The DNA Network

Personalized Genetics: Crystal Ball? [ScienceRoll] Posted: 25 May 2008 04:29 PM CDT The world of personalized medicine must be much more than a crystal ball. Here are some new articles about the steps that have to be made and some aspects that might help us : Workman’s Compensation, Stereotypes and GATTACA (The Gene Sherpa): I think this is the best post Steve Murphy has ever written. Young person goes to 23andME/Navigenics/ETC (They just may add this immediately)….gets predictive testing indicating that he is at a 300 fold increased risk of herniating a disc in his back. Avoids manual labor (plays video games all day) never herniates the disc. Did we do society a service? Some would argue yes….I say no. Genomic Medicine: An Educational Resource from Helix Health (Highlight Health): A good definition from Walter Jessen. A Four-Part Series About Personal Genomics at Condé Nast Portfolio - Are Genetic Tests Really Useful? (The Genetic Genealogist) It’s not as bloody as you think. Helping the Desert Bedouins with Genetic Testing (Jeffrey Dach): Very soon, the cost for routine whole human genome sequencing will become cheaper, and some day will be offered during routine clinical testing along with the CBC, blood count and chemistry panel. Also, we will very soon have a greater understanding of gene variation and disease risk, which will hopefully allow intelligent and useful interpretation of the routine clinical sequencing of the entire human genome. As of May 2008, we are not quite there yet. Tell me Everything: How To Use SNPedia for 23andMe and deCODEme (Think Gene) Crystal Ball” Personal Genomics Contest (The Medical Quack): An incredible contest.

Sharing of chromosomal segments to analyze human colonization [Yann Klimentidis' Weblog] Posted: 25 May 2008 02:28 PM CDT via Dienekes, an interesting looking paper that includes some "fun" movies that describe the results of their modeling of the spread of humans around the globe. Inferring Human Colonization History Using a Copying Model Garrett Hellenthal, Adam Auton, Daniel Falush PLoS Genetics 4(5): e1000078 Abstract: Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments between populations and uses the pattern of sharing to reconstruct a detailed colonization scenario. We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006). Our results are consistent with the consensus view of a single "Out-of-Africa" bottleneck and serial dilution of diversity during global colonization, including a prominent East Asian bottleneck. They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native South Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native North Americans, implying multiple waves of migration into the Americas. A detailed depiction of the peopling of the world is available in animated form.

TED talks: Teaching [Mailund on the Internet] Posted: 25 May 2008 01:42 PM CDT Here’s a few more TED talks, this time (somewhat) about teaching: Table of contents for TED Talks TED talks: Biology TED talks: IT TED talks: Space TED talks: statistics TED talks: physics TED talks: Teaching Previous in series

Gene Genie #32 is Live [adaptivecomplexity's column] Posted: 25 May 2008 01:07 PM CDT Gene Genie #32 is up at Highlight Health, showcasing some great blogging on human genes, genetics, and genetic diseases. Go on over and browse some great Sunday Science reading.

Around the web - May 25, 2008 [business|bytes|genes|molecules] Posted: 25 May 2008 11:42 AM CDT Linkfest Digital formats for long term preservation Follow Paulo’s open science activities Gapminder launches a community Zappos; paying employees to quit Bora talks to JCB about open science (any interview with links to BBGM has high chances of showing up here ) Multimedia ccNeLaS is a music blog I follow regularly. Does a great job of finding creative commons licensed music Data Center porn FLOSS Weekly with Dan Ingalls - A must listen. Blogspotting Bloody Fingers - a geeky blog from an atmospheric scientist Events Infoscale 2008 OATV Startup Camp - Would be great to attend this one Seattle Scalability Conference - I will most likely be there Self Assembly The highlight is probably the FriendFeed room that I created. The conversation on FriendFeed has been great. I hope it stays that way as it goes beyond the early adopter crowd. Been pretty active on the tumblelog Showed up on Gene Genie, which is all about GOOG ShareThis

Growing Human Heart Tissue from Embryonic Stem Cells [adaptivecomplexity's column] Posted: 25 May 2008 10:40 AM CDT We understand in amazing detail how a heart develops - in mice. Whether the same processes that produce mouse heart tissue also generate heart tissue in humans has been unclear, because we obviously can't do the required experiments on human embryos. But a paper published on Thursday in Nature describes research that used human embryonic stem cells to generate human heart cells, and in the process demonstrated that human and mouse stem cells use similar molecular signaling pathways to develop, or differentiate, from stem cells to various types of heart cells. What this means is that we now have the molecular recipe needed to grow heart tissue from embryonic stem cells. Having that recipe in hand brings us a step closer to an embryonic stem cell-based treatment for damaged hearts. Human Cardiac Cells - Figure 4c from Yang, et al., Nature 453 (2008) doi:10.1038/nature06894 read more

