genomics
sporte | December 18, 2007How do you go about researching a genetic disease?
This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio.
A bit of background
Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the conversation turns to Woody, and someone asks the question that no one wants to touch. Does Arlo's girlfriend know about Huntington's? ...dead silence... Now, I did see the movie quite a few years ago, so my…
mikethemadbiologist | December 12, 2007Earlier this week, I attended the International Human Microbiome Consortium Meeting (the human microbiome consists of the organisms that live on and in us). I'm not sure to make of the whole microbiome initiative, but one thing is clear to me: this is being driven by the wrong group of scientists.
Instead of being directed by biologists (medical primarily) who have devised a set of important questions, and want to use the power of high throughput genomics, including metagenomics which sequences of all the DNA in a specimen--bacteria, viruses, fungi, protozoa, and, yes, human (which raises…
mikethemadbiologist | December 10, 2007Since I'm attending a human microbiome meeting today, I'll repost this question about the utility of metagenomics:
NIH, in about six months, will release a huge sum of money to fund the study of the human 'microbiome': those microorganisms that live on or in us. One of the things that will be done with this money is metagenomics which is "the study of genomes recovered from environmental samples as opposed to from clonal cultures." (In this case, the samples would be fecal, vaginal, your mouth, etc.). In other words, we can sample the 'community' of genomes (or perhaps we should call it the…
sporte | December 5, 2007If you like ham and bacon, you might be interested in this. GenomeWeb reports that researchers at the University of Barcelona have developed an assay that tests 46 SNPs and can be used to trace the origin of your pork dinner.
According to GenomeWeb, the test identifies both the breed and origin of the animal.
The university and the company said meat traceability is necessary to ensure consumer safety, particularly in cases of infectious disease outbreaks or accidental feed contamination.
No more doubts about the home of your Jamón.
evolgen | December 5, 2007There are two recent genetics related posts on other blogs that evolgen readers might find interesting:
First, check out Query Gene (via ScienceRoll). This web-ap allows you to couple a nucleotide blast search with a Google search for a term related to your blast query. Here is how the creators describe it:
Query Gene is a web-based program that searches for information about genetic sequences on the web. It is distinctive because it is not limited to a single database, but instead captures genetic information on the entire Internet using Google. Query Gene works by taking a gene sequence in…
evolgen | December 4, 2007
I previously described where in a genome we would expect to find sexually antagonistic genes. Briefly, depending on whether a gene is male-biased or female-biased and whether beneficial mutations are dominant or recessive, we can predict whether these sexually antagonistic genes will be on X chromosomes or autosomes. As I mentioned in that post, the theoretical results can only be translated into realistic predictions if we have reliable estimates of the relevant parameters. We do not have such estimates, but we can study the distribution of sex-biased genes throughout genomes. The results…
sporte | December 3, 2007'Tis the holiday season and, according to ancient lore, the time when miraculous events are most likely to take place.
One of those well-known and miraculous events of ancient days was the birth of a son to a young girl, who, although she was married (Okay, I'm not sure about this part of the story) she was said to be a virgin and the birth to be a miracle.
Hmmm.
How do you think the news would be received if that sort of thing happened today?
Certainly, if the young girl were to produce a grilled cheese sandwich with a burn spot that vaguely resembled a woman in a robe, someone might be…
evolgen | November 27, 2007I came across two press releases yesterday, entitled:
Entire Yeast Genome Sequenced
and
University of Toronto scientists map entire yeast genome
Upon reading the first, I thought, hasn't the entire genome of Saccharomyces cerevisiae already been sequenced? And haven't other yeast genomes been sequenced as well? What in the world could they be referring to? Did yet another yeast species gets its genome sequence? Does that really warrant a press release (sorry Jason)? And the second made me think that the person in charge of titling the press release decided that genome sequencing is synonymous…
sporte | November 26, 2007GenomeWeb reports that Rite Aid drug stores on the West coast are now selling kits for doing paternity tests. The kits are made by Sorenson Genomics in Utah.
Sorenson Genomics calls it the "peace-mind-test." Really!
Each kit contains a swab for collecting cheek cells from the inside of your mouth and a container for mailing the sample to the lab.
