{bio,medical} informatics
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GenomeWeb
New Algorithm Could Automate Comparative Gene Mapping"Cornell University researchers have developed a comparative gene mapping algorithm that will soon be available in a software implementation, according to a university statement.
The algorithm draws on natural language processing techniques to remember the labels of genes and make decisions about what sequences go together on the basis of an overall trend.
The automated method should significantly speed the comparative gene mapping process, according to the university."
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The Register
Human genome data in hacker peril shocker"As if the attacks by crackers on credit card databases and even Microsoft's internal network wasn't bad enough, a firm of ebusiness integrators has outlined security holes on sites containing genetic research.
A report issued by BioExchange.com suggests there is lax security at the half-dozen online genomics companies who provide commercial-grade research tools and proprietary data sources for the biotechnology industry."
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The Independent
Genome project: 'This means new opportunities for medicine'"John Sulston, aged 58, is a former director of the Sanger Centre in Cambridgeshire and a leading member of the Human Genome Project team. This is his account of his breakthrough year."
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GenomeWeb
Nature Clarifies Role in GEML Community; Denies it 'Endorses' Standard "While the Nature Publishing Group has joined Rosetta Inpharmatics's Gene Expression Markup Language Community, the journal " is not taking sides or picking any standard over another," a Nature spokesman said Friday."
"This clarification of Nature's role in the GEML community came in response to Rosetta's recent public relations campaign, which claimed the journal " officially endorses" the GEML standard.
The announcement prompted the Microarray Gene Expression Database Group to send a letter to the journal stating that the Microarray Markup Language, which the MGED supports, has wider support in academia and industry."
redux [10.13.00]
"Imagine that your co-worker in the next cubicle has some information you need for a report that's due soon. She e-mails it to you, but the data are from a spreadsheet program, and all you have is a word processor, so there's no possibility of your cutting and pasting it into your document. Instead you have to print it out and type it in all over again. That's roughly the situation facing biologists these days. Although databases of biological information abound--especially in this post-genome-sequencing era--many researchers are like sailors thirsting to death surrounded by an ocean: what they need is all around them, but it's not in a form they can readily use.
To solve the problem, various groups made up of academic scientists and researchers from biotechnology and pharmaceutical companies are coming together to try to devise computer standards for bioinformatics so that biologists can more easily share data and make the most of the glut of information resulting from the Human Genome Project. Their goal is to enable an investigator not only to float seamlessly between the enormous databases of DNA sequences and those of the three-dimensional protein structures encoded by that DNA. They also want a scientist to be able to search the databases more efficiently so that, to use an automobile metaphor, if someone typed in "Camaro," the results would include other cars as well because the system would be smart enough to know that a Camaro is another kind of car."
"Eric Neumann, a member of both the Bio-Ontologies and BioPathways consortia, is a neuroscientist who is now vice president for life science informatics at the consulting firm 3rd Millennium in Cambridge, Mass. (no relation to Millennium Pharmaceuticals). He says Extensible Markup Language (XML) is shaping up to be the standard computer language for bioinformatics."
redux [09.15.00]
"With XML has come a proliferation of consortia from every industry imagineable to populate structured material with standard terms (see Appendix B). By one estimate, a new industry consortium is founded every week, perhaps one in four of which can collect serious membership dues. Rising in concert are intermediary groups to provide a consistent dictionary in cyberspace, in which each consortium's words are registered and catalogued.
Having come so far with a syntactic standard, XML, will E-commerce and knowledge organization stall out in semantic confusion?"
"How are semantic standards to come about?"
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EurekAlert
Science's Top 10: genome sequencing named top scientific advance of 2000 "The editors at the international journal, Science, have compiled their list of the Top 10 scientific developments for the year 2000, placing genome sequencing first on the list.
Science's Top 10 research advances, chosen for their profound implications for society and the advancement of science, appear in the journal's 22 December 2000 issue."
