The DNA Network |
| Gene Essence: what bad personal genomics looks like [Genetic Future] Posted: 29 Jun 2008 07:35 PM 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 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. |
| (Common) genetic vigilance [www.cancer-genetics.com] Posted: 29 Jun 2008 05:31 PM CDT Just wrote some notificaion on commercial tests in my “genetic testing” section: IMPORTANT NOTE. Some commercial tests for moderate/low cancer risk genetic predisposition are not verified/supported by independent experts or scientific evidence. Please consider these links with common sense and vigilance. Take care         |
| Sequencing the Cacao Tree Genome [The Genetic Genealogist] Posted: 29 Jun 2008 05:26 PM CDT Although it's not really genetic genealogy, this story was too interesting to pass up. Mars food company announced on Friday that it is partnering with IBM and the Department of Agriculture to sequence and analyze the entire cocoa genome. Mars will provide more than $10 million and will make the sequencing and analysis results freely accessible through the Public Intellectual Property Resource for Agriculture. Unfortunately for those of us that love chocolate, the cacao tree is under attack. According to an article in the Washington Post, "West Africa, which produces 70% of the world's cocoa, has been hammered by bad weather in the past few years." Additionally, the cocoa industry in Brazil has been almost completely destroyed by a fungus known as witches' broom. The cocoa genome is roughly 400 to 500 million base pairs, compared to 3 billion in the human genome. As a result, the scientists involved in the project estimate that it will take a year to sequence the cocoa genome. |
| Somatic mutations in cancer and genetic syndromes [www.cancer-genetics.com] Posted: 29 Jun 2008 03:38 PM CDT As for clinical geneticist, traditionally concerned more with germline (hereditary) mutations and disease, it might be strange to search through somatic mutation (or acquired) databases. But it is obvious that understanding of cancer genetics can not be limited to only germline or somatic mutations - it must be combined approach. And then you start to think in systemic way, or in other words, you think in pathways or patterns (pretty much the same way as main character from D. Aronofsky’s notorious “Pi” Anyway, currently I’m gliding through Ras-MAPK signaling pathway and in a future some posts will be related to it. Interestingly, lot of things in genetics are connected or in other ways, as a friend of mine once stated, “traditional genetics is dead” Just take a look: Ras-MAPK pathway is probably one of the most upregulated pathway in sporadic cancers. And there are bunch of syndromes with inherited altered mutations in a genes from there:
Among other symptoms, Neurofibromatosis type 1 have up to 13% risk for developing maligancy (mostly for MPNST), Costello syndrome have about 17% increased risk of cancer (particularly rhabdomyosarcomas, neuroblastomas and bladder Ca), in Noonan there is increased risk for juvenile myelomonocytic leukemia. Therefore lot of attempt must taken to perform targeted screening for these patients. LEOPARD (which is allelic for Noonan s. and stands for lentigines, ECG anomalies, ocular hypertelorism, pulmonic stenosis, abnormal genitalia, retarded growth and deafness) and CFC syndrome seems do not have increased cancer risk. For somatic mutation in cancer invaluable tool seems to be COSMIC database - Catalogue of Somatic Mutation In Cancer by Wellcome Trust institute. COSMIC is designed to store and display somatic mutation information and related details and contains information relating to human cancers. Enjoy.         |
| Building scientific communities [business|bytes|genes|molecules] Posted: 29 Jun 2008 01:59 PM CDT
I will start with something I have quoted all too often
That quote by Jon Udell, channeling Jeff Jonas is one that, to me at least, defines what the modern web is all about. Too many people tend to put the people first, but in the end without common data to commune around, there can be no communities. Science is an intellectual pursuit, whether it is formal academic science or just casual common interest. That’s where all the tools available today come into the picture. The data has always been there. Whether at the backend, or at the front end, we can think about how to get everything together, but being able to discovery and find some utility is very important. One of the reasons the informatics community seems to thrive online, apart from inherent curiosity and interest in such matters, is that we have a general set of interests to talk about, from programming languages, to tools to methods, to just whining about the fact that we spend too much time data munging. Successful life science communities need that common ground. In a blog post, Egon talks about JMOL and CDK. Why would I participate in the CDK community, or the JMOL one? Cause I have some interest in using or modifying JMOL, or finding out more about the CDK toolkit and perhaps using it. Successful communities are the ones that can take this mutual interest around the data and bring together the people. So my advice to anyone building a scientific community (the one that jumped out at me during the workshop was the EcoliHub) is to think about what the underlying data that could bring together people is first. Data here is used in a general sense. Not just scientific raw data, but information and interests as well. Then trying and figure out what the goals are that will make these people come together around the data and then figure out what the best mechanism for that might be. Don’t put the cart before the horse. In most such cases, you need a critical mass to make a community successful, to truly benefit from the wealth of networks. In science that’s often hard, so any misstep in step 1, will usually end up in a community that has little or no traction.  |
