences.  The comparison suggests that Ötzi belonged to a previously uncharacterized subclade of Haplogroup K, now termed K1ö.

Strange Conclusions - Otzi has NO living relatives?

Now, as any genetic genealogist knows, when your mtDNA doesn’t match anyone you conclude that you have to wait until more people get tested.  This is especially true if you believe that your relatives would be in continental Europe - for some reason those continental Europeans have very little interest in genetic genealogy.  The authors point out that Ötzi’s mtDNA line might have died out in the past 5,000 years, but they also acknowledge that the comparison database was small and further testing in Europe might reveal more examples of this new subclade.

As Kambiz points out in the comments to his post on this new paper, the media isn’t quite as careful as the authors of the paper.  See "Iceman May Have No Living Relatives" by National Geographic, for example.  Although they do a decent job of discussing the article and all the aspects I mention, the title is so bad that it makes my teeth hurt.

Or Does he?

But see this article: "DNA shows Otzi the Iceman has kin."  According to the article, Alan Cooper - head of the University of Adelaide’s Australian Center for Ancient DNA - has also sequenced Otzi’s mtDNA and stated that "We have found someone very, very closely related."  I’m looking forward to comparing the mtDNA genome obtained by the two research groups.  Will they be the same?

A few points to remember:

  • Ötzi’s mtDNA belongs to a previously undiscovered subclade of Haplogroup K, but there is currently no data to suggest that this subclade has died out in present-day humans.  115 mtDNA genomes barely constitutes a database!
  • Remember that this is only mtDNA testing, which passes only from mother to child.  Even if there is no living person with mtDNA belonging to the K1ö subclade, Ötzi could still have 2 billion direct descendants!

The Paper:  Luca Ermini, Cristina Olivieri, Ermanno Rizzi, Giorgio Corti, Raoul Bonnal, Pedro Soares, Stefania Luciani, Isolina Marota, Gianluca De Bellis, Martin B. Richards, Franco Rollo (2008). “Complete Mitochondrial Genome Sequence of the Tyrolean Iceman” Current Biology, DOI: 10.1016/j.cub.2008.09.028.


Tales from the lab [Discovering Biology in a Digital World]

Posted: 30 Oct 2008 05:15 PM CDT

Reposted in honor of the holiday.

What's it like when you work in the lab on Halloween?

It started out innocently enough.

"Go get some BHK cells," he said, "then transform the cells with these plasmids and use G418 to kill the cells that didn't get transformed."

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what did you think of the Obamamercial? [the skeptical alchemist]

Posted: 30 Oct 2008 05:02 PM CDT

As somebody who is not American... I thought it was so American. It had just the right amount of cheesiness to fly and be received well by the American people. It also reiterated some of the major points of the Obama campaign, and boasted support from people in charge in some of the swing states, as well as a retired general.

The day before, Obama also appeared among the converted as a (satellite) guest on the Daily Show - I have posted a link to the video right below.

Canadian readers, you can watch the interview on the Daily Show here; American readers, on the other hand, can watch the interview here.

On the other hand, here is the infomercial, just in case you missed it last night [link]

The thing I liked the most as a non-American watcher was the way the family portraits were done. These were all people who worked hard and were successful in life according to their own definition of success: some worked for a factory following in the steps of their fathers, another was a widow with children who still managed to keep the family steady, and so on. They were very real, and at the same time very average - really, I have to say, they were not even middle class, but working class families who seemed to do just fine before, but whose vulnerabilities were uncovered by the deteriorating economic situation.

I could have done away with the cheesy music and the wheat field, but somehow that appeals just to that classic American iconography so often recalled by Sarah Palin and the Republican ticket, and will maybe have a good emotional impact with the undecided voters.

But I am afraid he will never manage to convince that remaining 10% of Americans who still think he is an Arab... that no matter his roots, he grew up in America as an American.

