Genomics

Blaine Bettinger has an absolutely wonderful post where he compares his results for type 2 diabetes from 23andMe and DeCODEme. I really liked his post and I appreciated the way he showed the data from the two companies and elaborated on their interpretation of his genotype and his risk. Interestingly, his story goes beyond a simple relationship, where one base changes, one amino acid changes, and voila! you've got the disease. Bettinger describes what happens when there are changes in ... Read more
An NSF post on Twitter this morning described an interesting study from the University of Pennsylanvia and Cornell University, that found that some people who call themselves "African Americans" may only be 1% West African, according to their DNA. The University of Pennsylvania press release contains other interesting findings as well. 365 individuals were studied and 300,000 genetic markers were examined. Some of the findings were:
  • If you're African American, the genes most likely to have an African origin are those on your
  • ... Read more

You might think the coolest thing about the Next Generation DNA Sequencing technologies is that we can use them to sequence long-dead mammoths, entire populations of microbes, or bits of bone from Neanderthals.


... Read more
One of the interesting things I learned today was that many people are calling for the genome sequences of the chimps and Macaques to be finished. This is especially amusing because the human genome isn't quite done. We're primates, too! Why not finish our genome? [I blame these new-found revelations on Twitter. Despite my youngest daughter's warning that only old people use Twitter, I've joined my SciBlings and taken the plunge. (you can even follow me! @digitalbio). Now, I get to indulge my geeky tendencies while waiting ... Read more
Warfarin, a commonly used anti-clotting drug, sold under the brand name of Coumadin, has a been a poster child for the promise of pharmacogenomics and personalized medicine. The excitement has come from the idea that knowing a patient's genotype, in this case for the VKORC1 and CYP2C9 genes, would allow physicians to tailor the dose of the drug and get patients the correct dose more quickly. And it seems obvious that a test that would allow doctors to predict your ability to metabolize warfarin, would be a great thing, right?

No more delays! BLAST away!

Time to blast. Let's see what it means for sequences to be similar. 

First, we'll plan our experiment.  When I think about digital biology experiments, I organize the steps in the following way: 

           A.  Defining the question

B.  Making the data sets

           C.  Analyzing the data sets

D.  Interpreting the results

I'm going intersperse my results with a few instructions so ... Read more

We had a great discussion in the comments yesterday after I published my NJ trees from some of the flu sequences. If I list all the wonderful pieces of advice that readers shared, I wouldn't have any time to do the searches, but there are a few that I want to mention before getting down to work and posting my BLAST results. Here were some of the great suggestions and pieces of advice; 1. Do a BLAST search. Right! I can't believe I didn't do that first thing, I think the ... Read more

Watching the chIPs roll in, then I watch them roll away again, I'm just sitting on the DNA, wasting time (sung to the tune of "Sitting on the dock of the bay" by Otis Redding) Hesselberth et.al. recently published a paper about digital genomic footprinting that blew me away because it has so much potential. The authors used DNAse I and Next Generation DNA Sequencing to map every site in the yeast genome where a protein might be sitting. Since I used to do similar kinds of experiments, albeit on a much, much smaller scale, this sort of publication boggles my mind. ... Read more
For the past few months, the shake-up that began with Next Generation DNA Sequencing has been forcing me to adjust to a whole new view of things going on inside of a cell. We've been learning things these past two years that are completely changing our understanding of the genome and how it works and it's clear we're never going back to the simple view we had before. What's changed? The two most striking changes, to me at least, are the new views of the way the genome is put together and what the cell does with the information. They just don't assemble chromosomes like ... Read more
What do the missing Romanov children, genetically engineered humans, financial risk taking, and poop have in common? You can read about all these topics from this month's Gene Genie carnival at Mary Meets Dolly. Who would have thought that mutations could be so much fun? Read more

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