The DNA Network |
| Coming soon to a SNP panel near you? [genomeboy.com] Posted: 26 Jun 2008 08:07 PM CDT Will Saletan parses last week’s paper on sexually antagonistic selection as an explanation for the persistence of male homosexuality through the ages:
Bring on the genome-wide association studies… |
| Comp Sci SINS of Biologists [Think Gene] Posted: 26 Jun 2008 07:46 PM CDT Bits per BaseA commenter asked why nucleotide bases don’t take 7 bits to store. NO! 7 bits is the encoding for ASCII characters, which are used to store literal “A T C G”s in a text editor. There are 4 bases, so one only need 2 bits (22 = 4 bases). These bases could be numbered like this: 00 = A 01 = G 10 = C 11 = T This encoding further has the convenient property that the bits can be inverted to get the complementary DNA strand. Storing bases as ASCII is OK for small, human readable files, but otherwise, it’s a gross waste of storage, bandwidth, and processor resources (about a 350% waste). AbbreviationsThere’s a joke that biologist’s don’t have any new math, so they invent vocabulary to keep others out of their field. Josh will disagree because “biologists don’t use the Internet” and “base 2 is for nerds,” but PLEASE, define all your acronyms and unit abbreviations in a glossary! I was reviewing “A Short Guide to the Human Genome” by Cold Spring Harbor Lab Press, and in a table of chromosome sizes, the data is measured as Mb (with no explanation). What is “Mb?” DATA: “Mb” means “megabits,” which is 220 bits. Each base is two bits, so 219 = 524288 bases per unit “Mb.” BIOLOGY: “Mb” means “megabases,” or 1,000,000 bases per unit “Mb.” Either interpretation is valid, and this is a serious problem as biology and computation continue to merge. If NASA and Lockheed Martin can bungle units at the cost of a $327MM Mars Climate Orbitor extraterrestrial face plant, you can certainly bungle a genomic experiment due to mislabeled units, too. |
| A Phylogenomic Study of Birds Reveals Their Evolutionary History [HENRY » genetics] Posted: 26 Jun 2008 07:23 PM CDT Today’s Science sees the publication of a phylogenomic study of 196 bird species, which has some rather marked differences to the traditional phylogenies of bird species. Abstract says -
Abstract is here. Much news coverage will be forthcoming, I suspect, and I’ll link to some of these as they come through. Update: GrrlScientist has covers the paper excellently (although, not enough phylogenetic details for my liking :) |
| ABC, Misinformation and Government Regulation [The Gene Sherpa: Personalized Medicine and You] Posted: 26 Jun 2008 06:59 PM CDT I have to comment on George Stephanopoulos. ABC news tonight covered the whole drama in California.....But they really didn't. In fact they gave 20 seconds (approx) to the fact that the government... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| MD, finaly… [www.cancer-genetics.com] Posted: 26 Jun 2008 05:11 PM CDT Apologize for such long silence - was finishing my residency. And it is done - already received MD (clinical genetics). Now searching for the best way to practically realize my interest in familial cancer genetics - and to set up service which is virtually non existent in Lithuania. Hopefully, July will bring what I wish and move to a new working place, which will be more creative and simply better.         |
| Palm PCR: Finally, Biotech Has Its Own iPod. [] Posted: 26 Jun 2008 04:45 PM CDT
Check out the Palm PCR gadget from Korea’s Ahram Biosystems. We saw this at Bio2008 and we couldn’t keep our hands off of it. Flip it open, juice the micropores with your glass pipette, and press play. This is the kind of Blade Runner-esque personal biotechnology that gets us all excited. Comes in three nifty colors! Wow! We want one!
