Sunday, October 26, 2008

The DNA Network

The DNA Network

Evidence Based Healthcare and Baseball [The Tree of Life]

Posted: 26 Oct 2008 05:15 PM CDT

Love the Op Ed piece in the Friday New York Times entitled "How to take American Healthcare from Worst to First."  First, one reason I love this article is it is discussing how we need to move to more "Evidence Based" medicine.  You may be amazed to know that much of medicine is not evidence based but that is the sad truth.  When I first heard about how not all medicine was evidence based medicine (in a talk by David Cox when I was a grad. student) I was blown away.  Anyway, the article is worth a read from this point of view.  

More amazingly is the author list -- Billy Beane (general manager of the Oakland A's), Newt Gingrich, and John Kerry.  What a combination.  They make the argument that medicine needs a wholesale change in the way it is done just like baseball is shifting to more evidence based decisions.  It is a nice analogy.  Too bad the current administration believes that simply thinking about something is the equivalent to evidence.  And also too bad that McCain-Palin seem to be following in the trend of Bush to not hold "evidence" in high regard.  I wonder what Newt (who is a big science and technology advocate) thinks of the recent anti-science push of the Republicans in power.

What lessons can we learn from teaching with a wiki? [Discovering Biology in a Digital World]

Posted: 26 Oct 2008 02:28 PM CDT

Experimenting with on-line worksheets

I know some people who always teach their classes the same way, semester after semester, year after year.. Not me. I always want to experiment and try new things.

This fall, I'm experimenting with using a wiki in the classroom, in addition to my blog. This wont be my first wiki experience. We've long used wikis where I work, and I've used them to collaborate with people in different locations, but this is the first time that I'll try one in a teaching situation.

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Getting RESTive [business|bytes|genes|molecules]

Posted: 26 Oct 2008 01:27 AM CDT

I am getting frustrated by the number of people calling any HTTP-based interface a REST API.

Those words come from the man who put REST on the map, one Roy Fielding in a bit of a rant against what people call REST today. The post is worth reading for anyone who is into the REST architecture (or isn’t).

Also wanted to point to a couple of responses to Roy’s post. Sam Ruby, who co-authored the book that exposes most of us to REST, is amused by people’s attempts to try and figure out what Roy is saying.

You have to read Leigh Dodd’s post as he channels WALL-E to present his understanding of REST.

Me, I am still trying to get my head around Roy’s post (his writing style isn’t exactly one that lends itself to easy understanding). The one thing that’s clear is this part

if the engine of application state (and hence the API) is not being driven by hypertext, then it cannot be RESTful and cannot be a REST API

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Press Conference Video Footage featuring the PGP-10 [The Personal Genome]

Posted: 23 Oct 2008 01:22 PM CDT

After an all day meeting of talks and discussion, the PGP-10 participated in a press conference. NECN has some video footage from that event:

Scot Yount. Researchers intend to build online DNA database. NECN, October 21, 2008.

Mr. Green Genes glows on video [Discovering Biology in a Digital World]

Posted: 23 Oct 2008 11:47 AM CDT

This video from WDSU shows Mr. Green Genes, the transgenic kitty, in the dark and in the light.

There's also an interview with Dr. Betsy Dresser, who very briefly talks about the work at the Audubon Center for Research on Endangered Species.

Other than clips of the cat, and Dr. Dresser, the video mostly shows people taking frozen samples out of liquid nitrogen, but there's an interesting bit towards the end where they show a pipette transferring material into the nucleus of an egg cell. Mr. Green Genes is certainly a cute cat.

glowing_kitty.pngYou can see more pictures from the Times Picayune: here and here.

Thanks go to David Ricks for sending links to the photos and video.

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DNA Testing on Unusual Samples: Paraffin Blocks Now Accepted [DNA Testing Blog]

Posted: 23 Oct 2008 10:39 AM CDT

DDC is pleased to announce that it is now accepting paraffin-embedded tissue samples as a source of DNA for paternity testing. This may be very useful in cases where the alleged father or child is deceased or missing, and a medical examiner, coroner, or hospital pathologist has previously collected tissue samples and preserved them in [...]

PGP volunteers note: it's hard to hide your APOE status [Genetic Future]

Posted: 23 Oct 2008 10:22 AM CDT

When James Watson's genome sequence was publicly released earlier this year, Watson famously kept only one region of his DNA a secret - the region encoding the APOE gene, which contains common variants that contribute substantially to the risk of late-onset Alzheimer's, and also affect predisposition to other diseases.

A recent article in the European Journal of Human Genetics shows something that shouldn't have come as a surprise to anyone familiar with human genetics: simply removing the APOE gene was not enough to prevent someone from inferring whether or not Watson carries the riskier versions of this gene, because other markers around the gene can also indirectly convey this information through the magic of linkage disequilibrium.

The authors kindly don't reveal Watson's APOE status, and in fact note that they warned Watson prior to publishing their paper so that he had time to take appropriate actions. He has since responded by removing an additional 2 million bases around the APOE gene from his public sequence.

That action largely removes the possibility of inferring his risk genotype using linkage - in fact, the authors note with dry Australian understatement that the removal of 2 million bases is "likely excessive". Watson could have used linkage information from the HapMap project to delineate the smallest required region, but apparently decided that overkill was the best policy.

It's worth noting that once we have complete genome sequences from sufficient individuals it will be straightforward to determine which DNA positions provide linkage-based information about a particular risk polymorphism (in a specific population, at least). That would allow the clean excision of only those bases that are absolutely required, thus having a smaller impact on research into the rest of the genome. (Of course, that relies on at least some people releasing their APOE sequence into the public domain, even if it turns out to carry the riskier version - I guess it's lucky for us we have anonymous genome sequencing projects like 1000 Genomes.)

The whole episode must be raising questions in the mind of some of the Personal Genome Project volunteers as they consider the prospect of releasing their own genome sequences to the world (participant number 8 has already raised the prospect of redacting his APOE sequence, while Misha Angrist is reserving the right to hold back, well, anything). Are there genes they should be hiding? If so, how much sequence do they need to delete? Ultimately, how do projects like the PGP reconcile the desire for partial genome privacy with the need to get sequences out there in the public domain to further genomic research?

Mind you, given the quality of the sequence data released so far, they probably don't need to worry too much for the moment...

Subscribe to Genetic Future.

Dale R Nyholt, Chang-En Yu, Peter M Visscher (2008). On Jim Watson's APOE status: genetic information is hard to hide European Journal of Human Genetics DOI: 10.1038/ejhg.2008.198

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