Gene Genie #32 at Highlight HEALTH [ScienceRoll] Posted: 25 May 2008 06:02 AM CDT The  32nd edition is up at Highlight HEALTH with the title: Googling the Genie. A great compilation of articles and blogposts about human genetics and personalized medicine. Thank you, Walter Jessen, for hosting Gene Genie. Gene Genie is the blog carnival of genes and gene-related diseases. Our plan is to cover the whole genome before 2082 (it means 14-15 genes every two weeks). We accept articles on the news of genomics and clinical genetics. The news and articles of personalized genetics are also included. Check out Gene Genie for more about this unique field of medicine. Many thanks to Ricardo Vidal for the logo! Next edition is due to be published at Neurophilosophy on the 8th of June. Don't forget to submit your articles via the official page. Here are all the issues of Gene genie: Issue #1: Scienceroll Issue #2: Sciencesque Issue #3: Genetics and Health Issue #4: Sandwalk Issue #5: Neurophilosophy Issue #6: Scienceroll Issue #7: Gene Sherpa Issue #8: Eye on DNA Issue #9: DNA Direct Talk Issue #10: Genomicron Issue #11: Med Journal Watch Issue #12: My Biotech Life Issue #13: The Genetic Genealogist Issue #14: MicrobiologyBytes Issue #15: Cancer Genetics Issue #16: Neurophilosophy Issue #17: The Gene Sherpa Issue #18: Eye on DNA Issue #19: Scienceroll Issue #20: Bitesize Bio Issue #21: BabyLab Issue #22: Sandwalk Issue #23: Scienceroll Issue #24: biomarker-driven mental health 2.0 Issue #25: The Gene Sherpa Issue #26: Sciencebase Issue #27: DNA Direct Talk Issue #28: Greg Laden's Blog Issue #29: My Biotech Life Issue #30: Gene Expression Issue #31: Adaptive Complexity Issue #32: Highlight HEALTH

Synthetic Biology has a long way to go [business|bytes|genes|molecules] Posted: 24 May 2008 11:58 PM CDT At least till it catches up with Systems Biology in search popularity Technorati Tags: Systems Biology, Synthetic Biology, Google Trends ShareThis