Last but not least, I am not sure of how well this immense campaign expense will be perceived. America has not seen this kind of infomercial since maybe the Eighties, and spending $4 mil per spot might not necessarily fly so well with those same people who are struggling right now, and who he is appealing to.

What did you think of the infomercial?

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23andMe named Time's invention of the year [Genetic Future]

Posted: 30 Oct 2008 04:50 PM CDT

Personal genomics company 23andMe has been named Time magazine's Invention of the Year. The fairly lengthy citation notes that "[a]lthough 23andMe isn't the only company selling DNA tests to the public, it does the best job of making them accessible and affordable."

It's yet more public exposure for the personal genomics industry, pushing recreational genetic testing closer towards becoming a mainstream pursuit.

I note that 23andMe has wasted no time giving the award a central position on their home page.

HT: the ever-readable Attila.

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Changing habits with technology [business|bytes|genes|molecules]

Posted: 30 Oct 2008 04:31 PM CDT

Lots to blog about, so I will just put up something that came to me in the flight from LA to SEA that I took earlier today. First time this sort of occurred to me was a couple of weeks ago at work.

Like many geeks, I carry a moleskine notebook around with me (a small one in my travel bag, a bigger one at work) to scribble down notes just in case, especially in situations where a laptop might be inappropriate or inconvenient. With the iPhone and Evernote, I seem to have stopped doing that. On the plane today, I was writing down all kinds of ideas, except that I wasn’t writing, but typing and this time, the notes would actually be legible afterwards.

Just an example of how our devices and web services are changing our habits, especially as we get better at the interface of online and offline, of syncing across devices, etc. Just the other day, I saw someone launch a big compute job in the cloud using the iPhone as the launch interface. Fascinating times.

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Take that atta boy Back! Time to use sound judgement against 23andMe. [The Gene Sherpa: Personalized Medicine and You]

Posted: 30 Oct 2008 10:13 AM CDT

I would like to take the Atta Boy back. Huh? Yes, the one I gave 23andMe. Yes I commended them for destroying a DNA sample and confirming that they are only testing your DNA, one time and then...

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RECOMB Systems Biology Conference [The Seven Stones]

Posted: 30 Oct 2008 09:01 AM CDT

The RECOMB Satellite on Regulatory Genomics, RECOMB Satellite on Systems Biology, and DREAM reverse engineering conferences are currently held jointly at the MIT, in Boston.

Some of the talks are currently 'live-blogged' on FriendFeed and can be followed below or in the "Recomb-Sat/DREAM 08" room.

Genome scans for the whole family: 23andMe research director talks about genotyping her kids [Genetic Future]

Posted: 30 Oct 2008 07:36 AM CDT

One of the ethical quandaries raised by direct-to-consumer genetic testing is the possibility that customers may send in DNA samples for analysis from other people who haven't provided informed consent - prospective spouses, for instance, a la Gattaca - and then use that genetic information for nefarious purposes. In the past, personal genomics company 23andMe has responded to this possibility by arguing that it's not really the company's responsibility to prevent its customers from performing illegal acts; they have also (quite convincingly) pointed out the difficulties of extracting 2 mL of saliva from an unwilling victim without arousing suspicion.

However, there is one class of potential customers who are legally unable to provide informed consent, but who could usually be convinced quite easily to give up a tube full of spit: customers' children. And in this case 23andMe's view seems to be extremely relaxed - they even have a non-judgmental warning about the difficulty of collecting the required saliva from infants under 3.

In fact, judging from a recent entry on 23andMe's corporate blog The Spittoon, the company is actively encouraging customers to bring their own kids into the happy 23andMe family. This is a bold move, and one that is likely to provoke considerable controversy (and outrage). But rather than shying away from this debate 23andMe seems determined to confront the issues head-on.