[summary - can be viewed for free once registered]
"2000 was a banner year for scientists deciphering the "book of life"; this year saw the completion of the genome sequences of complex organisms ranging from the fruit fly to the human. Science marks the production of this torrent of genome data as the Breakthrough of 2000; it might well be the breakthrough of the decade, perhaps even the century, for all its potential to alter our view of the world we live in.”
redux [10.17.00]
[requires 'free' registration]
"What can people expect from biotechnology and genomics? Ten luminaries from the biomedical arena, law, and journalism grappled with issues related to that question at the City University of New York's Graduate Center on Sept. 20. In attendance was an audience of 350 whose research, medical, and counseling careers could hinge on how such issues are resolved. Syracuse University's Gene Media Forum (www.genemedia.org) sponsored the event.
The recurring theme was biological predictability. Eric Lander, director of the Whitehead Institute Center for Genome Research, in Cambridge, Mass., noted that in the past century, biologists "worked out a disease by being clever enough to figure out what was wrong." The systematic approach of genomics, he continued, would render research largely predictable.
Panelists stressed, nevertheless, that genomics would not yield answers easily. Harold Varmus, president of Memorial Sloan-Kettering Cancer Center in New York, said that biologists were used to studying one gene at a time. Now, he added, "you've got all the parts of the clock dumped on the table, and you can look at them. But, you know, it's a lot harder to put back together, too."
A consensus emerged that much of the public--including many journalists, behavioral scientists, and physicians--either were unaware of this newfound complexity or twisted it into misguided support for genetic determinism. "
redux [06.26.00]
""How it's going to help me develop drugs or do anything, I really don't have a clue," said Craig Rosen, executive vice president for research and development at Human Genome Sciences."
""It's like being given the best book in the world, but it's in Russian, and it's incredibly boring to read," said Ewan Birney, a team leader at the European Bioinformatics Research Institute, part of the Sanger Centre, one of the major labs working on the Human Genome Project."
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The Washington Post
U.S. Moves To Cloak Medical Records"The Clinton administration will issue broad new regulations today to safeguard the confidentiality of Americans' medical records, establishing the first federal protections aimed at limiting what information doctors, hospitals and health plans can divulge without patients' consent.
The rules are significantly more far reaching than those proposed by the White House a year ago, covering not only electronic medical records, as was initially outlined, but also paper records and oral communications. They also require patients' written consent for even routine disclosure of information, something not covered in the administration's earlier plan, and close a loophole that would have allowed large self-insured employers access to medical records without patient approval."
"The Clinton administration's move will not come without controversy. Medical industry representatives have argued that limiting how patients' records can be used will boost costs and hamper research that could lead to more advanced treatments."
"Accompanying the current debate over health care reform is an equally important debate about the privacy of medical records. No information is more sensitive or potentially more stigmatizing than personal health records. At the same time, medical data have enormous value to researchers and health care providers, offering insight for the epidemiologist and quantitative assessment of health care effectiveness. Striking this balance is not an easy task. Understandably, the medical profession has followed closely the privacy discussion associated with proposed administrative reforms, but many of these issues are complex, and the policy proposals are often not clear."
"Researchers, members of institutional review boards (IRBs), and health advocacy groups have acknowledged the fact that we can no longer guarantee privacy and confidentiality in an age of electronic medical records. The logistic hurdles associated with medical- and research-record gatekeeping make errors inevitable. Because of this reality, it is more important than ever to ensure the use of informed-consent procedures that convey this potential loss of privacy as one of the risks of research. And because the misuse of genetic information could be especially damaging, we need public policies that specifically address genetics research.
Although there are greater costs associated with recontacting individual subjects and gaining renewed consent for any additional research uses of tissue samples or medical records, this is a price we must be willing to pay. Much valuable research will still be able to go forward, and society will not be harmed in any meaningful fashion.