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| Biotechnology Trade Show Toys: Bio2008 Conference Exhibition Hall Booth Bait. [] Posted: 26 Jun 2008 04:20 PM CDT
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| Finally, High Througput Sequencing put to good use [Next Generation Sequencing] Posted: 26 Jun 2008 02:50 PM CDT Today, a U.S. Department of Agriculture team, funded with more than $10 million from Mars Inc., announced that they will start sequencing the cocoa genome. The results are likely to help in the battle against cocoa plant diseases and, much more importantly, they could also lead to better-tasting chocolate. A lot of people would probably also [...] |
| AMA looks at paying donors for organs [Mary Meets Dolly] Posted: 26 Jun 2008 02:35 PM CDT Thanks to Bioethcs.com, I found this MSNBC article that frankly scares me:
This is disturbing, not because I do not want all the people waiting for transplants to get organs, but because I worry about what a financial incentive for organs would do to the declining respect for human life. If I have said it once, I have said it a million times, once we exploit one member of our species for parts, then the rest of us will follow. If human embryos are commodities, then we, and consequently our organs, become commodities as well. |
| Inter-Plant Communication [Bayblab] Posted: 26 Jun 2008 02:35 PM CDT After hearing about the plot of "The Happening", I wondered how much evidence there is for inter-plant communication. Surprisingly there is quite a bit. The most interesting of which is the use of chemicals to attract carnivorous predators of herbivores. Check out a summary of the evidence for inter-plant communication. From the Figure Legend of the picture: Plants respond to herbivory with the emission of chemical cues above and below ground, which can elicit responses in (1) carnivorous enemies of the herbivores, (2) herbivores and (3) neighbouring plants. The plant–plant interactions comprise interactions among conspecifics and heterospecifics. The red broken arrow represents herbivore attack on a plant; the blue arrows represent the emission of chemical cues that affect other organisms. The thickness of the blue arrows indicates the relative knowledge of the interactions. |
| Combinging two of my favorite things - chocolate and genomes [The Tree of Life] Posted: 26 Jun 2008 02:28 PM CDT Well, the Mars company has really done it now (see Unwrapping the Chocolate Genome -from washingtonpost.com). They are planning to sequence the cacoa genome. Genomes and chocolate. Man are they going to get every bioinformatics person I know to apply to help out with this project ... Some little notes on the project:
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| Genomic Medicine and Warfarin Dosing: Webcast [ScienceRoll] Posted: 26 Jun 2008 12:17 PM CDT Steve Murphy at Helix Health is ready to organize the second webcast about genomic medicine. The first one focused on breast cancer and was fascinating.
Now they will focus on warfarin dosing. According to the American Food and Drug Administration, health care providers can use genetic tests to improve their initial estimate of what is a reasonable dose for patients (details here).
I encourage you to register here. The topics they plan to cover:
The speakers:
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| Sacred Heart Radio Interview [Mary Meets Dolly] Posted: 26 Jun 2008 11:23 AM CDT
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| Urban Birdwatching: Red-winged Blackbird [Bayblab] Posted: 26 Jun 2008 09:27 AM CDT  The Birds is one of my favorite Hitchcock movies (apparantly it's being remade in 2009). Bird attacks aren't that uncommon, particularly if you live in a nesting area for the Red-winged Blackbird. This common species (IUCN: Least Concern) inhabits grassy areas, both dry and wetlands. The males of the species (pictured) have distinctive red shoulders, giving the bird its name. Females are a brown-black colour and lack the distinctive red markings. If you live or commute near a Red-winged Blackbird nest, watch the skies: During nesting season, as some of our readers can tell you first hand, the males become fiercely territorial and will swoop down and peck at unsuspecting pedestrians or cyclists if they should wander too close. Nesting season runs from late May to mid-July. |
| Posted: 26 Jun 2008 07:36 AM CDT California and New York regulators have been in the news lately (such as here and here), with their attempts to crack down on the nascent direct-to-consumer genetic testing industry. These states argue that companies like 23andMe, Navigenics, and several others, are offering unproven and unlicensed clinical tests directly to consumers. Are the services offered by these companies clinical tests, subject to the normal regulations of other clinical tests? Should the government be able to stop you from getting your DNA sequenced? The answer to the second question is a flat-out no. The government has no legitimate reason to prevent you from getting genotyped. The technology used by these personal genetics companies is very good - in the future, this technology will be