As far as I can tell, you buy the kit for $29.99, take a sample, fill out the consent forms, and mail the sample to Sorenson along with the $119 lab fee.
Maybe I'm too imaginative, but I'm a little puzzled by some of the information that wasn'…
sporte | November 19, 2007The genie is out of the bottle. Personal genomes are not just for Venter and Watson anymore.
Three competing companies, 23andme, Decode, and Navigenics are betting that you want to do a little better than reading your horoscopes and playing with tea leaves. They think that you want to know something about your destiny and take control of your future. And when I look at the 23andme web site, I want it, too. I want it so badly, it makes me drool.
But is it really such an unequivically good thing?
There's been a long-standing debate between companies and at least some scientists and the…
sporte | November 14, 2007Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread.
Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used to look at ancestry.
Genetic markers in the mitochondrial DNA are used to trace ancestry through the maternal line and markers on the Y chromosome can be used to learn about one's father.…
evolgen | November 13, 2007Is it just me or does every analysis that looks for over-represented gene ontology (GO) terms turn up transcription factors? It doesn't matter if the study is looking for genes under positive selection or something else. It just seems like transcription factors are enriched in every dataset.
sporte | November 9, 2007Last year I wrote about an experiment where I compared a human mitochondrial DNA sequence to primate sequences in the GenBank. Since I wanted to know about the differences between humans, gorillas, and chimps, I used the Entrez query 'Great Apes' to limit my search to a set of sequences in the PopSet database that contained gorillas, bonobos, chimps, and human DNA.
A week ago, I tried to repeat this experiment and...
It didn't work.
All I saw were human mitochondrial sequences. I know the other sequences match, but I didn't see them since there are so many human sequences that match…
evolgen | November 7, 2007What happens when I mention a paper describing two more Drosophila genomes? Well, I get a comment telling me that the 12 Genomes Papers have gone live over at Nature. They have provided a nifty 12 Genomes Portal for us to navigate the articles published by Nature based on data from the 12 Genomes Project. Now, these aren't the only papers published from the 12 Genomes Project -- look for 12 Genomes Papers in the November issues of Genetics (currently not web-available), PLoS Genetics (also not up on the website), and the December issue of Genome Research.
The 12 Genomes Papers include two…
evolgen | November 7, 2007The world of genomics is changing. It was initially about sequencing the genome a single representative individual from a particular species. Now, there's a large focus on polymorphism -- that is, sequencing multiple individuals from a single species to study the genomic variation in that species. That's well under way in humans, with HapMap and various other projects designed to generate DNA polymorphism data on a genome-wide scale.
That approach has made its way to Drosophila genomics with the publication of a paper describing polymorphism across the entire genome of D. simulans, a sibling…
sporte | October 28, 2007Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome.
Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out who else shares our bodies, and lives in our skin, in our stomachs, and other places where the sun doesn't shine. Craig Venter used metagenomics when he sailed around the world and sequenced DNA samples from the Sargasso Seas.
In this…
sporte | October 26, 2007We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles.
The general process is this:
1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is good, and measure how good it is, but it cannot turn bad data into good data. And, there's no point in wasting time with…
sporte | October 21, 2007Welcome Bio256 students!
This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a subject that you can really grasp without getting your fingers dirty. So, this course will include a lot of hands-on work.
My friend and collaborator at Johns Hopkins University has given me data sets from the past three years and we…
sporte | October 16, 2007A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much.
I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million.
That was an estimate, of course. But what did it really cost?
Genome Technology asked J. Craig himself. In the October 2007 issue of GT, JCV estimates that the cost from the first Celera human genome project (guess who?) was about $100 million and that the cost of his most recent genome project was at least $70 million.…
evolgen | October 16, 2007Previous entries:
Part 1 - Introduction
Part 2 - The Backstory
Part 3 - Obtaining Sequences
Part 4 - Obtaining More Sequences
Part 5 - Examining the Outgroups
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 6 of this series (Evolutionary Relationships) can be found below.
Evolutionary Relationships
While we were probing the outgroup genomes for copies of aldolase genes using TBLASTX (Examining the Outgroups), we discovered that there are two excellent matches to aldolase genes in the honeybee,…