As we move to create better public policies in this area, we must retain our tradition of protecting human subjects and their right to consent or to refuse to consent before any use is made of their medical information for research.”
redux [06.15.00]
"DNA molecules are entirely separate from medical records. In the future, however, the DNA molecule and the medical record are likely to merge into one when it becomes possible to sequence a person's entire genome and put that information on a computer chip or disk. This is not deCODE's current project, but we should not wait until this step is taken to explore its implications. The most important questions would then be who has the authority to make such a disk in the first place; who owns the disk; who controls the use of the disk; and whether the disk containing the genome should be treated as specially protected medical information, as is the case for psychiatric and drug-dependency records? In clinical settings, it seems reasonable to treat such a disk as containing particularly private and sensitive medical information. It also seems reasonable to permit patients to agree to have their entire genome scanned without detailing the tens of thousands of tests that would be run. This is akin to consent to a battery of tests during an annual physical examination.
On the other hand, in a research setting, or when a specific genetic disorder is suspected, the creation and use of an individual patient's genome disk should be subject to the informed consent of the patient. And since they can be both separated from the medical record and readily recreated, research subjects should retain the right to have the files containing their genetic information destroyed at any time.
Iceland's experience with deCODE provides a useful catalyst for formulating fair and ethical rules for research on genetic variation. The Icelandic experience demonstrates that people are concerned about how genetic research is done, that medical-records research and DNA-based research are not the same, that community consultation is necessary but not sufficient to justify DNA-based research ethically, that the probable benefits of such research should be spelled out as clearly as possible, and that international standards for consent to and withdrawal from research should apply directly to research on human genetic variation. Rules for such research will retain their relevance even after it becomes possible to transfer all the genetic-sequence information in a DNA molecule to a computer disk."
redux [02.13.00]
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.
The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.
Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."
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USNews.Com
Slicing and dicing the facts of life"Christian Burks spent a good part of the past four years hunting for an elusive fruit-fly gene that could lead to new treatments for human cancer. But Burks wasn't peering down a microscope or, indeed, doing anything traditionally considered biology. Instead, he led a team that used computers to sift through massive amounts of DNA data, then exploited mathematical tools to predict which of the fly's 13,000 genes was likely to be a tumor suppressor.
Burks is a top practitioner in the crucial new field of "bioinformatics," the marriage of information technology and biology. Thanks to rapid advances in deciphering the genetic code, scientists are generating an exploding volume of biological data that can be stored and analyzed only by computer–for instance, billions of bits of information on gene sequence, individual genetic differences, and protein structure. A bioinformatics specialist helps other scientists work more efficiently–the kind of behind-the-scenes role that usually gets little credit in science, where oversize egos are as common as in Hollywood."
redux [09.19.00]
"If job searching were a poker game, Alan Williams would be sitting pretty with a full house.
Fresh out of graduate school, he happens to have a rare combination of skills that drives employers to offer hefty salaries, stock options and bonuses. And it's not even a dot-com job.
Williams has a combination of computer programming and molecular biology know- how. His job is to use computers to mine the vast store of data in the human genome model."
redux [09.01.00]
[requires paid registration]
"Since Next Wave last covered bioinformatics, in our July 1996 Profiles of Bioinformaticians and February 1997 Bioinformatics Skills features, the prominence of the bioinformatician's role in modern biology has only increased. This month, Next Wave provides a comprehensive picture of the current state of bioinformatics, from the funding situation in Europe and the U.S. to the new bioinformatics degree programs and the immediate hiring needs of industrial and academic labs around the world.”
redux [07.25.00]
"Are you a hacker? Do you yearn for something more important to work on than yet-another-gnome-applet? Are you annoyed that you can't find a problem that is fun to code and stretches your brain in new ways... bioinformatics might be the answer."