cheaper and cover more variants in your genome, but what is available right now is very good. And there are reasonable non-clinical reasons to get yourself sequenced, out of sheer curiosity, or for genealogy purposes, for example. More importantly, this sequence data is a permanent resource for you. Although we may not have very good clinical tests for complex genetic diseases right now, we'll have them in the future, and any DNA sequencing you get done now will be suitable for these future analyses. Once you have your raw DNA data in hand, it's there if you need it in the future. So, as things stand now, the genotyping serviced offered by 23andMe, DecodeMe, and Navigenics have enough non-clinical use to justify themselves, and these services should not be blocked by state regulators. But simply offering people DNA sequencing is one thing - making disease risk predictions is another. |
| Gene Essence: what bad personal genomics looks like [Genetic Future] Posted: 26 Jun 2008 07:17 AM CDT  I mentioned yesterday that one of the companies recently targeted by the California health department was an outfit called Gene Essence. Gene Essence is a 23andMe-style genome scan service launched back at the end of March (covered by Hsien) by Biomarker Pharmaceuticals, a company that aims to develop "genomic and proteomic aging-intervention technologies" to "provide interventions that will extend a healthy human lifespan by slowing the process of aging, and delaying the onset of age-related diseases."I haven't heard anything about Gene Essence since its launch was announced, so I was curious to see how the service had evolved. The first signs were good: the company is using the Affymetrix 6.0 SNP array, a solid platform that provides information on around 1 million genetic variants throughout the genome - although I can't find any information on where the testing is actually being performed. Unfortunately, it's all downhill from there. The company thoughtfully provides a demo report allowing customers to see what they'll be getting for their $1,195 - and based on what that shows me I can't imagine anyone purchasing this service, especially given that both 23andMe and deCODEme both offer infinitely superior products at a lower price. To see just how bad Gene Effects' service is, first check out the 23andMe and deCODEme demo versions, here and here. Now take a look at the demo page where Gene Effects displays your "genetic susceptibility" for a set of different common diseases. Apparently the demo sample has a genetic susceptibility of 100% for atherosclerosis; but does that mean he is 100% likely to get atherosclerosis, that he has the maximum possible genetic risk for the disease, or simply that he has the riskier version all of the known polymorphisms associated with the disease? It's impossible to tell from the page itself - and if you click on the bar for that condition you end up on this absolutely incomprehensible "detail page", which is no help at all. OK, so let's try reading the manual. The "How to Read This Report" page is unhelpful, but the "Sample Reports" page provides some useful detail - and after a bit of digging it becomes clear that the "genetic susceptibility" score is an indicator of how many of the known risk variants a person carries, scaled by the relative effect of each variant on disease risk. We're supposed to be using the "adjusted trend" column, which "takes into account the fact that for each condition, a different proportion of the population will have a genetic trend value lower than yours". This doesn't make it any clearer what this actually means in terms of risk prediction; but rather than provide a useful clarification the page goes on to lay out a series of generic disclaimers (e.g. "SNPs are simply markers for the disease or condition and do not necessarily carry any predictive value in terms of assessing one's susceptibility to a given disease"). In other words, the company provides a series of alarming and confusing predictions, and then simply tells you they don't necessarily mean anything. There's no estimate of the individual's actual risk of the disease (as you would find in a 23andMe, deCODEme or Navigenics report), no indication of the fraction of the total variance in disease risk that is captured by the polymorphisms in your report, and no reference to whether the described associations are actually reliable and well-validated (for instance, it gives you information on 14 different variants associated with bipolar disease, not one of which has actually been independently replicated). That renders the information essentially meaningless and potentially seriously misleading for the typical customer. By this stage anyone that Gene Essence somehow convinced to purchase their product would be desperately looking for a way to get some return on their $1,195 purchase. Well, they could always download their raw data and run it through Promethease, which would give them access to the information on each of their genetic variants from the public SNPedia database - except when they click on the "Complete SNP Data" page they'll find no straightforward way to download their entire