Gene Genie #32 - Googling the Genie [Highlight HEALTH] Posted: 24 May 2008 11:01 PM CDT Welcome to the 32nd edition of Gene Genie, a blog carnival devoted to genes and genetic conditions. This edition includes some excellent articles on genes and gene-related diseases, genetics, genomics and personalized genetics. logo credit: Ricardo @ My Biotech Life Google Health launched publicly this week and to recognize the event, the last section of the carnival is devoted to articles specifically about the service. Google, financial backer of 23andMe, also funds the Personal Genome Project, which plans to unlock the secrets of common diseases by decoding the DNA of 100,000 people in the world’s biggest gene sequencing project [1]. With the vast number of genetic data points collected for each genome sequenced, a digital system for the movement and storage of personal health information is critical for the widespread use of individualized healthcare. Google’s entrance into the online personal health records market may thus help to accelerate the era of personalized medicine. With these thoughts in mind, let’s get to this month’s edition of the Genie. Genes and gene-related diseases The term gene refers to an inheritable trait that is typically accompanied by a phenotype (meaning an observable characteristic); this is called an allele. Most genes code for proteins and many play a role in health and disease. However, researchers are challenging the one gene, one protein concept, suggesting that perhaps each gene sequence overlaps the next [2]. Like most things in biology, the closer we look, the more complexity we find. Dr Shock MD PhD Rates of depression and other psychiatric disorders are higher in people who have two copies of a genetic variant of the serotonin transporter gene as a function of exposure to increasing levels of stressful life events. A recent study examined the biological reactivity to stress in people with two copies of the allele [3]. Dr. Shock asks How Can Genes and Stress Cause Depression?. Genetics & Health Researchers in Canada recently tested the hypothesis that DNA methylation plays a role in alterations in gene expression in the suicide brain [4]. Elaine Warburton describes Suicide - Genetic Changes in Brain as a Result of Childhood Abuse. Think Gene Schwann cells insulate nerves in the peripheral nervous system and can dedifferentiate with injury to accelerate healing. A recent study demonstrates that c-Jun is an important regulator of this plasticity [5]. Josh Hill reports that c-Jun is Turning Back the Clock for Schwann Cells. Eye on DNA Hsien-Hsien considers the possibility of 23andMe showing personalized ads for personalized medicine, and hopes that the Parkinson's Institute and Clinical Center will have compliant study participants when 23andMe Collaborates on Study of Parkinson's Disease Genetics. Retail Genomics Simon Lin also writes about the collaboration between 23andMe and the Parkinson’s Institute. 23andme is Shaking up Clinical Research, and Simon’s happy to see the combination of consumer genomics and clinical trials. The Skeptical Alchemist Mice laking the glucose transporter gene Glut2 fail to control their food intake, suggesting a role for glucose sensing in the brain. Steppen Wolf reviews a study in humans showing that individuals with a genetic variant of the same glucose transporter, GLUT2, have a higher daily intake of sugar [6]. Now there’s Finally an Excuse for My Sweet Tooth!. The Spittoon A recent genome-wide association study in Asians found an association between a SNP of the gene PSCA and an increased risk of diffuse-type gastric cancer [7]. Erin Cline reviews the study in SNPWatch: Researchers Find SNP Associated with Diffuse-type Gastric Cancer. Genetics Genetics — the study of how physical and behavioural traits are inherited and the variations between organisms — has changed dramatically in the last 50 years. Genetics focuses on how genes specify the structure and function of an organism, and how that information is replicated and passed on to subsequent generations. Genetics is central to biology and is far-reaching, affecting medicine, agriculture, identity and privacy. Nimravid's Weblog The foundation of comparative genomics is that genes that are shared between closely related species have similar function and cause similar phenotypes when deleted from the genome. Nimravid reviews a systematic examination of this hypothesis [8]. Are You a Human or a Mouse? Greg Laden’s Blog A method for increasing the power of genetic studies in canines is to sample dogs of the same breed but from different geographic areas. A recent study assessed the genetic variation among dogs of the same breed collected from different geographic regions [9]. Greg Laden reviews the study and describes genetic variation, disease-connected alleles and dogs in his article Evolutionary Genetics of Canine Population Structure. Adaptive Complexity A review of genome-wide association studies highlights the knowledge gained and challenges that remain as researchers work to identify sequence variation and disease predisposition [10]. Adaptive Complexity covers The First Report Card for Genome Wide Association Studies. PredictER Blog Jere Odell writes about a genetic counselor’s response to a Nature article reporting the genomic DNA sequence of James D. Watson [11]. Dr Watson’s Genetic Counselor: Witty or Insulting? Sciencebase David Bradley discusses Genetic Manipulation and asks, “Do the GM pros outweigh the cons?” Genomics Genomics is the study of an organism’s entire genome to determine biological markers predisposing an individual to disease. Here at Highlight HEALTH, I explain the difference between genetics and genomics in my article Genomic Medicine: An Educational Resource from Helix Health. Genomicron T Ryan Gregory explores the multiple meanings of the term genome, clarifying “what is a genome?” and “Whose Genome was sequenced?” Gene Sherpas: Personalized Medicine and You Timing is everything. Steve Murphy highlights two major impacts on the future of Genomic Medicine last week when he writes about Timing, GINA is Law and the Future of Genomic Medicine. Giovanna Di Sauro A recent study used transgenesis to evaluate the function of sequences obtained from an extinct species in transgenic mice [12]. Giovanna Di Sauro tells us about Jurassic Park in the real world with her article Tasmanian Park: Extinct Mammalian DNA Back to Life. Next Generation Sequencing The NGS blog reports that the Genome Reference Consortium Launched. The consortium’s goal is to correct the small number of regions in the reference that are misrepresented, to close as many gaps as possible and to produce alternative assemblies of structurally variant loci. Personalized Genetics There’s much discussion about personalized genetics right now as a number of companies that can test your DNA are being launched around the world. 