"The amount of data is growing faster than anyone expected and only a handful of people can both remain with academic ideals and coding potential. We need hackers to join any number of projects out there. And there are a host to join. If you just liking hacking perl or you prefer compiler technology, there is something to suit you. "
redux [06.27.00]
"A fast-growing field known as bioinformatics uses computing to analyze the vast amount of biological, genomic, and related research to make sense of things too complex for the human brain to fathom.
But bioinformatics is also a bottleneck for many drug and biotech companies that can't find enough talented software engineers who combine sophisticated analysis tools with an understanding of genomics.
''We resolve the bioinformatics issue [by hiring] two people: one who understands computer science and the biologist or researcher,'' said Kenneth Fasman, vice president and global head of informatics of AstraZeneca LLC in Waltham."
"...according to Dr. Donald Johnson, a pathologist at the Nebraska University Medical Center. He estimated there are about 60,000 jobs available to scientists and managers versed in bioinformatics."
redux [05.10.00]
"As expected, salaries for the most part climb as the level of training rises, starting in the $40,000-$50,000 range for BAs and reaching over $100,000 for one post doc. But there are exceptions. For example, two of the three undergraduates who were placed received salaries between $50,0000 to $60,000. This is higher than that earned by seven of the masters students, although ten of the nineteen masters students for whom we have salary information earn more than $60,000. One masters student received a starting salary of over $100,000. Reported salaries for five hires at the doctorate level are over $70,000. One is between $80,000 to $90,000; another is over $100,000; yet another is between $60,000 to $70,000. Three post docs received placements with a salary between $80,000 to $90,000. One post doc was placed at a salary of over $100,000. One institution reported that one or more masters student(s) received a signing bonus.""The results of our current survey make it clear that the majority of these jobs are not being filled by graduates of formal programs—who by our count represent about 15 percent of the positions advertised in 1997. And, we believe the 15 percent figure to be an overestimate given that ads have been growing over time and our most recent ad count is for 1997, a year earlier than our hiring data. This leads us to infer that most of the advertised positions are being filled by individuals trained in informal programs and by individuals who change jobs. The distinct possibility exists that a number of these jobs remain vacant for a period of time, an issue not studied here. Furthermore, our pipeline estimates (see Table 2) lead us to conclude that the number of individuals currently enrolled in formal programs falls far short of the number of positions that have recently been advertised."
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The Informatics Review
"Computers and Biomedical Research" to become "The Journal of Biomedical Informatics""Computers and Biomedical Research (CBR) is being reborn in 2001 under the name "The Journal of Biomedical Informatics" (JBI). "
"Under its new title, JBI will continue the volume numbers from CBR and thus its historical ties to the first 33 volumes will not be lost. The change in title reflects our desire to emphasize informatics rather than the broad area of computers in biomedicine. We need to focus more in one area and the journal is intended to complement JAMIA by emphasizing informatics methodology rather than descriptions or evaluations of completed systems. Formative evaluation articles, and papers emphasizing innovative methodologies and their generalizability, will be encouraged. Graduate students may find JBI a particularly suitable venue for articles on PhD dissertation work, for example. We aim to make it an invaluable resource for medical informatics scientists/researchers and educators."
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MSNBC
Supercomputer tackles DNA project"The world’s fastest commercial supercomputer will soon be devoted exclusively to solving the world’s most powerful puzzle. A new IBM supercomputer will be made available to companies trying to ask questions of the recently decoded human genome."
"The new supercomputer will be capable of performing 7 1/2 trillion calculations per second. That’s 600 times faster than the IBM computer that defeated chess champion Gary Kasparov in 1997. The machine — actually a cluster of computers — will consist of 1,250 IBM servers supported by 2.5 terabytes of memory, 50 terabytes of online disk storage and a high-bandwidth networking infrastructure."
"The 7.5-teraflop computing cluster that IBM is building for Atlanta-based NuTec Sciences will give IBM a “distinct advantage” in the genomics marketplace, an IBM spokesperson said Monday"
"Some market watchers speculated that IBM, whose computers are historically among the more expensive, might have cut NuTec a deal in order to secure a stronger foothold in the genomics sector.