data-set, but rather a box in which they can type a SNP identification number and download their genotypes one by one. A million of those is going to take some time, even if this feature was actually working (which it isn't, at least for the demo account). In summary: based on the demo (which is all a potential customer would have to go on) this service is currently seriously bad; I find it hard to imagine that any potential personal genomics customer would pick it over its vastly more professional-looking, rigorous and user-friendly rivals. The fact that Gene Essence actually charges more for its service than 23andMe is utterly absurd. This is an example of what happens when a company tries to jump on the genome scan bandwagon without investing sufficiently in the knowledge-base and user interface required to present extremely complex data to a customer with a limited understanding of genetics. This hardly inspires any further confidence in the company: A person who declined to identify herself and who answered the phone at the number listed on Gene Essence's Web site said she didn't know anything about that business or Robert Danielzadeh, identified by the state as its chief executive.I suggested yesterday that the best outcome in California might be a compromise, in which respectable personal genomics companies are allowed to continue operating (with slightly increased regulatory oversight) while amateurish efforts like Gene Essence - and downright scams like the nutrigenetics companies - slide quietly out of existence. While I don't agree with Steve Murphy that a doctor's explicit permission should be required to authorise a genome scan, there should be a minimum standard of validation and information reporting - and the current version of Gene Essence falls well below that standard.  Subscribe to Genetic Future. |
| How Much Data is a Human Genome? Not Much. [Think Gene] Posted: 26 Jun 2008 03:43 AM CDT I recently noted in Napster of Medicine that an entire human genome would fit on a music CD. How much data IS a human genome?
(1 human genome) * (3,080,400,000 bases / 1 human genome) * (2 bits / 1 base) * (1 byte / 8 bits) * (1 MB / 1,048,576 bytes) = 734.4 MB per uncompressed human genome. Easily enough to fit on a 700 MB with basic file compression like gzip. Actually, while writing this post I invented a technique to get the file size down to about 10MB, but I need to file a patent before disclosing. Sorry. (yes, 10MB, as in, the size of an mp3 song) NOTE: Commenter “neandrothal” noted that this is the size of a haploid human genome. Humans are diploid: they two of each autosome and two sex chromosomes. So this is the size of a reference haploid human genome, not a complete human individual genome, which would be twice as much data. (2 music CDs) Thanks, neandrothal! [1] Scherer, Stewart. 2007. A Short Guide to the Human Genome. 6. MB = megabytes Mb = megabase |
| forgive the politics… [Epidemix] Posted: 26 Jun 2008 12:15 AM CDT …but this op-ed in the New York Times, by Gary Hart, really strikes me as a profound framing of what the future bodes. Regardless of your politics, you have to consider his list of challenges that the next president - whoever he may be - will face:
As a framing device, this is a brilliant list. We really are at a point in the nation & in the world where our politics have fallen far out of step with reality. Just consider, for instance, the stuff that this blog typically trafficks in - genomics, public health, infectious disease, science in general. To my mind, these are the things that will force our future, yet how often do any of them come up in political dialogue? Viral pandemics, for instance, are a perfect example of what our politicians should be protecting us against - a perfect role for government, really, where the free market will be unlikely to react - yet how often does the topic come up? Anyway, as I say, forgive the politics, but definitely worth a read. |
| The Upside of High Food Prices [Highlight HEALTH] Posted: 26 Jun 2008 12:04 AM CDT As the price at the gas pump continues to climb, so does the cost of diary, grain and meat products. Why? Because increasing fuel prices make it more expensive to grow, harvest, transport, process and package food. Indeed, food costs rose by 4 percent in 2007, the highest annual increase since 1990 [1]. In 2008, the U.S. Department of Agriculture predicts the consumer price index for all food will increase 4.5 to 5.5 percent as retailers continue to pass on fuel costs to consumers [1]. There is, however, an upside to the increasing cost of food. Michael Pollan, author of the book In Defense of Food: An Eater’s Manifesto, argues that as the price of fuel and commodities rise, nutritionally questionable, high-profit ingredients like high-fructose corn syrup will also cost more [2]. And as prices rise, consumer demand for products containing such ingredients will fall. This is good news for producers of sustainable foods — locally grown produce and locally raised meat — that don’t rely on fossil fuels. Locally grown foods are fresher, better tasting and healthier than food that’s been shipped or flown in from further