The post is by Stanford Assistant Professor Joanna Mountain, who heads a genetic anthropology research group and also serves as senior director of research at 23andMe. In the post Mountain describes the process of registering her two sons (aged 7 and 12) for analysis of several hundred thousand genetic markers at 23andMe - and while she acknowledges the ethical issues associated with analysing children's genetic data, such concerns don't seem to have weighed heavily on her mind:

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The Retail DNA Test Named the #1 Invention of 2008 by TIME Magazine [The Genetic Genealogist]

Posted: 30 Oct 2008 06:56 AM CDT

Image representing 23andMe as depicted in Crun...

Old 23andMe logo via CrunchBase

The latest issue of TIME Magazine lists the top 50 inventions of 2008, and the invention of the year is the Retail DNA Test.  The article is mostly about the product currently offered by 23andMe.  From the article:

“We are at the beginning of a personal-genomics revolution that will transform not only how we take care of ourselves but also what we mean by personal information. In the past, only élite researchers had access to their genetic fingerprints, but now personal genotyping is available to anyone who orders the service online and mails in a spit sample. Not everything about how this information will be used is clear yet — 23andMe has stirred up debate about issues ranging from how meaningful the results are to how to prevent genetic discrimination — but the curtain has been pulled back, and it can never be closed again. And so for pioneering retail genomics, 23andMe’s DNA-testing service is Time’s 2008 Invention of the Year.”

As the past year has shown, many people are opposed to this type of product for various reason, including that the test doesn’t involve genetic counseling, it isn’t ordered or interpreted by your personal doctor, and issues of genetic discrimination.  However, the article doesn’t shy away from these issues and provides a brief but interesting look into both sides.

This award highlights the fact that we are in the midst of a vast genetic revolution.  We are the first generation to be able to peer into the DNA inherited from thousands of previous generations.  Yes, the road will undoubtedly be bumpy, but I’m looking forward to the ride.  And so, I give my congratulations to 23andMe for this honor.

Powerpoint: Lose the bullets [Bitesize Bio]

Posted: 30 Oct 2008 05:40 AM CDT

Powerpoint is a double-edged sword. There’s no doubt it makes putting together a presentation easier. Those who worked with slides, overhead projector films and the like in the years B.P. (Before Powerpoint) will testify to that.

But Powerpoint’s ease of use also makes it easy to abuse, and bullet points are the most abused feature of all.

Bullet points should be used very sparingly, if at all, in Powerpoint and only ever to highlight crucial information.

But unfortunately most people spray bullet points around in Powerpoint like a gung-ho machine-gunner rather than a well-trained sniper, and that’s guaranteed to make your Powerpoint more of a hinderance than a help in trying to get your message across.

The most common reasons for bullet point overuse are that the presenter:

1. Plans his/her talk in Powerpoint itself, typing the main points out like a list
2. Wants to use the Powerpoint content to prompt him/herself during the presentation.
3. Thinks that saying what they are saying will somehow be emphasised by repeating in in text form on the screen.

All of these completely miss the point of Powerpoint.

Firstly, Powerpoint is not a planning tool and so it’s best not to use it as one. Planning is better done using pen and paper, well away from Powerpoint. Only then can you distill out the main points you are trying to get across and work out an appropriate way to illustrate them.

Secondly, Powerpoint should never, never be used as an autocue. Well, I suppose you could use it in that way, but you’d be better turning off the projector and giving a speech only presentation.

Your presentation should be designed from the audience’s perspective, not from your own, in such a way that it helps your audience understand your message.

Thirdly, It’s easy to parrot your presentation content as series of bullet points, but how does duplicating what you are saying in text help your audience?

It doesn’t. It only distracts your audience.

Instead you should design your slides with the idea that your audience should get most of it’s information from what you say, and that information should be enhanced (not just repeated) by the content of your presentation.

So, next time you create a Powerpoint presentation, consider leaving out the bullet points and replacing them with visual aids that enhance what you are saying.

Things like graphs, illustrations, even photos are ideal. The trick is to think about the key message you are trying to get across and focus the slide on that, rather than all of the individual points you are talking about.

If you can do that, and get good at it, your audiences will be much more receptive (and impressed).

Do you agree?

