MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'genomics'. Sat, 03 Sep 2011 01:52:59 +0100 http://www.medworm.com/index.php?rid=5096365&cid=t_104578_109_f&fid=38950&url=http%3A%2F%2Fwww.shockmd.com%2F2011%2F08%2F03%2Fwhy-personal-genomics-didnt-live-up-to-the-expectations%2F Buffer George Church talks about where the future of personal genomics is headed and what research has yielded so far. Decoding the human genome did not yield what people initially expected. In this lecture George Church talks about where the future of personal genomics is headed and what research has yielded so far. Buffer   No related posts. (Source: Dr Shock MD PhD) Dr Shock MD PhD blogs http://www.medworm.com/rss/comments.php?id=5096365 Wed, 03 Aug 2011 05:49:06 +0100 5096365 http://www.medworm.com/index.php?rid=5077688&cid=t_104578_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fcan-pharmacogenomic-tests-help-to-improve-public-health%2F2011.07.29 Adverse drug events are a serious public health problem. Consider the following facts: an estimated 82% of American adults take at least one medication and 29% take five or more; 700,000 emergency department visits and 120,000 hospitalizations are due to adverse drug events annually; $3.5 billion is spent on extra medical costs of adverse drug events annually; at least 40% of costs associated with adverse drug events occurring outside hospitals can be prevented. How can genomics help? Pharmacogenomics is the study of genetic variation as a factor in drug response, affecting both safety and effectiveness. The intended applications of pharmacogenomics research include identifying responders and non-responders to medications, avoiding adverse events, optimizing drug dose and avoiding unnece... Better Health blogs http://www.medworm.com/rss/comments.php?id=5077688 Fri, 29 Jul 2011 12:00:10 +0100 5077688 http://www.medworm.com/index.php?rid=4953226&cid=t_104578_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FgVptTyL-3Q8%2F [via Teun Boekhout] This year looks like another great lineup of speakers for the EMBO Comparative Genomics of Microorganisms: ‘Understanding the Complexity of Diversity’ 15-20 Oct 2011 Sant Feliu de Guixols, Spain. Andrew Allen J. Craig Venter Institute US Anders Blomberg Göteborg University SE Chris Bowler École Normale Supérieure FR Gertraud Burger University of Montreal CA Bernard Dujon Institut Pasteur FR Toni Gabaldón CRG, Barcelona ES Ursula Goodenough Washington University US Michael Gray Dalhousie University CA Joseph Heitman Duke University US Christiane Hertz-Fowler University of Liverpool UK Regine Kahmann Max Planck Institute DE Patrick Keeling University of British Columbia CA Nicole King UC, Berkeley US Edda Klipp Humboldt Univers... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4953226 Mon, 20 Jun 2011 20:18:12 +0100 4953226 http://www.medworm.com/index.php?rid=4841830&cid=t_104578_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F05%2F18%2Fhow-to-create-a-partial-ucsc-genome-mysql-database%2F File under: simple, but a useful reminder UCSC Genome Bioinformatics is one of the go-to locations for genomic data. They are also kind enough to provide access to their MySQL database server: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A However, users are given fair warning to “avoid excessive or heavy queries that may impact the server performance.” It’s not clear what constitutes excessive or heavy but if you’re in any doubt, it’s easy to create your own databases locally. It’s also easy to create only the tables that you require, as and when you need them. As an example, here’s how you could create only the ensGene table for the latest hg19 database. Here, USER and PASSWD represent a local MySQL user and password with full privileg... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4841830 Wed, 18 May 2011 04:54:10 +0100 4841830 http://www.medworm.com/index.php?rid=4829301&cid=t_104578_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FlA5ZtOLK-m0%2F Good morning, everyone. A spot of rain is falling on the Pharmalot corporate campus this morning, but our spirits remain sunny. After all, as the Morning Mayor used to say: Every brand new day should be unwrapped like a precious gift. So while you tug on the ribbon, please join us for a cup of stimulation and take a moment to scan the news of the world. Hope your day goes well and you remain dry… Merck To Close Inspire HQ And Lay Off Workers (Raleigh News-Observer) Gingrich Says Alzheimer’s Research Will Save US Money (Associated Press) Pfizer Lung Cancer Drug To Get FDA Priority Review (Reuters) Mylan Must Pay $24M To Ipsen Over Pill Marketing (Bloomberg News) Actos Diabetes Drug Linked To Bladder Cancer (Reuters) Alexion To Expand Plant And Add Jobs In Rhode Island (WPRI) Gla... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4829301 Tue, 17 May 2011 11:52:04 +0100 4829301 http://www.medworm.com/index.php?rid=4775398&cid=t_104578_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fwhy-double-mastectomies-are-popular-watchful-waiting-is-too-difficult%2F2011.05.01 The rise of prophylactic double mastectomy in women with increased risk of breast cancer has been a topic of recent discussion. In particular, this trend has been observed amongst women with the diagnosis of unilateral carcinoma in situ, or pre-invasive breast cancer. While it has been known that in women with genetic cancer syndromes, including BRCA1 and BRCA2, double mastectomy reduces risk, the efficacy of the approach is uncertain in women with other risk profiles, yet more women and surgeons seem to be doing it. Knowing when to test, treat and act is part of art of medical practice. The ability to convey this information effectively is also an art. Both patients and doctors may have a hard time embracing watchful waiting with respect to many forms of cancer and pre-cancer. In the case... Better Health blogs http://www.medworm.com/rss/comments.php?id=4775398 Sun, 01 May 2011 13:00:00 +0100 4775398 http://www.medworm.com/index.php?rid=4714227&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2011%2F04%2Fphylogenetics-and-phylogenomics-for-microbial-genomes.html from Luo et al (2011) in Microbial Population GeneticsGenerally, microorganisms, in particular prokaryotes often lack morphological and behavioral characters amenable to phylogenetic analysis. Such a lack of information in these areas makes gene sequence information the most prevalent source of data for phylogenetic analysis in pre-genomic era. Molecular phylogenetics based on single genes, in particular the small-subunit rRNA (SSU rRNA) , has laid the foundation for a modern classification system, conceptually represented by the 'universal tree of life'. However, phylogenetic trees based on single genes or gene families may show conflict results due to a variety of problem, such as mutational saturation of the single genes and horizontal gene transfer. Consequently, although SSU rRNA gene... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=4714227 Fri, 15 Apr 2011 04:00:12 +0100 4714227 http://www.medworm.com/index.php?rid=4676317&cid=t_104578_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FYgb2d_p5qu4%2F This week’s addition to the virology toolbox was written by Chris Upton Sequence Searcher is a Java program that allows users to search for specific sequence motifs in protein or DNA sequences. For example, it can be used to identify restriction enzyme cleavage sites or find similar sequence patterns among multiple sequences. Most searches run in a few seconds. Sequence Searcher is part of the Virology.ca suite of programs available at the University of Victoria. Help files: Quick start How-to Some of the key features of Sequence Searcher include: Searching through multiple sequences Use of regular expressions or fuzzy search patterns. Searching for patterns on both strands of a DNA sequence Graphical representation of results and ability to save search results It can run on multiple ... virology blog blogs http://www.medworm.com/rss/comments.php?id=4676317 Mon, 04 Apr 2011 19:14:42 +0100 4676317 http://www.medworm.com/index.php?rid=4577940&cid=t_104578_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2011%2F03%2F12%2Freport-from-amia-all-diseases-will-become-orphan%2F The first speaker I heard at the American Medical Informatics Joint Summit was Kenneth Buetow from the National Cancer Institute. In his typical provocative manner, he challenged the audience on the transition day from the Translational Bioinformatics to the Clinical Research Informatics Summits.  He began with promoting the P4 Medicine as the new model for healthcare: personalized, predictive, preemptive, participatory. Although throughout the conference little was articulated on the participatory aspects with one exception. More on that later. Buetow talked about defining cancer on the molecular level and the challenge of the exponential number of patients required to do genetic screening for a single disease. He referred to Pharma 3.0 from the Ernst and Young report on Progressions 20... eHealth blogs http://www.medworm.com/rss/comments.php?id=4577940 Sat, 12 Mar 2011 07:18:27 +0100 4577940 http://www.medworm.com/index.php?rid=4507281&cid=t_104578_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fthe-human-genome-turns-10%2F2011.02.22 The human genome has been around for a bit more than ten years, but on February 15, 2001, the first complete human genome sequence was published. This was nothing short of a revolution within medicine. Since then, great advancements have been made in our understanding of genetics and its associations with human traits and diseases. Nature is celebrating this tenth birthday with a special titled “Human Genome at Ten.” In it, multiple papers reflect on what we learned and discovered, what is still unknown, and what we can expect for the near future. Best of all, Nature has packaged the special in a free iPad app for everyone to read, which features interactive graphs, videos, and audio commentaries. Nature special: The Human Genome at Ten… iTunes link: Nature Human Genome S... Better Health blogs http://www.medworm.com/rss/comments.php?id=4507281 Tue, 22 Feb 2011 18:00:52 +0100 4507281 http://www.medworm.com/index.php?rid=4477802&cid=t_104578_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2F6skMEuKLIcg%2Fstrategic_plans_and_genome_seq.php This morning I attended a "bloggers-only" conference call with Dr. Eric Green and the folks from the NIH Human Genome Research Institute (NHGRI) to hear about NHGRI's new strategic plan. The new plan represents a shift away from viewing the genome through a lens marked "for research use only" and towards the goal of making the genome useful as a clinical tool. As a consequence, we will see a greater emphasis on funding activities that support clinical work. For example, it's not always clear how variations in the genome are related to disease. NHGRI might fund projects that help sort and categorize this information. It's certainly not clear yet what NHGRI should do to help patients and physicians handle the genetic information onslaught, particularly in the area of personal genomics. Pers... Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=4477802 Mon, 14 Feb 2011 20:36:50 +0100 4477802 http://www.medworm.com/index.php?rid=4455409&cid=t_104578_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F10%2Fconservative-with-a-small-c-research%2F This is really interesting. I’m reading it at work so I can’t tell you if it’s behind the paywall, but I sincerely hope not; it deserves to be read widely: Edwards, A.M. et al. (2011) Too many roads not taken. Nature 470: 163–165 doi:10.1038/470163a Most protein research focuses on those known before the human genome was mapped. Work on the slew discovered since, urge Aled M. Edwards and his colleagues. The article includes some nicely-done bibliometric analysis. I’ve lifted a few quotes that illustrate some of the key points. More than 75% of protein research still focuses on the 10% of proteins that were known before the genome was mapped Around 65% of the 20,000 kinase papers published in 2009 focused on the 50 proteins that were the ‘hottest’ in... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4455409 Thu, 10 Feb 2011 02:02:48 +0100 4455409 http://www.medworm.com/index.php?rid=4450452&cid=t_104578_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FsUICiC0b8Ac%2F Announcing an upcoming conference in October. Comparative Genomics Of Eukaryotic Microorganisms: Understanding The Complexity Of Diversity It will be held in Sant Feliux, Spain October  15-20, 2011. The website has more details including an impressive slate of speakers. I can attest to it being a great meeting from my attendance 2 years ago. A great venue and excellent speakers and plenty of time to linger and discuss ideas and research over meals and coffee breaks.   (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4450452 Tue, 08 Feb 2011 18:00:05 +0100 4450452 http://www.medworm.com/index.php?rid=4285301&cid=t_104578_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FrYtx4OOtgDY%2F Though a bit cliche, I think the metaphor of “presents under the tree” of some new plant pathogen genomes summarized in 4 recent publications is still too good to resist.  There are 4 papers in this week’s Science that will certainly make a collection of plant pathogen biologists very happy. There are also treats for the general purpose genome biologists with descriptions of next generation/2nd generation sequencing technologies, assembly methods, and comparative genomics. Much more inside these papers than I am summarizing so I urge you to take look if you have access to these pay-for-view articles or contact the authors for reprints to get a copy. These include the genome of biotrophic oomycete and Arabidopsis pathogen Hyaloperonospora arabidopsidis (Baxter et al). Wh... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4285301 Thu, 23 Dec 2010 16:11:50 +0100 4285301 http://www.medworm.com/index.php?rid=4229035&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F12%2Fcomparative-genomics-of-metabolic-pathways-in-microbial-genomes.html from Luo et al (2011) in Microbial Population GeneticsUnderstanding the regulatory mechanisms should allow the examination of engineering pathways with pre-determined expression patterns (i.e. expression is activated by a given compound or in a specific environmental or physiological condition). Metabolic pathways have evolved to execute their function efficiently, while tolerating perturbations, such as changes in environmental parameters or in the physiological status of the cell. Below we describe some of the databases and programs for integrated analyses of metabolic pathways.KEGGKEGG (Kyoto Encyclopedia of Genes and Genomes) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking ge... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=4229035 Sat, 04 Dec 2010 05:00:08 +0100 4229035 http://www.medworm.com/index.php?rid=4224706&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F12%2Fcomparative-genomics-microarray-analyses-technology.html from Luo et al (2011) in Microbial Population GeneticsThe advent of DNA microarray technology has greatly expanded our ability to monitor changes in the abundance of transcripts. Such a development has been a milestone in several areas of microbiology. In clinical microbiology, microarrays are used for microorganism detection and identification and gene-expression analysis. DNA microarrays have allowed us to monitor the effects of pathogens on host-cell gene expression in a much greater depth and on a significantly broader scale than previous single gene studies. The results generated by these studies are complex, and few systematic studies have been carried out to compare results among studies. Comparative transcriptomics - whole genome mRNA transcript profiling using microarrays.Whole-ge... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=4224706 Fri, 03 Dec 2010 12:34:05 +0100 4224706 http://www.medworm.com/index.php?rid=4189707&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F11%2Fanalytic-tools-in-comparative-genomics.html from Luo et al (2011) in Microbial Population GeneticsThe rapid accumulation of bacterial genome sequences has opened up a new field of research, that of comparative genomics. Interpretation of raw DNA sequence data involves the identification and annotation of genes, proteins, and regulatory and/or metabolic pathways. Therefore, there is a natural shift towards the creation of tools for viewing and manipulating data in a comparative genomics context. In addition, genome annotations need to be reprocessed on a regular basis to take into account the newly characterized functions of genes. Furthermore, large-scale functional analyses generate additional data that contribute to the interpretation of genomic data. These considerations are driving the research community to think about how to ma... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=4189707 Mon, 22 Nov 2010 17:23:46 +0100 4189707 http://www.medworm.com/index.php?rid=4133898&cid=t_104578_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F11%2F02%2Finnovation-summit-obesity-diabetes-the-metabolic-crisis%2F This week I attended the Cleveland Clinic Innovation Summit and contributed to the live tweeting of the event. There was substantial discussion of devices in the pipeline and drugs for diabetes but a less optimistic outlook on drugs for obesity with some being shut down by the FDA. The most scientific yet controversial presenter was JefferyFriedman, who referred to his 2009 Newsweek article on “The Real Cause of Obesity” as a summary of his position that most of obesity is genetically determined.  Many referred to the recent prediction posted by the CDC that the current incidence of diabetes being around 10% of the population with the potential of growing to 20 – 30% by 2050. At the end of day two, the annual announcement of Top 10 Innovations. The final day will include... eHealth blogs http://www.medworm.com/rss/comments.php?id=4133898 Wed, 03 Nov 2010 01:51:32 +0100 4133898 http://www.medworm.com/index.php?rid=4121910&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F39444424%2Ftough_fibers_from_transgenic_silkworms.php silk fibers from transgenic wormsA startup company - Kraig Biocraft Laboratories - were able to make made genetically modified silkworms that produce fibers incorporating spider-silk proteins. The product fibers are a lot stronger and flexible and finer than silk made by normal silkworms. Kraig Biocraft believes that they will be able to match the properties of spider silk within the next year and hopes to sell the first generation of fibers to companies that will make stronger everyday silk products. Their ultimate goal ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=4121910 Sun, 31 Oct 2010 04:39:33 +0100 4121910 http://www.medworm.com/index.php?rid=4045278&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F10%2Fkif-6-genetic-findings-useful-medicine.html Way back in 2008 I mentioned an article, which I hoped would pan out. Or at least I hoped it would point the way to a model of PGx research which would be followed by pharma and alike to find associations to help us target the right medication for the right patient.While the similar model followed through with Plavix, the initial study did not. Which is why when the Berkeley Heart Lab guy came last week, I told him I would not be testing for Kif6. It had not been replicated in further GWAS.Heck, I don't even use the 9p21.3 test......Why?A VAP cholesterol panel, a HsCRP, a family history and a blood pressure can help me predict risk much better.The problem and backlash facing DTCG and DTMD genetic test purveyors is the 'Ol "Your million dollar major study now rushed to market has just been ... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=4045278 Fri, 08 Oct 2010 22:37:00 +0100 4045278 http://www.medworm.com/index.php?rid=4045394&cid=t_104578_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FHTtxY7fTDCU%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? And here is something that’s become a regular feature. Send us a photo and we will spotlight a different person each week. This time around, we note that Scrip Intelligence hired Christopher Bowe as US healthcare analyst. Before joining the information service, he worked in strategic affairs at Schering-Plough, and was previously US healthcare correspondent and Chicago co... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4045394 Fri, 08 Oct 2010 12:12:56 +0100 4045394 http://www.medworm.com/index.php?rid=4031293&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F39444424%2Faggressive_skin_cancer_gene_found.php © EmmaLeeSnowCutaneous squamous cell carcinoma (SCC) is an aggressive kind of skin cancer that usually spreads to other parts of the body. Now, according to a study published by the Arizona Cancer Center, Mayo Clinic and the Translational Genomics Research Institute (TGen), he loss of a gene known as INPP5A could predict the onset and track the progression of cutaneous squamous carcinoma. Targeting the said gene - INPP5A - will provide physicians with better ways of preventing and treating this aggressive skin cancer. ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=4031293 Mon, 04 Oct 2010 12:06:24 +0100 4031293 http://www.medworm.com/index.php?rid=3969040&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fpreeclampsiapredicting_metabolic_markers_newly_found.php © mahalieFourteen simple metabolites that predict preeclampsia in early pregnancy with high accuracy have been detected by a team of international scientists. Marked by high blood pressure and excess protein in a pregnant woman's urine after 20 weeks of pregnancy, preeclampsia can lead to serious and even fatal complications for both the mother and the baby when left untreated. At the moment, there is no test that predicts preeclampsia and there is also no cure other than the baby's delivery. Reporting in Hypertension: ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3969040 Tue, 14 Sep 2010 21:50:08 +0100 3969040 http://www.medworm.com/index.php?rid=3954322&cid=t_104578_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F09%2F09%2Fp4-medicine-revolutionizing-healthcare%2F I attended a presentation by Leroy Hood of the Institute for Systems Biology today on P4 Medicine. The 4 Ps are: Prediction Prevention Personalized Participatory In the presentation, he demonstrated studies (in mice) of looking at the complete process of illness: genotype, phenotype including biological networks and molecular machines.  He is even examining the organ specific blood footprints and miRNA as markers of disease progression. He predicts that in the future there will be a virtual cloud of data points for each person, billions of data points for billions of people, and that healthcare IT must prepare to address this. The real core of something like P4 is prediction. The complexity of achieving this level of analysis for many diseases is a challenge. One audience member questio... eHealth blogs http://www.medworm.com/rss/comments.php?id=3954322 Fri, 10 Sep 2010 02:04:34 +0100 3954322 http://www.medworm.com/index.php?rid=3993044&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fgenome-of-streptomyces.html%23unique-entry-id-195 Genome Architecturefrom Ralph Kirby and Carton W. Chen writing in Streptomyces: Molecular Biology and BiotechnologyLinear replicons are relatively uncommon among bacteria and their preponderance among the Actinomycetales, and within the Streptomyces in particular, poses some interesting questions. These novel bacterial replicons are capped by terminal proteins that are covalently bound to the 5' ends of the linear DNA and these terminal structures are directly involved in replicating and protecting the ends of the linear genome. In addition and perhaps related to their linear nature, these genomes are among the largest bacterial chromosomes. As far as can be ascertained at present, these large genomes have a specific organizational structure in terms of their genes. The genome structure ca... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3993044 Wed, 08 Sep 2010 23:00:00 +0100 3993044 http://www.medworm.com/index.php?rid=3876651&cid=t_104578_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fthe-phd-illustrated%2F2010.08.17 I started my Ph.D. in clinical genomics last year and sometimes it really feels like what is shown in this figure. Click HERE for the full series of pictures. *This blog post was originally published at ScienceRoll* (Source: Better Health) Better Health blogs http://www.medworm.com/rss/comments.php?id=3876651 Tue, 17 Aug 2010 20:00:51 +0100 3876651 http://www.medworm.com/index.php?rid=3865464&cid=t_104578_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F-qsv1lAFCb0%2F And so yet another work week will soon draw to a close. And not a moment too soon, yes? This means, of course, the time is drawing near to catch up on sleep, sundry chores and spending time with some of the short people. What about you? Planning a trip to the beach or a big night out? Maybe read a book (or is that called a Kindle these days?) Whatever you do, have a great time and be safe. Catch you soon… Gene Testing May Have Saved Obesity Drug (Reuters) Sharing Data Leads To Progress On Alzheimer’s (The New York Times) Are You Ready For A World Without Antibiotics? (The Guardian) FDA Warns Glaxo’s Lamictal May Cause Meningitis (Associated Press) Roche Faces New Type Of Patent Lawsuit (Indianapolis Business Journal) (Source: Pharmalot) Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3865464 Fri, 13 Aug 2010 11:46:29 +0100 3865464 http://www.medworm.com/index.php?rid=3848910&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FDhhEhj-Px1k%2Flack-of-neutrality-in-bacteria-and.html Pseudogenes, which are in essence regions of the genome that used to be genes but no longer able to produce a functional unit, have long been considered to be models of the genetic equivalent of Switzerland's neutrality. With this assumption of neutrality in hand, researchers have used studies of pseudogenes to better understand what happens to DNA when it is not visible to any form of natural selection. That is, pseudogenes have been thought to be neither harmful (as in, they are not under negative selection) or helpful (i.e., they are not under positive selection).And from this assumption we have supposedly learned about mutation rates and patterns (because if they are neutral then the changes in pseudogenes should be reflective of mutational processes, not selection) as well as all sort... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3848910 Tue, 10 Aug 2010 06:51:58 +0100 3848910 http://www.medworm.com/index.php?rid=3816448&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FLpfJM5_CjjE%2Fhuman-genome-project-oversold-sure-but.html Well, the piling on the human genome project continues, it seems at an accelerating pace.  I think most of this comes from the fact that we are in the range of the 10 year anniversary right now.   Here are some examples of recent stories suggesting the human genome project (or projects, if you count the public effort and Craig Venter's effort as separate) have had little benefit: 7/31/10: The Human Genome Project: 10 Years Later, Progress but Still a Puzzle - WNYC. Interesting piece by Sarah Kate Kramer discussing the limited clinical value of the HGP.  Includes some criticisms of personalized genomic medicine.  7/29/10: Spiegel interview with Craig Venter with the headline "We have learned nothing from the genome".  Has lots of interesting tidbits. &nbsp... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3816448 Tue, 03 Aug 2010 16:18:29 +0100 3816448 http://www.medworm.com/index.php?rid=3790742&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Fhomepage.mac.com%2Fjonathan_eisen%2FPDFs%2F5.Eisen.SNF2.1995.pdf Just got an announcement regarding this challenge: Automated Function Prediction SIG 2011 featuring the CAFA Challenge: Critical Assessment of Function Annotations | Automated Function Prediction 2011 July 15-16 2011, Vienna, Austria Here is a description: CAFA is a community-driven effort. We call upon computational function prediction groups to predict the function of a set of proteins whose true function is sequestered. At the meeting, we will reveal the functions, and discuss the predictions. The CAFA challenge goals are to foster a discussion between annotators, predictors and experimentalists about methodology as quality of functional predictions, as well as the methodology of assessing those predictions. Registration for CAFA starts July 15, 2010 and the CAFA challenge will t... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3790742 Mon, 26 Jul 2010 23:08:52 +0100 3790742 http://www.medworm.com/index.php?rid=3718109&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fviral-sequences-plant-genomes.html%23unique-entry-id-150 Endogenous Viral Sequences in Plant Genomesfrom Pierre-Yves Teycheney and Andrew D.W. Geering writing in Recent Advances in Plant VirologyEndogenous viral sequences from members of two virus families, the Caulimoviridae and Geminiviridae, have been discovered in several monocotyledonous and dicotyledonous plant species. For the most part, these sequences are replication-defective but those capable of causing infection have been discovered in tobacco (Nicotiana edwardsonii), petunia (Petunia hybrida) and banana and plantain (Musa spp.). Activation of endogenous caulimovirid sequences is one of the major impediments to international banana and plantain breeding efforts. Research on endogenous viral sequences in plants is still in its infancy, with little known about the contributions of thes... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3718109 Tue, 29 Jun 2010 23:00:00 +0100 3718109 http://www.medworm.com/index.php?rid=3702972&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fhuman_collagen_production_from_tobacco_plants.php © minnemomResearchers have succeeded in producing a replica of human collagen from tobacco plants, possibly making the production of commercially produced collagen for use in surgical implants and many wound healing devices in regenerative medicine. Currently, commercial collagen is produced from farm animals such as cows and pigs as well as from human cadavers and are thus prone to harbor human pathogens such as viruses or prions and, in the case of human cadavers, may possesses serious ethical issues. Producing human recombinant type I ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3702972 Mon, 28 Jun 2010 01:56:47 +0100 3702972 http://www.medworm.com/index.php?rid=3695182&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fmeningococcus-vaccine.html%23unique-entry-id-124 The First Vaccine Obtained Through Reverse Vaccinology: The Serogroup B Meningococcus Vaccinefrom Jeannette Adu-Bobie, Beatrice Aricò, Marzia M. Giuliani and Davide Serruto writing in Vaccine Design: Innovative Approaches and Novel StrategiesNeisseria meningitidis was isolated over one hundred years when Anton Weicshelbaum identified the causative agent of cerebrospinal meningitis. Since its isolation in 1887, N. meningitidis has been recognized to cause endemic cases, case clusters, epidemics and pandemics of meningitis and devastating septicaemia. Despite over one century since its discovery, scientists have yet to identify a universal vaccine for this deadly bacterium. Although vaccines exist for several serogroups of pathogenic N. meningitidis, serotype B (MenB) has eluded scien... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3695182 Wed, 23 Jun 2010 23:00:00 +0100 3695182 http://www.medworm.com/index.php?rid=3683798&cid=t_104578_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F06%2F22%2F23andme-yes-me-part-3%2F Results! The email is titled “Your Genetic Profile is Ready at 23andMe!” It arrived on June 21, a shade under 5 weeks after sample arrival and well ahead of the estimated 6-8 weeks. This is what we’ve been waiting for. OverviewWelcome to me!On logging in to the 23andMe website, you’re presented with a news feed which confirms that your results are ready. To the left is a navigation menu divided into 4 main sections: My Health, My Ancestry, Sharing & Community and 23andWe. The first 3 are the most relevant with regard to your genomic data. My Health The Health menu has 5 sub-menus: Disease Risk, Carrier Status, Drug Response, Traits and Health Labs. Disease Risk Marker EffectsClicking on “Disease Risk” presents 3 summary tables for elevated, decrease... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3683798 Tue, 22 Jun 2010 06:17:33 +0100 3683798 http://www.medworm.com/index.php?rid=3683582&cid=t_104578_87_f&fid=34902&url=http%3A%2F%2Fwww.futurepundit.com%2Farchives%2F007268.html If you are low in vitamin D it might be due to your genes. An international research consortium has identified four common gene variants that are associated with blood levels of vitamin D and with an increased risk of vitamin D deficiency. The report from the SUNLIGHT consortium – involving investigators from six countries – will appear in The Lancet and is receiving early online release. "We identified four common variants that contributed to the risk for vitamin D deficiency," says Thomas Wang, MD, of the Massachusetts General Hospital (MGH) Heart Center, a co-corresponding author of the Lancet report. "Individuals inheriting several of these risk-associated variants had more than twice the risk of vitamin D deficiency as was seen in... (Source: FuturePundit) FuturePundit blogs http://www.medworm.com/rss/comments.php?id=3683582 Sun, 20 Jun 2010 23:00:00 +0100 3683582 http://www.medworm.com/index.php?rid=3706721&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fbiomarker_for_severity_and_recurrence_of_breast_cancer.php © AmazonResearchers have identified a biomarker in the blood which can predict the severity of breast cancer in patients, distinguish breast cancer patients with a greater risk of disease recurrence, and may enable clinicians to track patients throughout the course of their treatment. The research, funded by Science Foundation Ireland (SFI) and Breast Cancer Ireland (BCI) investigated the protein changes in breast cancer that is resistant to treatment and found a higher level of a protein called HOXC11 and the presence of a secreted molecule ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3706721 Sat, 19 Jun 2010 02:58:29 +0100 3706721 http://www.medworm.com/index.php?rid=3695206&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fsalmonella-evolution.html%23unique-entry-id-99 Evolutionary trends associated with niche specialization as modeled by whole genome analysis of egg-contaminating Salmonella enterica serovar Enteritidisfrom Jean Guard, Devendra Shah, Cesar A. Morales and Doug Call writing in Salmonella: From Genome to FunctionThe mosaic nature of the Salmonella enterica genome facilitates its access to multiple environments. Many large scale genomic events have been described that contribute to the combinatorial complexity of the pathogenic Salmonellae. However, the impact of small scale genetic change occurring at the level of single nucleotide polymorphism (SNP) on the emergence of niche specialization is just now becoming appreciated. A recent review describes concepts behind the evolution that culminated in the remarkable ability of Salmonella enteri... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3695206 Tue, 15 Jun 2010 23:00:00 +0100 3695206 http://www.medworm.com/index.php?rid=3695205&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fsalmonella-pathogenesis.html%23unique-entry-id-100 We describe the molecular basis of Salmonella Typhi pathogenesis, in particular where genomics has contributed to our understanding in the past decade. Potentially important S. Typhi-specific virulence determinants include the Vi polysaccharide capsule, the type IV pilus, and a unique repertoire of fimbria. These may account for key differences in the disease outcome of this pathogen compared with non-typhoidal serotypes. Genome comparison with the closely related serotype S. Paratyphi A identifies a core set of pseudogenes, some of which emerged independently, that may define important features of genome degradation associated with host restriction and pathogenesis of invasive disease. Geo-phylogenetics of S. Typhi constructed from single nucleotide polymorphism data from high throughput ... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3695205 Tue, 15 Jun 2010 23:00:00 +0100 3695205 http://www.medworm.com/index.php?rid=3695203&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fsalmonella-fimbriae.html%23unique-entry-id-102 Fimbrial signature arrangements in Salmonellafrom Sean-Paul Nuccio, Nicholas R. Thomson, Maria C. Fookes and Andreas J. Bäumler writing in Salmonella: From Genome to FunctionThe complement of fimbrial operons held within a genome represents one of the key differentiating features of the sequenced Salmonella serovars and one of the single largest sources of genetic diversity. Generically described as filamentous non-flagellar surface appendages, fimbriae (also known as pili) typically imbue an adhesive trait to the cells expressing them. While much is known about the general biology of fimbrial assembly mechanisms, the role of these structures in Salmonella pathogenesis remains poorly characterized. Here we present fimbrial operon data gathered from the seventeen completed Salmonella g... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3695203 Tue, 15 Jun 2010 23:00:00 +0100 3695203 http://www.medworm.com/index.php?rid=3695202&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fsalmonella-flagella.html%23unique-entry-id-103 New insights into the role and formation of flagella in Salmonellafrom Rasika M. Harshey writing in Salmonella: From Genome to FunctionThe flagellum of Salmonella enterica serovar Typhimurium is the best studied of all flagellar systems. The major function of the flagellum is to enable swimming and chemotaxis in liquid media, and swarming on surfaces. New structural information, along with biochemical, physicochemical and genetic analyses has greatly accelerated our understanding of the self-assembly of this highly sophisticated nano-machine. The study of swarming motility is a relatively new field, but has begun to reveal new roles for the flagellum, new functions for motility genes and new regulatory circuits that control the decision between motility and sessility. Morphological and fun... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3695202 Tue, 15 Jun 2010 23:00:00 +0100 3695202 http://www.medworm.com/index.php?rid=3686834&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fsalmonella-evolution.html%23unique-entry-id-99 Evolutionary trends associated with niche specialization as modeled by whole genome analysis of egg-contaminating Salmonella enterica serovar Enteritidisfrom Jean Guard, Devendra Shah, Cesar A. Morales and Doug Call writing in Salmonella: From Genome to FunctionThe mosaic nature of the Salmonella enterica genome facilitates its access to multiple environments. Many large scale genomic events have been described that contribute to the combinatorial complexity of the pathogenic Salmonellae. However, the impact of small scale genetic change occurring at the level of single nucleotide polymorphism (SNP) on the emergence of niche specialization is just now becoming appreciated. A recent review describes concepts behind the evolution that culminated in the remarkable ability of Salmonella enteri... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3686834 Tue, 15 Jun 2010 23:00:00 +0100 3686834 http://www.medworm.com/index.php?rid=3665702&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fsalmonella-genome.html%23unique-entry-id-97 Comparison of Salmonella genomesfrom Ye Feng, Wei-Qiao Liu, Kenneth E. Sanderson, and Shu-Lin Liu writing in Salmonella: From Genome to Function:Salmonella contains over 2600 known lineages, each with distinct biological characteristics, including differences in the niche in which they dwell and the nature of diseases they may cause in their hosts. Genomic sequence analysis is beginning to reveal the genetic basis that determines the phenotypic differences among them. Comparison of eight sequenced genomes of Salmonella subgroup I lineages, which infect warm-blooded animals including humans, demonstrates that these pathogens share about 90% of their genes (the "core" genome), with the remaining ca. 10% genes being unique to each of the lineages (the "accessory" genome). Prophages and Salmon... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3665702 Tue, 15 Jun 2010 23:00:00 +0100 3665702 http://www.medworm.com/index.php?rid=3658922&cid=t_104578_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2010%2F06%2F14%2Ffda-to-regulate-genetic-testing-by-dtc-companies-like-23andme%2F Direct-to-consumer (DTC) genetic testing refers to genetic tests that are marketed directly to consumers via television, print advertisements, or the Internet. This form of testing, which is also known as at-home genetic testing, provides access to a person’s genetic information without necessarily involving a doctor or insurance company in the process. [definition from NLM's Genetic Home [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=3658922 Mon, 14 Jun 2010 02:25:05 +0100 3658922 http://www.medworm.com/index.php?rid=3655735&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F06%2Fi-am-glad-we-can-all-put-this-behind-us.html As you now may be aware. DTCG is considered a medical diagnostic according to the FDA. I look forward working with companies who may now allow me to use their tests for medicine. The Sherpa Says: If we work together, we can deliver the best preventative and personalized care in the world! (Source: Gene Sherpas: Personalized Medicine and You) Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3655735 Fri, 11 Jun 2010 17:46:00 +0100 3655735 http://www.medworm.com/index.php?rid=3599474&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fdna_vaccine_against_dll4_protein_slows_down_cancer.php © WIkipediascientists at the Karolinska Institutet have a developed a DNA vaccine targeted at a protein known as 'Delta-like ligand 4' (DLL4), which has recently been identified as an important component in regulating the formation of new blood vessels. By blocking the expression of DLL4 in a tumour, new, but non-functional, blood vessels, are formed, slowing down tumor growth. Results from an animal trial have shown that vaccination against DLL4 causes an immunological antibody response to DLL4, hindering the growth of breast cancer in ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3599474 Wed, 26 May 2010 01:04:00 +0100 3599474 http://www.medworm.com/index.php?rid=3590450&cid=t_104578_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F23%2F23-and-me-%25e2%2580%2593-yes-me-%25e2%2580%2593-part-2%2F Sample journey and arrival Spitting across the PacificMy tube of spit arrived at the lab on May 19. Six days door-to-door via Guangzhou, Anchorage and Memphis to LA. 23andMe raw data menuOn arrival, a confirmatory email: “The spit sample you recently submitted to 23andMe for the person listed above has been received by the laboratory and is now pending analysis; the process usually takes 6-8 weeks. You will receive another email notification from us as soon as the data for this sample are ready to be accessed through your 23andMe account.” In the meantime, there’s plenty to explore at the 23andMe website. Anyone can create a demo account, which allows you to explore anonymous sample data to get a feel for what you’ll see when your own sample is processed. Naturally,... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3590450 Sun, 23 May 2010 04:04:41 +0100 3590450 http://www.medworm.com/index.php?rid=3590449&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F05%2Fthomas-goetz-has-wrong-debate-fda.html I think everyone in this space has been way off base as to what the problem is with FDA and Congress wanting to investigate the DTC Genomics companies. The whole mindset is wrong. What I hear from this debate is "It's my data, mine, mine, mine. Gimmee, Gimmee, you can't keep me from my data Big Brother!"From Mr Goetz's Blog"The controversy seems to have stirred the FDA to assert its authority – and that of physicians – over any and all medical metrics." "To me, getting access to this information is a civil rights issue. It’s our data." This is a straw man argument that has been set up to make regulating these companies seem unseemly and an invasion of privacy. IT IS A DEAD WRONG ARGUMENT and I will not stand for it being perpetuated anymore. This is not about getting access to your d... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3590449 Sat, 22 May 2010 18:49:00 +0100 3590449 http://www.medworm.com/index.php?rid=3581780&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F05%2Fhow-bad-can-house-investigation-be-for.html Ok, so you've been summoned to Congress to testify It won't be that bad if you know what you are in for. So let's review.1. A chart listing the conditions, diseases, consumer drug responses, and adverse reactions for which you test;2. All policy documents, training materials, or written guidance materials regarding genetic counseling and physician consultations, including documents regarding what conditions, diseases, drug responses, or adverse reactions trigger the need for genetic counseling or physician consultation, and documents governing communications with consumers regarding individual genetic testing results;3. All documents relating to the ability of your genetic testing products to accurately identify consumer risk, including:a. internal and external communications regarding the... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3581780 Thu, 20 May 2010 12:16:00 +0100 3581780 http://www.medworm.com/index.php?rid=3563958&cid=t_104578_87_f&fid=38368&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FDisruptiveWomenInHealthCare%2F%7E3%2FUHjGKILo-L8%2F By Archelle Georgiou. On Wednesday, the FDA suddenly decided to impose their regulatory authority on personalized genetic test kits after Walgreens and Pathway Genomics announced they’d be selling them in local pharmacies. But, what triggered this response from the FDA? Are they new? No. These kits have been available to consumers via the Web for 3 years. Have they been off the regulatory radar screen? No. As far back as 2008, the rapid emergence of genetic testing fueled the passage of GINA, a federal law prohibiting health insurers and employers from discriminating on the basis of genetic information. Have these companies been quietly launching their strategy and staying invisible? No. They have made major investments in marketing with an abundant amount of media coverage in women&... Disruptive Women in Health Care blogs http://www.medworm.com/rss/comments.php?id=3563958 Fri, 14 May 2010 11:57:24 +0100 3563958 http://www.medworm.com/index.php?rid=3564133&cid=t_104578_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F14%2F23-and-me-yes-me-part-1%2F Until recently, I was not even aware that there is a DNA day. Nor can I tell you exactly when and where I noticed that 23andMe, the personal genomics company, launched a sale to celebrate the day – I imagine it flashed by on Twitter or FriendFeed. I can tell you that like many others I decided that finally, I could justify the expense, signed up (with around 15 minutes to spare – thanks to the 17 hour Sydney/California time difference) and I’m now waiting for sample arrival and processing. I thought it might be interesting to blog the experience and provided that I don’t discover anything disturbing (finding out that I’m actually a woman, for example), I’ll share some of my data here. Related posts will be tagged with “23andme” and here is pa... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3564133 Fri, 14 May 2010 03:52:33 +0100 3564133 http://www.medworm.com/index.php?rid=3538090&cid=t_104578_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fdo-you-own-your-genome%2F2010.05.06 As the costs of sequencing our DNA shrink and the roles of digital media in our lives expand, we will need to understand who (or what) controls the ownership, access and use of our genomic information. From state regulation to Google to Facebook, who controls the acquisition, transmission and replication of our genomic information and material will become an important battle in the 21st century. (more…) *This blog post was originally published at Phil Baumann* (Source: Better Health) Better Health blogs http://www.medworm.com/rss/comments.php?id=3538090 Thu, 06 May 2010 14:00:11 +0100 3538090 http://www.medworm.com/index.php?rid=3537840&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fmetagenomics-book-review.html%23unique-entry-id-67 I am pleased to provide the following excerpt from a book review of Metagenomics: Theory, Methods and Applications:"the book is recommended for life science researchers and all students in biology and medicine wishing to learn more about this new and very interesting field" from Arzneimittelforschung/Drug Research (2010) 60: 226-227 read more ...Metagenomics: Theory, Methods and Applications Edited by: Diana MarcoISBN: 978-1-904455-54-7Publisher: Caister Academic PressPublication Date: January 2010Cover: Hardback"an excellent resource for students, researchers, and scientists ... a valuable resource on the newly evolving biological field of metagenomics, making contributions to ecology, biodiversity, bioremediation, bioprospection of natural products, medicine, and other disciplines." (Doo... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3537840 Wed, 05 May 2010 23:00:00 +0100 3537840 http://www.medworm.com/index.php?rid=3529824&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FcY05id7YMY8%2Fholy-lateral-transfer-batman-amazing.html As many know, I generally do not write a lot about papers in non open access journal because I like readers to be able to access all the papers which I write about. But this is one of the exceptions to my normal rule. An amazing paper was published a few days ago in Science by Nancy Moran and Tyler Jarvik. Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids -- Moran and Jarvik 328 (5978): 624 -- ScienceI first found out about this from Ed Yong's blog post here (just a note - his Not Exactly Rocket Science is such a frigging incredible blog). He really does the whole story on this so I am just posting a bit here.Anyway Moran and Jarkiv paper focuses on genes in the aphid genome that encode enzymes for carotenoid synthesis. These enzymes are involved in red and/or ... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3529824 Mon, 03 May 2010 19:33:26 +0100 3529824 http://www.medworm.com/index.php?rid=3569861&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fgenetic_variations_linked_to_caries_and_gum_disease.php © robtxgalDental school researchers have found out that certain genetic variations may be linked to higher rates of tooth decay and aggressive periodontitis. Apparently, the rate of dental caries was influenced by individual variations, or polymorphisms, in a gene called beta defensin 1 (DEFB1), which plays a key role in the first-line immune response against invading germs. For the study, the researchers analyzed nearly 300 dental records and accompanying saliva samples, and assigned each case a DMFT score based on the presence of decayed ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3569861 Mon, 03 May 2010 02:31:58 +0100 3569861 http://www.medworm.com/index.php?rid=3487284&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Fblogs.discovermagazine.com%2Fgnxp%2F2010%2F04%2Fof-pigs-people%2F Jared Diamond famously argued in Guns, Germs and Steel that only a small set of organisms have the characteristics which make them viable domesticates. Diamond’s thesis is that the distribution of these organisms congenial to a mutualistic relationship with man shaped the arc of our species’ history and the variation in wealth that we see (though his a human-centric tale, we may enslave them, eat and use them as beasts of burden, but these are also species which have spread across the world with our expansion). This thesis has been challenged, but the bigger point of putting a focus on how humans relate to their domesticated animals, and the complex co-evolutionary path between the two, is something that we need to consider. In a plain biological and physical sense animals have... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3487284 Tue, 20 Apr 2010 13:25:50 +0100 3487284 http://www.medworm.com/index.php?rid=3471968&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Fblogs.discovermagazine.com%2Fgnxp%2F2010%2F04%2Fthe-ideal-diversity-to-infect-you-the-case-of-p-vivax%2F In this study they established the existence of this group rather clearly, but is it due to the peculiarities of Madagascar’s population mixture and history? True, Brazil also has an admixed population whose Duffy allele frequencies are interchangeable with that of Madagascar, but Brazil has been settled for only the past ~300 years or so, with much of the population being of more recent origin (Brazil had the highest slave attrition rate on the American mainland, which explains the African nature of Afro-Brazilian culture. Many of the slaves were from Africa, or first generation, at emancipation). A lower bound for Madagascar is ~1,000 years, and the coexistence of Barito and African populations is likely closer to ~2,000 years. So the existence of P. vivax lines which can penetrate... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3471968 Thu, 15 Apr 2010 15:01:08 +0100 3471968 http://www.medworm.com/index.php?rid=3471783&cid=t_104578_87_f&fid=38368&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FDisruptiveWomenInHealthCare%2F%7E3%2FVfbpbwFJYZ8%2F I’ve been called many names…and, most of the time, I ignore it and let it roll off my back. But last week, I got the ultimate compliment. I was ordained as one of the “Disruptive Women in Healthcare,” a blog site that invites anyone, particularly women, to speak up and challenge the health care status quo. Since I got formal permission to be disruptive (as if I really needed to have someone tell me it’s okay), I am going to allow myself to be a bit irreverent in this blog entry. I apologize in advance. The focus of this week’s blog is on the health benefits of personal genetic testing–an emerging area of medicine that intrigues many people when they read about it, but scares them too much to get tested themselves. Yes, the blog last week had a simi... Disruptive Women in Health Care blogs http://www.medworm.com/rss/comments.php?id=3471783 Wed, 14 Apr 2010 23:43:06 +0100 3471783 http://www.medworm.com/index.php?rid=3463629&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fpatient_genetics_and_warfarin_coumadin_dosing.php © gregor_yPrevious studies have indicated that individual genetic variation affects how warfarin is tolerated and broken down by the body, and scientists have developed several formulas that take genetic information into account when calculating warfarin dosage. Now, a five-year, $3.7 million clinical trial is underway to investigate a formula that includes three gene variations that have been shown to influence a person's warfarin sensitivity or metabolism. "Without any anticoagulant, orthopedic patients have a nearly 50 percent chance of having a blood clot after hip ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3463629 Tue, 13 Apr 2010 07:23:51 +0100 3463629 http://www.medworm.com/index.php?rid=3460323&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Fblogs.discovermagazine.com%2Fgnxp%2F2010%2F04%2Fwhen-a-trait-isnt-a-trait-isnt-a-trait%2F One of the great things about evolutionary theory is that it is a formal abstraction of specific concrete aspects of reality and dynamics. It allows us to squeeze inferential juice from incomplete prior knowledge of the state of nature. In other words, you can make predictions and models instead of having to observe every last detail of the natural world. But abstractions, models and formalisms often leave out extraneous details. Sometimes those details turn out not to be so extraneous. Charles Darwin’s original theory of evolution had no coherent or plausible mechanism of inheritance. R. A. Fisher and others imported the empirical reality of Mendelism into the logic of evolutionary theory, to produce the framework of 20th century population genetics. Though accepting the genetic inh... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3460323 Mon, 12 Apr 2010 13:15:19 +0100 3460323 http://www.medworm.com/index.php?rid=3454198&cid=t_104578_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FHQM_IUWAu4Q%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? And here is something we hope to make a regular feature. Send us a photo and we will spotlight a different person each week. This time around, we note that Dendreon hired Varun Nanda as senior vice president of global commercial operations. He most recently served as the senior vice president and global head of oncology at Roche/Genentech. Nanda arrives, of course, in time ... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3454198 Fri, 09 Apr 2010 12:37:44 +0100 3454198 http://www.medworm.com/index.php?rid=3449059&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Fblogs.discovermagazine.com%2Fgnxp%2F2010%2F04%2Fheritable-yes-which-gene-another-issue%2F Dr. Daniel MacArthur points to a long article by Edmund Yong, Dangerous DNA: The truth about the ‘warrior gene’. Dr. MacArthur notes on his twitter account: “Nice piece on behavioural genetics…but should emphasize MOST behav. gene assocs are actually false.” I think he’s pointing to the winner’s curse; there are lots of people studying various topics, but only a subset of studies pass which yield appropriate effect sizes and p-values actually get published. A sequence of such may give a false sense of certitude as to the strength of the association between a locus and a trait, as negative results are not usually published. I hope David Dobbs keeps this in mind in relation to his new book on the ‘orchid hypothesis’. We have decades of re... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3449059 Thu, 08 Apr 2010 16:10:44 +0100 3449059 http://www.medworm.com/index.php?rid=3443913&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Fblogs.discovermagazine.com%2Fgnxp%2F2010%2F04%2Fthe-many-lives-of-an-inverted-genomic-region%2F About five years ago Kari Stefansson published an interesting paper, A common inversion under selection in Europeans. The basic thrust of the results was that a particular genomic region in Europeans exhibited a pattern of variation whereby there was one variant which was inverted in relation to the modal type. They labelled them “H2″ and “H1″ respectively.  The region in question is spans ~900 kilobases on chromosome 17 and has within it the MAPT gene which is implicated in several neurological diseases. Stefansson et al. argued that H2 and H1 were long coexistent lineages, prevented from recombining due to the molecular genetic constraints of the chromosomal inversion, and each preserved within several human populations by balancing selection dynamics. That is, n... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3443913 Mon, 05 Apr 2010 10:49:25 +0100 3443913 http://www.medworm.com/index.php?rid=3429362&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fgnxp%2F%7E3%2FH7kNQKBdC8o%2F Excellent post from Dr. Daniel MacArthur, Common copy number variation doesn’t explain much complex disease risk – but why not?: The Wellcome Trust Case Control Consortium has just published the results of a massive survey of common, large DNA duplications and deletions (collectively termed copy number variation, or CNVs) in 16,000 patients suffering from complex diseases and 3,000 controls. The results come as no surprise, but are nonetheless disappointing: the study identified absolutely no novel CNVs associated with complex disease. Although three such variants were found to alter disease susceptibility, all three had been identified from previous studies. The study’s findings suggests that – despite their size – common CNVs play very little role in the eti... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3429362 Thu, 01 Apr 2010 08:44:23 +0100 3429362 http://www.medworm.com/index.php?rid=3420577&cid=t_104578_113_f&fid=34623&url=http%3A%2F%2Fhealthnex.typepad.com%2Fweb_log%2F2010%2F03%2Fthe-analytics-virtual-center.html Over the course of 2009, IBM opened centers in Berlin, Beijing, London, New York, Tokyo and Washington D.C.  to advance the frontier of analytics: namely turning big data into new intelligence, predictive capabilities and insight. Healthcare is one area where analytics holds great promise. To support those physical solution centers we launched the Analytics Virtual Center (AVC) at the start of 2010, and welcome you to visit it, especially as we come up on the one year anniversary of the launch of our business analytics initiative. The AVC underscores a central tenet of Smarter Planet — how digital and physical worlds — databases and drydocks,  petabytes and powerplants — are weaving themselves together. Through it, people can extend their physical presence,... HealthNex blogs http://www.medworm.com/rss/comments.php?id=3420577 Tue, 30 Mar 2010 14:06:43 +0100 3420577 http://www.medworm.com/index.php?rid=3420670&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fgnxp%2F%7E3%2F2hc4HHcZGbM%2F It is famously noted that when Charles Darwin published The Origin of Species he had no plausible theory of inheritance to drive his hypothesis. Specifically, one of the major issues of the “blending” model whereby the phenotypes of the parents average out in the subsequent generation is that such mixing eliminates the variation which is a necessary precondition for natural selection. At the same time that Darwin was revolutionizing our conceptualization of how the tree of life came to be, Gregor Mendel was preforming the experiments which solidified his eponymous theory of inheritance. Though ignored in his own day by ~1900 Mendelism reemerged and offered a relatively parsimonious abstraction which could explain why variation was not eliminated through the fusion of sexual rep... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3420670 Mon, 29 Mar 2010 08:50:46 +0100 3420670 http://www.medworm.com/index.php?rid=3420672&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fgnxp%2F%7E3%2FsdoVPlbMcgM%2F A follow up to the post below, see John Hawks, Selection’s genome-wide effect on population differentiation and p-ter’s Natural selection and recombination. As I said, it’s a dense paper, and I didn’t touch on many issues. (Source: Gene Expression) Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3420672 Sun, 28 Mar 2010 18:31:46 +0100 3420672 http://www.medworm.com/index.php?rid=3420673&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fgnxp%2F%7E3%2FfcpVzeFsO0M%2F Last week Nature published a paper which may have found a new ‘branch’ of the hominin evolutionary bush which may have been coexistent which modern humans and Neandertals. I recommend The Atavism, Carl and John Hawks on this story. Interesting times. (Source: Gene Expression) Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3420673 Sun, 28 Mar 2010 07:41:48 +0100 3420673 http://www.medworm.com/index.php?rid=3420674&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fgnxp%2F%7E3%2F0-5hB0p-XtA%2F The following passage is from the epilogue of The Real Eve: Modern Man’s Journey Out of Africa by Stephen Oppenheimer: In this book I have offered a synthesis of genetic and other evidence. Everything points to a single southern exodus from Eritrea to the Yemen, and to all the non-African male and female gene lines having arisen from their respective single out-of-Africa founder lines in South Asian (or at least near the southern exit). I regard the genetic logic for this synthesis as a solid foundation, and I have based the rest of my reconstruction of the human diaspora upon it. Obviously, the ‘choice’ of starting point (mine or theirs) determined all the subsequent routes our ancestors and cousins took. Tracing the onward trails is only possible as a result of marked s... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3420674 Sun, 28 Mar 2010 07:15:38 +0100 3420674 http://www.medworm.com/index.php?rid=3411116&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FqF37R5CGGYE%2Fjgi-user-mtg-day3-notes-coming-up-rita.html Here are links to the Friendfeed Notes for today -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3411116 Fri, 26 Mar 2010 18:05:47 +0100 3411116 http://www.medworm.com/index.php?rid=3420678&cid=t_104578_131_f&fid=34995&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fgnxp%2F%7E3%2FJr_qmaJW7go%2F In conclusion, we have shown that genome-wide human population differentiation in allele frequencies is significantly correlated with recombination rate on a megabase scale, demonstrating that natural selection has had a profound effect on allele frequency distributions averaged over the last hundred thousand years. While these results likely reflect the effects of hitchhiking and background selection, disentangling the strengths of these two forces will require extending the analyses presented in this paper. One important direction is to use genetic maps that have fine spatial resolution, which may shed light on the detailed distribution of selective coefficients that have shaped allele frequency differentiation. A second direction in which these results can be extended is to compare more... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3420678 Fri, 26 Mar 2010 16:28:15 +0100 3420678 http://www.medworm.com/index.php?rid=3395178&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fyou_test_youtm_cancer_assessment_kit.php Nowadays it is possible for an individuals to detect if they have cancer while it is in its early stages without even having to make an appointment with a own doctor. Whether it's due to a general anxiety about developing cancer or increased exposure to risk factors associated with cancer, an individual can now have answers with the You Test YouTM Cancer Assessment kit. The test kit measures a marker called tFFDP (tumor fibrin and fibrinogen degradation products), which is associated with 18 different ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3395178 Sat, 13 Mar 2010 19:17:52 +0100 3395178 http://www.medworm.com/index.php?rid=3359215&cid=t_104578_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FCkbiyODkbig%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? Portola Pharmaceuticals promoted William Lis to ceo; BayBio Jeremy Leffler chief operating officer; Human Genome Sciences named David Southwell exec vp and cfo; Teva Pharmaceuticals named Phillip Frost as chairman; Sandoz promoted Don DeGolyer to head No. American commercial ops; Cornerstone Pharmaceuticals named Robert Shepard as chief medical officer; EUSA Pharma hired Ia... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3359215 Fri, 12 Mar 2010 13:00:53 +0100 3359215 http://www.medworm.com/index.php?rid=3354513&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F03%2Fproblem-with-comparative-whole-genomics.html I have been having this debate with a good friend and mentor. I think Complete Genome Comparison could be a Killer App.He thinks it could be a legal and scientific nightmare.I think he's right.Let's really think about this for a second. If history has anything to say about human behavior we need look no further than the secrecy with which gene sequences were hunted.Hell, even Science makes mention of it several times. The Article "Data Hoarding Blocks Progress in Genetics" might be a good read if you are interested.Guys like Daniel MacArthur over at Genetic future point out some good points about the difficulty in making sense of all the noise that exists in genomes. But the problems go even further than that. Hell, CNV can differ in IDENTICAL TWINS!!!! Say Wha?So what do we have to say ab... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3354513 Thu, 11 Mar 2010 15:11:00 +0100 3354513 http://www.medworm.com/index.php?rid=3346637&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F03%2Fwhat-difference-year-makes.html It has been one year since I commented on 23andMe's foray into clinical medicine. I was frankly blown away that such a move would be so blatant without integration of health care practitioners. I also was blown away that Myriad wouldn't sue the ever living bejesus out of 23andMe. A year later, no lawsuit. I am still surprised about this one. Don't you have to demonstrate protection of your patent to keep it?Maybe Google/23andMe are paying a VIG to Myriad? I don't know, but it hasn't shown up on Myriad's SEC reports yet......Why was I so surprised? Well, a few months after 23andMe launched the service AND Myriad did not sue, MYRIAD WAS SUED.I began to wonder if not suing Google/23andMe was a sign of weakness. I was certain Myriad would then shut down the DTC Genomics BRCA testing.To date, t... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3346637 Tue, 09 Mar 2010 12:58:00 +0100 3346637 http://www.medworm.com/index.php?rid=3311716&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FIzCtBZQjbQA%2Fgenome-sequencer-flx-bay-area-regional.html Just got this email - may be of interest to some: Genome Sequencer FLX Bay Area Regional User Group Meeting Roche 454 Life Sciences invites you to the Bay Area Regional Genome Sequencer FLX User Group meeting which will be held at Roche Diagnostics in Pleasanton, CA on March 8th and 9th. We will kickoff the meeting the afternoon of March 8 with interactive sessions with our BioInformatics Specialist Teri Mueller and Regional Applications Consultant Shamali Roy. Bring any questions or ideas you may want to address. Teri will present on the most recent upgrades to our Data Analysis software and Shamali will be available for experimental design advice. This will be a user driven question and answer event scheduled from 1:00-4:00 pm. Tuesday will feature local scientists presenting their 4... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3311716 Thu, 25 Feb 2010 20:39:20 +0100 3311716 http://www.medworm.com/index.php?rid=3275866&cid=t_104578_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F02%2F15%2Fdecision-tree-and-the-quantified-self%2F The article in Wired on Decision Trees and the new book also by Thomas Goetz has generated a greater interest in participatory medicine and quantifying one’s life and health. The title of the first chapter says it all: Living by the Numbers – How alot of science and a little self awareness can give you control of your health. Brian Ahier addresses these issues as well in his post on “Data Not Drugs: Taking Control of Your Health in the Age of Genetics.” While pointing out the host of tools available to manage your health, everything from WolframAlpha to GetUpAndMove, he discusses earlier adopters who will lead the way, knowing not only their genetic risk but also quantifiy their daily health status. He notes that with few blockbuster drugs in the pipeline, perhap... eHealth blogs http://www.medworm.com/rss/comments.php?id=3275866 Tue, 16 Feb 2010 02:01:35 +0100 3275866 http://www.medworm.com/index.php?rid=3235866&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FVfD-USDjqtw%2Fstory-behind-science-plos-genetics.html Conclusions: Lynch has eloquently argued that biologists are often too quick to assume that organismal and genomic complexity must arise from selection for complex structures and too slow to adopt non-adaptive hypotheses. Our results lend additional support to this view, and extend it to show that indirect and non-adaptive forces can not only produce structure, but also create an illusion that this structure is being conserved. We do not doubt that many aspects of transcriptional regulation constrain the location of transcription factor binding sites within enhancers. Indeed a large body of experimental evidence supports this notion, and we remain committed to identifying and characterizing these constraints. But if this process is to be fueled by comparative sequence analysis, as we belie... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3235866 Wed, 03 Feb 2010 15:53:35 +0100 3235866 http://www.medworm.com/index.php?rid=3231108&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F02%2Fmicrobial-phylogenetics-methods.html The purpose of phylogenetic analysis is to understand the past evolutionary path of organisms. Even though we will never know for certain the true phylogeny of any organism, phylogenetic analysis provides best assumptions, thereby providing a framework for various disciplines in microbiology. Due to the technological innovation of modern molecular biology and the rapid advancement in computational science, accurate inference of the phylogeny of a gene or organism seems possible in the near future. There has been a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods in public domain databases, literature and worldwide web space. Phylogenetic analysis has long played a central role in basic microbiology, for example in taxonomy and ecology. In a... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3231108 Tue, 02 Feb 2010 14:25:00 +0100 3231108 http://www.medworm.com/index.php?rid=3212358&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2F9KI32mDBUBc%2Fwantedfeedback-on-importance-of.html Discussion on Friendfeed to question from Michael BartonLANL finishing in the future meetingScivee talks from 2009 LANL meetingBlakesley, R., Hansen, N., Gupta, J., McDowell, J., Maskeri, B., Barnabas, B., Brooks, S., Coleman, H., Haghighi, P., Ho, S., Schandler, K., Stantripop, S., Vogt, J., Thomas, P., Comparative Sequencing Program, N., Bouffard, G., & Green, E. (2010). Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates BMC Genomics, 11 (1) DOI: 10.1186/1471-2164-11-21Fraser, C., Eisen, J., Nelson, K., Paulsen, I., & Salzberg, S. (2002). The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) Journal of Bacteriology, 184 (23), 6403-6405 DOI: 10.1128/JB.184.23.6403-6405.2002Chain, P., & et al. (2009). Geno... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3212358 Tue, 26 Jan 2010 23:29:50 +0100 3212358 http://www.medworm.com/index.php?rid=3208025&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F01%2Facclaim-for-new-aspergillus-book.html "an overview of the forefront of Aspergillus genomics - from bioinformatics and systems biology to gene regulation, secondary metabolism, and novel industrial applications ... (the book starts) with a superb holistic overview of the genus by its doyenne Joan Bennett ... a most stimulating volume ... The editors and publishers can be proud of having put together a volume that is produced to the highest scientific standards."from David L. Hawksworth in Mycological Research 113: 1444-1445Further reading: Aspergillus: Molecular Biology and GenomicsFull range of books on microbiology at Microbiology Books (Source: Microbiology Blog: The weblog for microbiologists.) Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3208025 Tue, 26 Jan 2010 09:04:00 +0100 3208025 http://www.medworm.com/index.php?rid=3182210&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fgenomics_of_sunflower.php © Esdras CalderanGenome Canada, Genome BC, US Departments of Energy and Agriculture, and France's INRA (National Institute for Agricultural Research) has undertaken a US$10.5 million research project that will create a reference genome for the sunflower family - currently the world's largest plant family, containing 24,000 species of plants, including many crops, medicinal plants, horticulture plants and noxious weeds. Th project, titled Genomics of Sunflower, will use next-generation genotyping and sequencing technologies to sequence, assemble and annotate the sunflower genome and to locate the ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3182210 Sun, 17 Jan 2010 15:57:57 +0100 3182210 http://www.medworm.com/index.php?rid=3163493&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F01%2Fretrovirus-book-published.html Published this month (January 2010):Retroviruses: Molecular Biology, Genomics and Pathogenesis Edited by: Reinhard Kurth and Norbert Bannert Published: 2010   ISBN: 978-1-904455-55-4Price: GB £159 or US $310 Written by the top retroviral specialists, this book reviews the genomics, molecular biology, and pathogenesis of these important viruses, comprehensively covering all the recent advances. Topics include: host and retroelement interactions, endogenous retroviruses, retroviral proteins and genomes, viral entry and uncoating, reverse transcription and integration, transcription, splicing and RNA transport, pathogenesis of oncoviral infections, pathogenesis of immunodeficiency virus infections, retroviral restriction factors molecular vaccines and correlates of protection, gamma... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3163493 Tue, 12 Jan 2010 08:56:00 +0100 3163493 http://www.medworm.com/index.php?rid=3159499&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F01%2Fmolecular-phylogeny-of-microorganisms.html A proper understanding of the diversity, systematics and nomenclature of microbes is increasingly important in many branches of biological science. The molecular approach to phylogenetic analysis, pioneered by Carl Woese in the 1970s and leading to the three-domain model (Archaea, Bacteria, Eucarya), has revolutionized our thinking about evolution in the microbial world. The technological innovation of modern molecular biology and the rapid advancement in computational science have led to a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods. Phylogenetic analysis has long played a central role in microbiology and the emerging fields of comparative genomics and phylogenomics require substantial knowledge and understanding of phylogenetic analy... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3159499 Mon, 11 Jan 2010 16:06:00 +0100 3159499 http://www.medworm.com/index.php?rid=3149251&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F01%2Fhackers-hitech-and-hipaa-in-dtc.html At our practice we run a pretty tight ship when it comes to security of patient records. Why do we do this? Well there are 2 big reasons.1. It's the right thing to do.2. The law will put you in the hurt locker if you don'tI want to talk about reason 2 a little bit. Why? With all of this protection of health information and DTC genomics companies going bankrupt, I begin to really wonder who a covered entity is. Daniel Vorhaus over at Genomics Law Review has a pretty good break down of it, but I think there may be some nuances not covered. As well as a notable lack of coverage of HITECH policies in the ARRA.Wha? Yes the recovery act has stuff on Health care privacy in it. In HIPAA DTC Genomics may not be covered, but I think in HITECH they are.Why have I been reading this stuff? Because it's... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3149251 Thu, 07 Jan 2010 13:45:00 +0100 3149251 http://www.medworm.com/index.php?rid=3120446&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Fhomepage.mac.com%2Fjonathan_eisen%2FPDFs%2F14.Eisen.PhD2.pdf Discussions here And I will post more links as they come up.  Below what I try to provide is some of the story behind the story: My personal interest in applied uses of phylogenetics stage 1: undergraduate preparation at Harvard As this paper is primarily about an applied use of phylogenetics (in selecting genomes for sequencing), I thought it would be worth going into some of how I personally became a bit obsessed with applied uses of phylogenetics. For me, my obsession began as an undergraduate at Harvard where I got exposed to the value of phylogeny as a tool from many many angles including but not limited to: Freshman year taking a course taught by Stephen Jay Gould where Wayne and David Maddison were Teaching Assistant's and where they were demoing their new phylogene... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3120446 Fri, 25 Dec 2009 09:35:53 +0100 3120446 http://www.medworm.com/index.php?rid=3092892&cid=t_104578_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2009%2F12%2F15%2Fprinceton-scientists-find-way-to-catalog-all-that-goes-wrong-in-a-cancer-cell%2F A team of Princeton University scientists has produced a systematic listing of the ways a particular cancerous cell has “gone wrong,” giving researchers a powerful tool that eventually could make possible new, more targeted therapies for patients. A team of Princeton University scientists has produced a systematic listing of the ways a particular cancerous cell has [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=3092892 Tue, 15 Dec 2009 22:53:24 +0100 3092892 http://www.medworm.com/index.php?rid=3122099&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fpeptide_identifies_tumors_and_penetrates_to_deliver_anticancer_compounds.php © kaibara87Researchers at Burnham Institute for Medical Research have identified a new peptide called iRGD that specifically recognizes and penetrates cancer tumors but not normal tissues. The peptide was also shown to deliver diagnostic particles and medicines into the tumor. This discovery stems from the previous discovery of "vascular zip codes," which showed that blood vessels in different tissues (including diseased tissues) have different signatures. These signatures can be detected and used to dock drugs onto vessels inside the diseased tissue. In addition to ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3122099 Tue, 08 Dec 2009 14:09:13 +0100 3122099 http://www.medworm.com/index.php?rid=3067242&cid=t_104578_131_f&fid=34994&url=http%3A%2F%2Fwww.gnxp.com%2Fblog%2F2009%2F12%2Ffinding-missing-heritability.php In a recent special issue of The Economist magazine, evolutionary psychologist Geoffrey Miller of the University of New Mexico writes that there is a "looming crisis in human genetics". Setting aside a number of mistakes Miller makes, a core truth he reports is that to date most genetic variants that have been associated with complex diseases such as diabetes and complex phenotypes such as height can account for only a small percentage of the estimated genetic contribution to population variation in these traits (~5% in total for the cases of type-2 diabetes and height). This residual unexplained variability has been dubbed the "missing heritability".The missing heritability is an open and fascinating research question, not a crisis, although it has become fashionable to characterize it as... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3067242 Mon, 07 Dec 2009 05:31:00 +0100 3067242 http://www.medworm.com/index.php?rid=3122100&cid=t_104578_107_f&fid=36584&url=http%3A%2F%2Fwww.biotech-weblog.com%2F50226711%2Fsoy_peptide_lunasin_has_anticancer_antiinflammatory_properties.php © Kanko*Two studies report that lunasin, a soy peptide present in effluents from soy-processing plants, may have important health benefits that include fighting leukemia and blocking the inflammation that accompanies such chronic health conditions as diabetes, heart disease, and stroke. In the cancer study, de Mejia's group identified a key sequence of amino acids—arginine, glycine, and aspartic acid, (the RGD motif)—that triggered the death of leukemia cells by activating a protein called caspase-3. "Other scientists have noted the cancer-preventive effects of the RGD ... (Source: The Biotech Weblog) The Biotech Weblog blogs http://www.medworm.com/rss/comments.php?id=3122100 Wed, 02 Dec 2009 14:57:39 +0100 3122100 http://www.medworm.com/index.php?rid=3035828&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F11%2Fselect-biosciences-conferences-2010.html January 20 - 21, 2010 Stem Cells World CongressSan Francisco, CA, USA Further information4th annual Stem Cells World Congress and exhibition. There will be two parallel tracks focused specifically on: (1) Stem Cells in Drug Discovery and Development and (2) Regenerative MedicineFebruary 11 - 12, 2010 Screening EuropeBarcelona, Spain Further information7th annual Screening Europe conference and exhibition, claimed to be the largest screening event in Europe with four conference rooms in 2010. Novel Screening Platforms and Drug Discovery Methods, High Content Screening, Fragment Based Screening, Label Free Screening, Enzymes as Drug Targets, Receptors as Drug TargetsSuggested reading: Biology BooksMarch 4 - 5, 2010 Advances in Synthetic BiologyLondon, UK Further information3rd annual Advance... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3035828 Fri, 27 Nov 2009 16:10:00 +0100 3035828 http://www.medworm.com/index.php?rid=3106762&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FLsv-QnGvKTg%2F1000-complete-bacterial-and-archaea.html 1000 Complete Bacterial and Archaeal Genomes in Genbank. Big MileStone. Good day for a microbial genome party. This whole thing is amazing to me. I moved to TIGR in 1998 in order to get in early on the "genome sequencing revolution" as we called it then. We were amazed when the 10th genome came out. We were then thrilled when TIGR sequenced its 20th genome. And now, there are 1000. Amazing.And as Nikos Kyrpides just told me (he is sitting next to me right now) - actually if you go to GOLD (Genomes Online) (Nikos runs this DB) you can see there are actually a few more than 1K there. Even more amazing.Posted using ShareThis -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short upd... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3106762 Tue, 24 Nov 2009 00:48:11 +0100 3106762 http://www.medworm.com/index.php?rid=3106757&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FQfnBNh9cpak%2Fbiologists-rally-to-sequence-neglected.html Nice little story in Nature News about the need to sequence "neglected" microbes. Biologists rally to sequence 'neglected' microbes : Nature NewsQuotes me and a few others. Love the fact that it quotes Steven Giovannoni in support of this notion:"The broad brush strokes of microbial diversity are not adequately represented in that first thousand," says Stephen Giovannoni, a microbiologist at Oregon State University in Corvallis. "It's absolutely important that we sequence more."I like this because Steve gave me enormous grief about this project at a conference last year. Though I argued with him and disagreed with him, his critiques helped guide much of our work on this project that helped make our paper on the work (which is in press) much better. Glad he generally is now in suppo... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3106757 Tue, 24 Nov 2009 00:48:11 +0100 3106757 http://www.medworm.com/index.php?rid=2999694&cid=t_104578_122_f&fid=36582&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FSharpBrains%2F%7E3%2FMRDJKneVQC8%2F Welcome to the 16th edition  of Scientia Pro Publica, the blog carnival  that celebrates the best science, nature and medical writing published in the blogosphere within the past 60 days. What are some of the fascinating topics you can explore and discuss with this group of bloggers? Science & Us The Evolving Mind: What’s the point of daydreaming? Credit: Johan Stigwall, via Flickr Generally Thinking: What is the brain impact of different types of meditation (focused, open monitoring, compassion)? The Emotion Machine: Can blogging help you control your environment and manage stress? Greater Good Magazine: Want to live longer and bettter? Collective Imagination: Can you share a powerful uncanny experience? Science & Friends via LiveScience Lab Rat: Pros and Cons of havin... SharpBrains blogs http://www.medworm.com/rss/comments.php?id=2999694 Mon, 16 Nov 2009 18:20:08 +0100 2999694 http://www.medworm.com/index.php?rid=3111605&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F11%2Flong-qt-syndrome-location-matters_1427.html I just saw a family who had Long QT with a KCNQ1 mutation ripping through them. Which is why I loved this email I received from one of my long time readers the day after I saw them.Closer Look at Genetic Testing in Long-QT syndromeOne of my favorite lines from this paper was"Nothing tests the tools of clinical risk prediction quite like sudden death."Ummmm......Uh Huh.They go on to say"The difficulties encountered in the clinical application of genetic data, even in inherited conditions such as the long-QT syndrome (LQTS), in which the transmitted risk of sudden death is several hundred-fold greater than that in the general population, highlight some of the hurdles that must be overcome if DNA diagnosis is ever to transform cardiovascular medicine. "The reader then went on to send me a rel... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3111605 Mon, 09 Nov 2009 14:47:00 +0100 3111605 http://www.medworm.com/index.php?rid=2970207&cid=t_104578_87_f&fid=38368&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FDisruptiveWomenInHealthCare%2F%7E3%2FVbmPZlSqcW4%2F This month, Disruptive Women welcomes Patrick F. Terry, a self-proclaimed “JAD” (Just A Dad), as our Man of the Month. Q: So, where should we start? You have been involved with founding a number of ground breaking biotechnology companies, life science research foundations, trade associations, philanthropic groups, and a whole host of public policy organizations. A: I enjoy thinking ahead and trying to do the next new thing to advance science, biomedical research, and the business of patient-centered health care. I’m very impatient for change. I consider myself an unrepentant insurgent, renegade, and rabble rouser. I think that is the most powerful disruptive technology there is. That’s why I love the Disruptive Women in Health Care Blog. But honestly, everything I do is i... Disruptive Women in Health Care blogs http://www.medworm.com/rss/comments.php?id=2970207 Fri, 06 Nov 2009 19:44:25 +0100 2970207 http://www.medworm.com/index.php?rid=3111606&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F11%2Fgood-enough-science-apparently-so-at_6680.html "A total of 61 individuals involved in five norovirus outbreaks in Denmark were genotyped at nucleotides 428 and 571 of the FUT2 gene, determining secretor status, i.e., the presence of ABH antigens in secretions and on mucosa. A strong correlation (P 0.003) was found between the secretor phenotype and symptomatic disease, extending previous knowledge and confirming that nonsense mutations in the FUT2 gene provide protection against symptomatic norovirus (GGII.4) infections." This from a report at 23andSerge's "Norovirus Resistance" report.I don't know what I would do with a Norovirus resistance report........Go on more cruises? Work in a daycare? Have more kids?I bring this up because I begin to wonder what level of science is good science.Is highlighting every article as useful as highli... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3111606 Thu, 05 Nov 2009 03:34:00 +0100 3111606 http://www.medworm.com/index.php?rid=2954209&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F11%2Fmicrobial-genomics.html Microbes are ubiquitous in the world in which we live. With the development of high throughput DNA sequencing technology, there has been an explosion of DNA sequence data on microbes. The major aim of future microbial genomics will be to identify the functional significances of individual gene and genomic fragments and to use the information to help improve human health and promote our society development. One current major undertaking to understand genomic information is the comparative analyses between genomes that are not only distantly related, but also closely related ones. Such comparative analyses between genomes that have diverged at different evolutionary time scales allow us to extract different types of information about biological functions and evolutionary processes (Xu, 2010)... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2954209 Tue, 03 Nov 2009 12:03:00 +0100 2954209 http://www.medworm.com/index.php?rid=3111608&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F11%2Faway-and-now-back-what-did-i-miss_5370.html 23andSerge has layoffs, big surprise. When Linda left, she had a tribe that left too. I am working on hiring one or 2 and will see what exactly was going on over there......Likely a huge cash bleedGAPPNet has their first meeting, which I missed.I will email Dr. Khoury and find out how it went.Daniel MacArthur pointing out that 23andSerge could have bashed bad science, yet instead promoted it......No surprise there either.It looks like 23andSerge fired the engineers and scientists.....and kept the PR and marketing wonks.......Well, in the end it is crystal clear It turns out the lawyers questioned this as well as Misha.....Turns out, if you took the genome, then you probably can sell it.......better yet, if you "acquired it via firesale" you also can probably sell it and break all kinds of ... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3111608 Mon, 02 Nov 2009 15:47:00 +0100 3111608 http://www.medworm.com/index.php?rid=2950913&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F11%2Faway-and-now-back-what-did-i-miss.html 23andSerge has layoffs, big surprise. When Linda left, she had a tribe that left too. I am working on hiring one or 2 and will see what exactly was going on over there......GAPPNet has their first meeting, which I missed.I will email Dr. Khoury and find out how it went.Daniel MacArthur pointing out that 23andSerge could have bashed bad science, yet instead promoted it......No surprise there either.It looks like 23andSerge fired the engineers and scientists.....and kept the PR and marketing wonks.......Well, in the end it is crystal clear It turns out the lawyers questioned this as well as Misha.....Turns out, if you took the genome, then you probably can sell it.......better yet, if you "acquired it via firesale" you also can probably sell it and break all kinds of "terms of service" What'... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2950913 Mon, 02 Nov 2009 15:47:00 +0100 2950913 http://www.medworm.com/index.php?rid=3111611&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F10%2Ffollow-up-to-yesterday-wtf-harvard-navi_5221.html So I was thinking about all of this hullabaloo and how Beth Israel Deaconess flipped the script by using non-clinically validated, non medical tests to teach residents about medical genetics..... Yes, that is pretty freaking preposterous in and of itself, but I have a deeper concern..... "Beth Israel has launched the Personalized Genomics and Next Generation Sequencing Training Program, which includes a series of lectures, discussions, and presentations, aimed at promoting a better understanding of the personalized genomics field and next-generation sequencing technologies." Ok, so my question is. Who will be giving the lectures? Let me put this another way..... "NewsFlash" (This is not true, however it is just as preposterous and written to illustrate a point) Harvard Medical School has ... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3111611 Thu, 22 Oct 2009 15:15:00 +0100 3111611 http://www.medworm.com/index.php?rid=3111612&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F10%2Fexcuse-me-harvard-and-navigenics-wtf_8525.html Ok,So I was blown away when I read this juicy little tid bit from Genome Web. NEW YORK (GenomeWeb News) – Navigenics and Beth Israel Deaconess Medical Center in Boston announced today that they will collaborate on training physicians in personal genomic testing.Amazing! I had spoken with Mike Murray up there a while ago and have neen involved in his training curriculum with CMEs for providers. I have always interpreted his opinion on the DTC companies to be suspect of what the hell the companies are doing.In fact when we, Mike and I presented together at the Association of Program Directors in Internal Medicine meeting in 2008 in New Orleans I assumed that their department as well as he didn't much support DTC genomic testing.Which is why the BID move had me puzzled, so I emailed him. Bu... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3111612 Wed, 21 Oct 2009 15:10:00 +0100 3111612 http://www.medworm.com/index.php?rid=3111614&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F10%2Ffew-months-late-to-party_4237.html In conclusion, this backlash will detract more from the movement than the hype added to it. The Sherpa Says: Why continue to support something that in the long run will damage credibility with community physicians and the public? Why? (Source: Gene Sherpas: Personalized Medicine and You) Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3111614 Thu, 15 Oct 2009 12:46:00 +0100 3111614 http://www.medworm.com/index.php?rid=2881194&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2009%2F10%2Fadopt-geba-genome-program-for-education.html The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “adopt” bacterial genomes, such as those sequenced as part of the "Genomic Encyclopedia of Bacteria and Archaea" (GEBA project), for analysis. This “Adopt a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. The organisms ideally provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and use gene ortholog neighborhoods for comparative genomics and annotate biochemical pathways, w... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=2881194 Sat, 10 Oct 2009 19:58:00 +0100 2881194 http://www.medworm.com/index.php?rid=2871608&cid=t_104578_87_f&fid=38368&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FDisruptiveWomenInHealthCare%2F%7E3%2FHa0wmbppsG4%2F Well – sadly it’s been one year since I have posted a blog with Disruptive Women in Healthcare so I really need to update you all on the fascinating science occurring in the genomics community. Shortly after I wrote my last blog in October 2008, I attended a meeting at one of our country’s finest scientific institutions– Cold Spring Harbor Laboratories – where some of the world’s foremost scientific discoveries have occurred. At this inaugural meeting entitled “Personal Genomes”, scientists discussed the tremendous potential for understanding the genome and translating this knowledge into our quest for the personalization of healthcare – yet at this meeting one year ago, we were acknowledging that we had sequenced less than a handful of genomes, the task at hand enorm... Disruptive Women in Health Care blogs http://www.medworm.com/rss/comments.php?id=2871608 Wed, 07 Oct 2009 11:05:33 +0100 2871608 http://www.medworm.com/index.php?rid=2851973&cid=t_104578_131_f&fid=34994&url=http%3A%2F%2Fwww.gnxp.com%2Fblog%2F2009%2F09%2Fsweeps-markov-models.php Detecting Selective Sweeps: A New Approach Based on Hidden Markov Models. Over at Mailund on the Internet. (Source: Gene Expression) Gene Expression blogs http://www.medworm.com/rss/comments.php?id=2851973 Wed, 30 Sep 2009 20:53:00 +0100 2851973 http://www.medworm.com/index.php?rid=2823675&cid=t_104578_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F09%2Fmetaproteomics.html Microbial ecology is currently experiencing a renaissance spurred by the rapid development of molecular techniques and "omics" technologies in particular. As never before, these tools have allowed researchers in the field to produce a massive amount of information through in situ measurements and analysis of natural microbial communities, both vital approaches to the goal of unraveling the interactions of microbes with their environment and with one another. While genomics can provide information regarding the genetic potential of microbes, proteomics characterizes the primary end-stage product, proteins, thus conveying functional information concerning microbial activity. Advances in mass spectrometry instrumentation and methodologies, along with bioinformatics approaches, have brought th... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2823675 Wed, 23 Sep 2009 16:10:00 +0100 2823675 http://www.medworm.com/index.php?rid=2800609&cid=t_104578_131_f&fid=34994&url=http%3A%2F%2Fwww.gnxp.com%2Fblog%2F2009%2F09%2Fpersonal-genomics-beyond-hype.php ScienceDaily has an interesting piece, Individual Genetic Data Illuminates How Genes Influence Human Health. Points to two papers, Epistasis and Its Implications for Personal Genetics and Genetic Population Structure Analysis in New Hampshire Reveals Eastern European Ancestry. If you read a weblog like Genetic Future you are probably cognizant of the fact that personal genomics firms are invested in overselling and hyping their current efficacy to serve their economic interests. And yet I was intrigued as to the disjunction between the present day capabilities of personal genomics and the perception of its power in the general media when listening to a recent episode of Plant Money. The hosts spoke as if personal genomics had already rendered health insurance obsolete because science had r... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=2800609 Tue, 15 Sep 2009 23:57:00 +0100 2800609 http://www.medworm.com/index.php?rid=2793358&cid=t_104578_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2Ft8b-RRiEZtg%2F A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation sequencing will enable and can start to imagine what happens when even cheaper 3rd generation sequencing technologies are applied. I’m behind in reviewing these papers for you, dear reader, but I hope you’ll click through and take a look at some of these papers if you are interested in the topics. In the following set of papers we have some nice examples of comparative genomics of closely related species and among a clade of species. The papers mentioned ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2793358 Mon, 14 Sep 2009 18:14:35 +0100 2793358 http://www.medworm.com/index.php?rid=2778620&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F09%2Fre-reviewing-national-academies.html After listening closely to Timothy Aitman of the Imperial College of London, it seems to me that the market for DTC is not in the United States.It is in Jolly 'Ol England. Timothy seems to be very Pro-DTC and Dr. Khoury(CDC), Dr. Ganz (UCLA) and Dr Korn (HARVARD) seem to firmly believe that regulations are needed and that they should be treated as one in the same with "Any other Clinical Laboratory that is offering similar services" Frederick Anderson asks, "How far does this go? Does this go to the interpretation or the testing? Or Both?" It seems to me that this panel is Pro-Regulation.Timothy BTW is just a presenter, not a member. My guess, National Academies will conclude that the regulation of these companies currently is not up to par. In fact, they may conclude it is an area in dire... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2778620 Wed, 09 Sep 2009 12:29:00 +0100 2778620 http://www.medworm.com/index.php?rid=2762088&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F09%2Fsome-confusion-exists.html I have a great comment string going on with Daniel MacArthur over at his blog Genetic Future I think there is some confusion going on here and I place blame on just about everyone in this space who has a mouthpiece.......But mainly I lay blame on the marketing teams for the Direct to Consumer Genomics companies.These companies have an interest in making you "think" that their products have some particular health relevance.Otherwise, no one in their right mind would waste their time with these tests.......Other than the HUGE field of ancestry buffs like Blaine Bettinger J.D. (woohoo) We need clarity here. From Daniel- "The American College of Medical Genetics is saying "Genetic tests of individuals or families for the presence of or susceptibility to disease are medical tests." The fine pri... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2762088 Thu, 03 Sep 2009 12:03:00 +0100 2762088 http://www.medworm.com/index.php?rid=2752079&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F09%2Fiom-not-webcast-today-why-not.html The IOM conference "Direct-to-Consumer Genetic Testing: A Cross-Academies Workshop" will not be webcast today? I wonder why not? Was it supposed to be and then submarined after Muin Khoury quoted an email I wrote him while he was presenting?Why is there no webcast for this important conference today?Maybe I am just a conspiracy theorist.But I would like IOM and the National Academies to explain why the cover one day but not the second.The second day by the way has some great topicsFrom the AgendaSession 5: The Impact of DTC Genetic Tests on the Medical System"If the medical system is no longer required to mediate genetic testing, how will the system cope with losing oversight (and reimbursement) of these services while retaining the full responsibility of caring for patients the services a... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2752079 Tue, 01 Sep 2009 12:43:00 +0100 2752079 http://www.medworm.com/index.php?rid=2748078&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F08%2Fnational-academies-and-iom.html Today and Sept. 1 the National Research Council and Institute of Medicine will hold a symposium to explore the health, policy, and ethical implications of direct-to-consumer genetic testingAUDIO WEBCAST: Morning sessions on Aug. 31 -- covering the history and likely evolution of direct-to-consumer genetic testing, as well as the regulatory framework -- will be available via live audio webcast at http://national-academies.org.Don't miss this. I am listening to Muin Khoury right now.BTW, the best question was just asked. "Do you think you are practicing medicine and if no, explain why not?"That is the crux of this whole DTC field. I have always thought, they are.......The Sherpa Says: I will cover this and the NIH conference over the week. (Source: Gene Sherpas: Personalized Medicine and You... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2748078 Mon, 31 Aug 2009 13:21:00 +0100 2748078 http://www.medworm.com/index.php?rid=2719896&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F08%2Fwhere-from-here.html This is the question I am asked so often.1. We have the steady progress towards cheap genomes. 2. We have the biggest supporter of personalized medicine running the NIH 3. We have "some" clinical awareness of personalized medicine 4. We have the government aware of the shenanigans of some unscrupulous DTC advertising, etc 5. We have several milemarkers under our belts with genome science..... We are moving in the "right" direction, but where do we go from here There are several areas we need to investigate. I would like to sum a few of them, both basic science and clinical. Basic Science first. 1. We need to understand precisely how gene regulation occurs in the face of certain common environmental exposures. Trans Fat, Tobacco Smoke, Alcohol, Stress. Is it RNA? Is it Methylation? What pr... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2719896 Thu, 20 Aug 2009 14:26:00 +0100 2719896 http://www.medworm.com/index.php?rid=2712292&cid=t_104578_131_f&fid=34994&url=http%3A%2F%2Fwww.gnxp.com%2Fblog%2F2009%2F08%2Fin-defense-of-big-genetics.php Greg Mayer, filling in for Jerry Coyne, has a post up on a somewhat odd objection to the appointment of Francis Collins as director of NIH: that he's a geneticist. The argument seems to be that diseases are complicated and not entirely genetic, and that Collins isn't hip to non-genetic subtleties. To be frank, this is silly--while it's sometimes a revelation to non-biologists that the "gene for X" way of framing things is inaccurate, Collins is not incompetent. If I had to guess what direction he's planning on taking the NIH, I'd look to what he's actually written.In the comments to the post, there's the additional worry that Collins represents "big science", which I suppose is considered to be a bad thing (apparently Collins thinks it would be nice to catalogue all the transcripts in a ce... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=2712292 Wed, 19 Aug 2009 03:19:00 +0100 2712292 http://www.medworm.com/index.php?rid=2699647&cid=t_104578_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2009%2F08%2Foverselling-genomics-award-6.html For those interested in so-called "third generation" DNA sequencing systems, this week has had some buzz with the release of a publication in Nature Biotechnology reporting the sequencing and analysis of a human genome using a Helicos Heliscope sequencer. In this paper Stephen Quake and colleagues generated short read sequences from Quake's DNA using this machine and then analyzed them by comparing them to reference human genomes.Certainly, what they did was cool. And the use of the Helicos equipment is a good thing for that company and it's development of single molecule sequencing. And given the "race" if you want to call it that for the $1000 genome, it is thus not surprising that this paper received a lot of coverage from all sorts of angles because they claim it involved the cheapest ... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=2699647 Thu, 13 Aug 2009 15:42:00 +0100 2699647 http://www.medworm.com/index.php?rid=2683960&cid=t_104578_131_f&fid=34994&url=http%3A%2F%2Fwww.gnxp.com%2Fblog%2F2009%2F08%2Fgenome-sequencing-shop-talk.php There's a nice post over at Genetic Future getting into the details of a recent paper using ABI SOLiD to resequence a human genome. The comments are quite instructive as well. For those not dealing with these sorts of technologies regularly, it can all seem a bit incomprehensible, but the outcome of these sorts of debates will determine who dominates the sequencing business for the next few years... (Source: Gene Expression) Gene Expression blogs http://www.medworm.com/rss/comments.php?id=2683960 Sat, 08 Aug 2009 17:43:00 +0100 2683960 http://www.medworm.com/index.php?rid=2649196&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F07%2Fpharmacogenetic-indication-for.html That's one way to market the newest medication to prevent stroke, heart attack or stent thrombosis. Wha? Yes, I mean, Prasugrel otherwise known as Effient is FDA approved for use in these patients. But one thing I was thinking is that, since the FDA put on the insert of Plavix that 2C19 testing may be useful to identify people who will not respond to Plavix (generic Clopidogrel)Perhaps, the marketing geniuses over at Eli Lilly could use this as an FDA suggestion that these 2C19 people may be better off with Prasugrel. Yes, it would be one of the most brilliant ways to market pharmacogenomics. I can only imagine the DTC genomics companies salivating over this "We offer the 2C19, test. Act now, save your life." Technically, It actually could. Yes, all the stops would be pulled out and it co... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2649196 Wed, 29 Jul 2009 12:01:00 +0100 2649196 http://www.medworm.com/index.php?rid=2645380&cid=t_104578_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2009%2F07%2F27%2Fwhat-is-it-like-to-receive-your-genetic-profile.aspx%3Fref%3Drss Now that online offerings for genetic testing is readily available, what is it like to order the test and then receive and open the results for the first time? Jen McCabe Gorman, the quintessential ePatient, shares her experience on YouTube as she opens her results from 23&Me. Here experience is filled with excitement, worry and questions - wondering who else in her family might have similar traits, what are the medical implications of mild tendencies, what are the implications for future medical treatment? This personal experience goes beyond anything you will find describing these online genetic testing. Technorati: Health 2.0 (Source: eHealth) eHealth blogs http://www.medworm.com/rss/comments.php?id=2645380 Tue, 28 Jul 2009 08:54:00 +0100 2645380 http://www.medworm.com/index.php?rid=2645476&cid=t_104578_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FSHq0DHhi37g%2F It looks like Proctor & Gamble scientists have just discovered the secret to youthful skin: it’s in 1,500 genes. Using data from the Human Genome Project, P&G scientists identified some 1,500 genes that are responsible for how skin ages. Of those, up to 700 genes control how skin collects and retains moisture. Genomics has key to keeping skin healthy and young. According to an article in the Daily Mail, there are separate ways that skin ages, and each of these are controlled by their own set of genes: Collagen (the protein that gives skin its structure and strength) degrades. Skin loses its ability to keep it hydrated. Fewer skin cells are produced with time. Wrinkles are produced when the skin becomes more inflamed. Age weakens our skin’s natural defense against free-radicals... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2645476 Tue, 28 Jul 2009 08:01:28 +0100 2645476 http://www.medworm.com/index.php?rid=2637951&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F07%2Fgo-see-gastro-doc.html I am so blown away at the desperation (def: recklessness arising from despair) of the DTC companies. Recently my iPhone has been flooded with all sorts of clinically inaccurate information designed to make people think that something miraculously has changed with DTC genomics tests. A change so impressive that it now appears as if you can actually do something about the results. The best is a video now on Navi's website2 sisters on the site taking about their results......likely plants...... The transcript includes these misleading words.......Sister 1: We both tested "High" For Colon Cancer! Sister 1: But the Crohn's disease was "really high" on my results. Which is interesting because, I didn't know we had that disease in our family...... Sister 2: It is a disease that is 75% genetic but... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2637951 Fri, 24 Jul 2009 14:32:00 +0100 2637951 http://www.medworm.com/index.php?rid=2630307&cid=t_104578_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FM-HrlX4ETbE%2F If you can make plans to head to Spain in October you should consider attending the EMBO conference on Comparative Genomics of Eukaryotic Microorganisms October 17-22 outside of Barcelona. Lots of very interesting speakers and I’ve got the chance to be there to speak about ideas and results using comparative genomics to study evolution of early diverging fungal lineages. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2630307 Wed, 22 Jul 2009 17:41:49 +0100 2630307 http://www.medworm.com/index.php?rid=2606153&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F07%2Ftruvalue-is-coming-valuation-of-gmg.html Valuation, it is a fickle beast. I love this post from AskTheVC.comValuation – especially for early stage companies – falls in the category of “more art than science.” While buyout investors who are acquiring companies with meaningful cash flow streams love their multi-sheet Excel models with 37 pivot tables, most early stage VCs can do valuations on a napkin (or – if they are good at simple math (e.g. addition and subtraction) – in their head.) In the early stages three things drive valuation: (a) ownership dynamics, (b) market terms, and (c) competitive deal dynamics. Remember Again - this is art - there is no scientific way to really value three guys and a powerpoint slide or a web service with 10,000 subscribers of which 250 are active (although no one can prove that only 2... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2606153 Thu, 16 Jul 2009 11:55:00 +0100 2606153 http://www.medworm.com/index.php?rid=2606154&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F07%2Fpathway-genomics-is-lab-not-algorithm.html Today an article came out in BioIT world about Pathway Genomics. (Sounds Eerily like Amway)With a tagline like, "Your Future, Only Better" I thought that maybe they were like Vanilla Sky or some Total Recall like service. I could only guess how in the world they could offer a better future through a SNP scan.....Yes another DTC Genomics/SNPscan Company in the game. Hopefully they will accept regulations and not try to manipulate the laws. I hope that they act responsibly with the data and samples. I hope that they will be transparent and honest.FROM Bio-IT"In common with other consumer genomics firms, Becker oversees an editorial team to review criteria from the latest peer-reviewed genome association studies. That team includes Victoria Magnuson, who trained with Francis Collins and John ... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2606154 Wed, 15 Jul 2009 14:16:00 +0100 2606154 http://www.medworm.com/index.php?rid=2591636&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F07%2Fgood-legal-advice-for-genomics.html I have often thought that the laws which currently govern genomics, medicine and direct to consumer products are prettty interesting.Which is why, when we started our medical practices we were going to do an internet distribution of testing and consultation........ This was back in 2005. We sat late up at night in my partners apartment plotting to take over the industry.We aligned some players and then we obtained some legal advice....... After that fateful day in 2005, we realized that this was a buzzsaw we did not want to mess with......Especially in New York, Our Market! So you can imagine my incredulity when we saw 3 companies planning to do precisely what we were advised legally not to do. The mistakes these companies made were exactly the issues we were advised to avoid. We spent a m... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2591636 Fri, 10 Jul 2009 12:52:00 +0100 2591636 http://www.medworm.com/index.php?rid=2561483&cid=t_104578_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F07%2Fno-gene-is-island.html This is a saying I have been using for about 4 years now.When someone asked about testing for HFE and why we don't do it as the first screening step anymore..... They often looked at me confused.....I then bring up the case of sickle cell disease.Most doctors have seen a sickle cell patient in the hospital.......They may have even seen a family in the hospital, brother and sister, Son and Mother......but what most don't know is that the majority of sicklers never go into the hospital..... That's when I ask, what is the mutation that the son and mother have? The answer Sickle-cell anemia is caused by a point mutation in the β-globin chain of hemoglobin, causing the amino acid glutamic acid to be replaced with the hydrophobic amino acid valine at the sixth position. Now what about the patie... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2561483 Wed, 01 Jul 2009 12:08:00 +0100 2561483 http://www.medworm.com/index.php?rid=2512405&cid=t_104578_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FHEThPiK8Qy0%2F What does mega-search engine Google and mega-genome services company 23andMe have in common? Two actually, and maybe more… First – investments and second, spouses. This week, Google invested $2.6 million in 23andMe on top of the $7 million invested so far. No surprise there, since Google’s co-founder Sergey Bring is the spouse of 23andMe’s co-founder Anne Wojcicki. But as CNN remarked, it’s one the perks of marrying Google.   In another news, biotech giant Illumina has launched a personal genome sequencing service. That is, you can have your entire genome sequenced – all 3 billion DNA - for a hefty price of $48,000. Unlike 23andMe and other genome-testing services where only genotypes are provided, Illumina will provide your entire DNA sequence. But you need a prescr... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2512405 Sun, 21 Jun 2009 06:58:59 +0100 2512405 http://www.medworm.com/index.php?rid=2511554&cid=t_104578_113_f&fid=34623&url=http%3A%2F%2Fhealthnex.typepad.com%2Fweb_log%2F2009%2F06%2Fsmarter-healthcare-channel-via-gbs-video-studio.html With healthcare reform taking centerstage in Washington in the weeks and months ahead, we wanted to share this section of clips in the IBM Global Business Services Video Studio, which debuted with the launch of IBM's new consulting organization, Business Analytics & Optimization. (Source: HealthNex) HealthNex blogs http://www.medworm.com/rss/comments.php?id=2511554 Fri, 19 Jun 2009 18:36:16 +0100 2511554 http://www.medworm.com/index.php?rid=2464333&cid=t_104578_131_f&fid=34994&url=http%3A%2F%2Fwww.gnxp.com%2Fblog%2F2009%2F06%2Fmobile-genetic-elements-in-wooly.php Cool new paper about ancient DNA, Mobile DNA Elements In Woolly Mammoth Genome Give New Clues To Mammalian Evolution: The woolly mammoth died out several thousand years ago, but the genetic material they left behind is yielding new clues about the evolution of mammals. In a study published online in Genome Research, scientists have analyzed the mammoth genome looking for mobile DNA elements, revealing new insights into how some of these elements arose in mammals and shaped the genome of an animal headed for extinction.The paper isn't online yet, but it will be here. Kind of mind-blowing that we might know so much about the genomics of an extinct organism. We've come a long way since E. B. Ford. (Source: Gene Expression) Gene Expression blogs http://www.medworm.com/rss/comments.php?id=2464333 Tue, 09 Jun 2009 06:27:00 +0100 2464333