23andMe is on a mission to be the world’s most trusted source of personal genetic information; Navigenics aims to help you live healthier, longer; and deCODEme claims that its never been so easy to learn about ancestry, disease risk and inheritance of physical traits as it relates to you and your genome. Scienceroll Berci Meskó discusses the recent improvements of individualized medicine in his article Personalized Genetics: Privacy and the Virtual Gene. PredictER Blog How would personalized genetic information change the perceptions of risk and behaviors of people making retirement plans? Jere Odell ponders Retirement and Risk: Betting on Your Genes? Think Gene Personalized genetic services test for SNPs, DNA sequence variations that occur when a single nucleotide — A, T, C or G — in the genome is changed, producing different alleles. Most services test between 500,000 and 1,000,000 SNPs, yet interpret less that 100 traits. Kevin Fischer demonstrates how to get more information about your genome. Tell me Everything: How To Use SNPedia for 23andMe and deCODEme. The Genetic Genealogist How reproducible are the results of genome scanning services? Blaine Bettinger evaluates the Accuracy of Large-Scale Genome Scanning Services. He follows the article up by assessing the Reproducibility of SNP Testing. DNA Direct Talk After speaking about competition in the lab testing space at the Executive War College on Laboratory and Pathology Management, Trisha Brown reports that It's Not Just the Test, It's the Service. Genetic Future Daniel reflects on a panel discussion on direct-to-consumer genetic testing of 23andMe, deCODEme and Navigenics at Cold Spring Harbor. Genome Alberta Education In an on-going blog series that serves as a ‘consumer guide to personal genotyping’, Mike Spear describes Genomics at Quinpool, recounting some comments and questions from the Youth Forum on Personal Genomics where students and a panel of experts looked at his personal genome test report and SNP file. Google Health The goal of Google Health is to organize health information and allow users to make their medical records available to doctors or pharmacies. Additionally, you can use the service to find out how medications might interact, refill prescriptions online or get personalized health information based on your profile. When asked if Google Health could make it easy to access personalized genetics services, they indicated that they “have some genetic partners where we’ve already been making investments. Genetics is much further out, and will be done at the control and discretion of the user” [1]. business | bytes | genes | molecules Deepak Singh gives the service a quick synopsis in his article Your Personal Health: Google Health is Live. TechCrunch Techcrunch gives Google Health A Quick Hands-On Look. ReadWriteWeb Richard MacManus reviews the limitations of Google Health in his article Google Health Launches - Cautious, Non-Innovative Entry into Health 2.0. e-patients.net As Google Releases Google Health, John Grohol expresses concern that an individual’s Google Health record may be an ideal way for other companies to market to them based on their specific health concerns. Pimm - Partial immortalization Attila Chordash gives us some background of Google Health’s product manager, asking that we Meet Dr. Google Health: Roni Zeiger, right from Stanford! Scienceroll Berci Meskó hopes he will never get pharma ads or spams from doctors based on his health profile when he announces Google Health: The First Steps. Conclusion That concludes the 32nd edition of Gene Genie. My thanks to everyone who submitted an article. You can find more information about the carnival as well as the hosting schedule and past editions at the Gene Genie Website. The next edition will be hosted at Neurophilosophy on June 8th. References Google Backs Harvard Scientist’s 100,000-Genome Quest (Update2). Bloomberg.com 2008 Feb 29. Pearson H. Genetics: what is a gene? Nature. 2006 May 25;441(7092):398-401. View abstract Gotlib et al. HPA axis reactivity: a mechanism underlying the associations among 5-HTTLPR, stress, and depression. Biol Psychiatry. 2008 May 1;63(9):847-51. Epub 2007 Nov 19. View abstract McGowan et al. Promoter-wide hypermethylation of the ribosomal RNA gene promoter in the suicide brain. PLoS ONE. 2008 May 7;3(5):e2085. View abstract Parkinson et al. c-Jun is a negative regulator of myelination. J Cell Biol. 2008 May 19;181(4):625-37. View abstract Eny et al. Genetic variant in the glucose transporter type 2 is associated with higher intakes of sugars in two distinct populations. Physiol Genomics. 2008 May 13;33(3):355-60. Epub 2008 Mar 18. View abstract The Study Group of Millennium Genome Project for Cancer. Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer. Nat Genet. 2008 May 18. [Epub ahead of print] View abstract Liao and Zhang. Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci U S A. 2008 May 13;105(19):6987-92. Epub 2008 May 5. View abstract Quignon et al. Canine population structure: assessment and impact of intra-breed stratification on SNP-based association studies. PLoS ONE. 2007 Dec 19;2(12):e1324. View abstract McCarthy et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008 May;9(5):356-69. View abstract Roche MI. A case of genetic counselling for Dr Watson. Nature. 2008 May 15;453(7193):281. View abstract Pask et al. Resurrection of DNA Function In Vivo from an Extinct Genome. PLoS ONE. 2008 May 21;3(5):e2240. View abstract Bookmark or Share Thank you for subscribing by RSS or email. I work hard to make the articles on Highlight HEALTH engaging and I truly appreciate your interest and readership! This article was published on Highlight HEALTH. Related articles Genomic Medicine: An Educational Resource from Helix Health The Best of Highlight HEALTH 2007 - The Year in Review HEALTH Highlights - October 23rd, 2007 HEALTH Highlights - September 10th, 2007 HEALTH Highlights - August 9th, 2007

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