Destroy the Sample....Save the World! [The Gene Sherpa: Personalized Medicine and You]

Posted: 30 Oct 2008 05:15 AM CDT

I am so very proud of 23andMe. There was some big issue with their consent and policy, in fact something I expressed grave concern about. That was the indication that 23andMe/Google would own your...

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the return of the Molecular and Cell Biology Carnival [the skeptical alchemist]

Posted: 30 Oct 2008 01:09 AM CDT

I have been away from the internet for a while, and as a consequence I was unable to organize the Carnival for the summer months. However, fall is here, and so is a nice broadband internet connection!

BlogCarnival is having problems again, so I suggest we stay away from it altogether. October is almost over, but November is coming up, and the next edition of the Carnival will be hosted on
November 9.

If you are interested in hosting, please consult the hosting guidelines and then leave a comment under this post. If you are interested in contributing your post, please consult the submission guidelines, and also leave a comment, with your post's URL, right here.

The upcoming editions will be published on the second Sunday of every month, and I am looking for hosts…so do get in touch!

Last but not least: you can find the latest edition of the MCB Carnival over at ScienceRoll! Thanks, and apologies for the late link!

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The technology gap in action: Second Life vs. College Instructors [Discovering Biology in a Digital World]

Posted: 29 Oct 2008 10:47 PM CDT

A bit of unsolicited advice for workshop presenters

I'm currently in Washington, D.C. at the Advanced Technology Education conference co-sponsored by National Science Foundation and the American Association of Community Colleges. The people here are an interesting mix of instructors teaching high tech stuff and instructors who sometimes seem more advanced in age than technological know-how.

Mind you, people are doing amazing things. Some colleges have nanotechnology, some microfabrication, some biotechnology, computer forensics, but some of the high tech programs are managed by some very low tech people.

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Richard Dawkins off the deep end [adaptivecomplexity's blog]

Posted: 29 Oct 2008 09:13 PM CDT

At long last I'm getting a paper out the door, which means my latest blog column's been delayed.

In the mean time, John Hawks (whose blog you should be reading) has some priceless stuff on Richard Dawkins' war on Harry Potter:

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On selection and disability []

Posted: 29 Oct 2008 09:17 AM CDT

With the help of the Personal Genetics Education Project’s Dana Waring Bateman, I have teamed up with Dr. Chris Korey at the College of Charleston. Both of us are teaching mavericky, genomicky classes this semester and Chris asked if his students could post on genomeboy in response to a series of questions he and Dana developed regarding the use of preimplantation genetic diagnosis to select for or against particular traits. “Anything to crowd out the spam,” I told him. I have modified the questions slightly to make them a bit bloggier.

  • When we select for or against a trait, does it change how we as a society view those traits?
  • How will the proliferation of sequenced personal genomes change our thoughts on what constitutes a disability?
  • How and whether genetic and genomic information ultimately leads to the expression of human traits remains unclear. How should that affect our use of this technology?
  • Should the government restrict the use of this technology for positive and/or negative selection?  Why or why not?
  • Is PGD a good idea? Make your case.

I confess I haven’t thought a whole lot about PGD, but I will say this: I see the emergence of this technology as inevitable and I think any attempts to ban it or drastically curtail it will fail. If parents want to select for or against a highly penetrant mendelian trait and they can’t do it in the US, they will go to China or Russia or the Cayman Islands or the UK. And it will only get cheaper. Thus, I think it would behoove regulatory agencies to get off their patooties and try to figure this out. The time for hand-wringing is long past.

Having said that, I worry about what we don’t know regarding the epigenetic effects of PGD and other assisted reproduction technologies. When we’re tiny balls of cells, we are extremely vulnerable. When we mess with a preimplantation embryo’s environment, we are likely to alter that embryo’s patterns of cell division, gene expression and/or morphology.

UPDATE: Will Saletan discusses the advent of increasingly sophisticated prenatal testing and its implications.

Please have at it in the comments.

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