away (we won’t even discuss heavily processed foods). Sustainable food producers haven’t felt the increasing cost of fuel like factory farms, making them more economically competitive in today’s marketplace. Even so, a recent Ohio State University study found that grocery store shoppers are willing to spend more for locally grown foods [3]. The study was published in the May issue of the American Journal of Agricultural Economics. Researchers evaluated data from 477 surveys at 17 Midwestern locations, including retail grocery stores, on-site farm markets and farmers markets. In the survey, shoppers were presented with two baskets of strawberries under 80 different combinations of price, freshness, farm location and farm type. After presenting the options, shoppers were asked which basket of strawberries they would buy. The average retail shopper was willing to pay 48 cents more for strawberries produced locally (in the study, local meant grown within Ohio). Shoppers at farm markets were willing to pay even more at 92 cents extra. Freshness was also found to be important factor for shoppers. Retail shoppers were willing to pay 54 cents more for fresh produce that was recently harvested. Again, farm market shoppers were willing to pay even more at 73 cents extra. According to Marvin Batte, Ph.D., a co-author of the study and professor of Agricultural, Environmental and Development Economics at Ohio State University [4]:
The Washington Post ran a great story earlier this week about the benefits of fruit and vegetables. To Produce Good Health, Bite Into Fruit and Veggies reveals some of the reasons why these food provide so many health benefits. The article also suggests that fresh fruits and vegetables are inexpensive and more accessible over the summer months:
Nobody likes to pay more for food. But if increased food costs force people to find locally grown alternatives and eat healthier, there is indeed an upside to the high price of food. For more information on farmers markets, family farms and other sources of sustainably grown food in your area where you can buy locally grown produce and grass-fed meats, visit LocalHarvest.org. What are your concerns about the cost of food? How are you dealing with increasing food prices? References
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| Closing the gap between fish and land animals [Think Gene] Posted: 25 Jun 2008 10:47 PM CDT New exquisitely preserved fossils from Latvia cast light on a key event in our own evolutionary history, when our ancestors left the water and ventured onto land. Swedish researchers Per Ahlberg and Henning Blom from Uppsala University have reconstructed parts of the animal and explain the transformation in the new issue of Nature. It has long been known that the first backboned land animals or “tetrapods” - the ancestors of amphibians, reptiles, birds and mammals, including ourselves - evolved from a group of fishes about 370 million years ago during the Devonian period. However, even though scientists had discovered fossils of tetrapod-like fishes and fish-like tetrapods from this period, these were still rather different from each other and did not give a complete picture of the intermediate steps in the transition. In 2006 the situation changed dramatically with the discovery of an almost perfectly intermediate fish-tetrapod, Tiktaalik, but even so a gap remained between this animal and the earliest true tetrapods (animals with limbs rather than paired fins). Now, new fossils of the extremely primitive tetrapod Ventastega from the Devonian of Latvia cast light on this key phase of the transition. “Ventastega was first described from fragmentary material in 1994; since then, excavations have produced lots of new superbly preserved fossils, allowing us to reconstruct the whole head, shoulder girdle and part of the pelvis”, says Professor Per Ahlberg at the Department of Physiology and Developmental Biology, Uppsala University. The recontructions made by Professor Ahlberg and Assistant Professor Henning Blom together with British and Latvian colleagues show that Ventastega was more fish-like than any of its contemporaries, such as Acanthostega. The shape of its skull, and the pattern of teeth in its jaws, are neatly intermediate between those of Tiktaalik and Acanthostega. “However, the shoulder girdle and pelvis are almost identical to those of Acanthostega, and the shoulder girdle is quite different from that of Tiktaalik (the pelvis of Tiktaalik is unknown), suggesting that the transformation from paired fins to limbs had already occurred. It appears that different parts of the body evolved at different speeds during the transition from water to land”, says Per Ahlberg. Source: Uppsala University Josh says: It’s too bad DNA doesn’t really get preserved in fossils. While reading this type of thing though, I can’t help but think how this is just another nail in the coffin for the creationists, such when a new “species” of E. coli recently evolved in the lab. However, even in light of such strong evidence, they still just call it fraudulant, even to the author’s face. |
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