| Medicine 2.0 carnival at Highlight HEALTH 2.0 [ScienceRoll] Posted: 29 Jun 2008 12:04 PM CDT The 27th edition is up at the Highlight HEALTH 2.0! Check out all the posts and news about the world of medicine 2.0 and health 2.0. Thank you, Walter Jessen, for hosting Medicine 2.0! Medicine 2.0 is a blog carnival about the impact of web 2.0 on medicine and healthcare.  Medicine 2.0 editions so far:
The next edition is due to be published on the 13th of July 2008 Scienceroll. Submit your blog article to the next edition of medicine 2.0 using our carnival submission form. And read about this interesting and emerging field here.         |
| Homosexual behavior due to genetics and environmental factors [Think Gene] Posted: 28 Jun 2008 08:49 PM CDT Homosexual behavior is largely shaped by genetics and random environmental factors, according to findings from the world’s largest study of twins. Writing in the scientific journal Archives of Sexual Behavior, researchers from Queen Mary’s School of Biological and Chemical Sciences, and Karolinska Institutet in Stockholm report that genetics and environmental factors (which are specific to an individual, and may include biological processes such as different hormone exposure in the womb), are important determinants of homosexual behavior. Dr Qazi Rahman, study co-author and a leading scientist on human sexual orientation, explains: “This study puts cold water on any concerns that we are looking for a single ‘gay gene’ or a single environmental variable which could be used to ’select out’ homosexuality - the factors which influence sexual orientation are complex. And we are not simply talking about homosexuality here - heterosexual behaviour is also influenced by a mixture of genetic and environmental factors. The team led by Dr Niklas Långström at Karolinska Institutet conducted the first truly population-based survey of all adult (20-47 years old) twins in Sweden. Studies of identical twins and non-identical, or fraternal, twins are often used to untangle the genetic and environmental factors responsible for a trait. While identical twins share all of their genes and their entire environment, fraternal twins share only half of their genes and their entire environment. Therefore, greater similarity in a trait between identical twins compared to fraternal twins shows that genetic factors are partly responsible for the trait. This study looked at 3,826 same-gender twin pairs (7,652 individuals), who were asked about the total numbers of opposite sex and same sex partners they had ever had. The findings showed that 35 per cent of the differences between men in same-sex behavior (that is, that some men have no same sex partners, and some have one or more) is accounted for by genetics. Rahman explains: “Overall, genetics accounted for around 35 per cent of the differences between men in homosexual behavior and other individual-specific environmental factors (that is, not societal attitudes, family or parenting which are shared by twins) accounted for around 64 per cent. In other words, men become gay or straight because of different developmental pathways, not just one pathway.” For women, genetics explained roughly 18 per cent of the variation in same-sex behavior, non-shared environment roughly 64 per cent and shared factors, or the family environment, explained 16 per cent. The study shows that genetic influences are important but modest, and that non-shared environmental factors, which may include factors operating during fetal development, dominate. Importantly, heredity had roughly the same influence as shared environmental factors in women, whereas the latter had no impact on sexual behavior in men. Dr Rahman adds: “The study is not without its limitations - we used a behavioral measure of sexual orientation which might be ok to use for men (men’s psychological orientation, sexual behavior, and sexual responses are highly related) but less so for women (who show a clearer separation between these elements of sexuality). Despite this, our study provides the most unbiased estimates presented so far of genetic and non-genetic contributions to sexual orientation.” Source: Queen Mary, University of London Josh says: I’m glad studies like this are coming out (pun not intended). Once someone’s neurological structure is such that they’re gay, then it cannot be changed; the same goes for someone who is straight. I think many aspects of intelligence work this way as well - there is a proportionally smaller genetic component, but environmental factors during neurological development play the largest role. |
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