IBM software for web application serving, information portals, and data integration will also be included in the system. NuTec Sciences will use the system to manage, mine and integrate genetic data from a wide variety of sources, and share this information via the Internet with the global life sciences community."
NuTec plans to run several massively parallel applications on the cluster. Morrissey said that a combinatorics algorithm that NuTec is developing in collaboration with the NIH to analyze disease-causing gene combinations is particularly compute-intensive. This algorithm is running as a test set on the company’s IBM computer in Houston, but Morrissey said they’re awaiting delivery of the supercomputer before it can be scaled up to optimal efficiency."
"While many genetic research techniques are the equivalent of monumental exercises in alphabetizing, the NuTec machine also will be useful for another sort of genetics research, into the creation of proteins, Morrissey said. Protein research typically exercises the mathematical abilities of a computer, something that chips from Compaq and IBM are better at handling than Intel chips.
Meanwhile, the Linux operating system is making headway in another type of supercomputer called a Beowulf cluster.
Linux Networx, based in Salt Lake City, has sold a 40-processor computer to Lawrence Berkeley National Laboratory for genetics research, the company said Thursday.
The lab is using the cluster to analyze the genome of the fruit fly Drosophila, a common subject for genetics experiments.
Rosetta Inpharmatics also is using a Linux Networx system, spokesman Brad Rutledge said."
"Inpharmatica, a leading innovator in the application of structural bioinformatics in pharmaceutical research, announced today that it has more than doubled the power of its in-house computer facilities. Correctly-used computer power is an essential part of present and future techniques involved in discovering the drugs of tomorrow and in analysing the enormous amounts of data now generated by the Human Genome Project. Inpharmatica's 1,100 processor system is the most powerful commercial installation in Europe dedicated to bioinformatics, the use of computer techniques in drug discovery."
""Historically, companies wanting to do large scale processing-intensive computing have had to rely on specialist high performance computing vendors with high-cost proprietary solutions," said Pat Leach, IT director at Inpharmatica. "The use of Linux and the low cost of standard PC components has enabled Inpharmatica to achieve 'more for less'."
"The massive amount of data computation inherent in genome research requires either large supercomputers or cluster systems. Cluster technology links multiple inexpensive PCs together to form a powerful, unified system that delivers the computational performance of supercomputers for a fraction of the cost.
"The Linux NetworX cluster is much more cost efficient than the systems we've used in the past," said Erwin Frise, systems manager and biomedical scientist, Lawrence Berkeley National Laboratory. "Comparing the price/performance of the cluster to supercomputers and other options available on the market made Linux NetworX the obvious choice for our research.""
""Historically, companies wanting to do large scale processing-intensive computing have had to rely on specialist high performance computing vendors with high-cost proprietary solutions," said Pat Leach, IT director at Inpharmatica. "The use of Linux and the low cost of standard PC components has enabled Inpharmatica to achieve 'more for less'."
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The Street
Biotech Today, Part 2: Is the Human Genome Land Grab Over?"For years, Dr. J. Craig Venter has been saying that the human genome probably had fewer than 60,000 genes. Heck, Dr. C. nailed most of them when he worked in partnership with Human Genome Sciences (which said back in 1996 that they'd found 96% of the human genes). Now Eric Lander of the famed Whitehead Institute at M.I.T. --- a man who has had his differences with Craig --- has also come out and said that there are fewer than 50,000 genes in the human genome.
The fact that these words have been on the airwaves for years doesn't mean that most investors have heard them. (The axiom "there are 100,000 genes in the human genome" has been pretty deeply drilled into a lot of our brains.) So at our shop, we've been proceeding under the assumption that the big genome land grab happened years ago but a large number of investors haven't noticed that fact. We also assume that most of what will transpire over the next few years will be lawsuits and cross-licensing: We refer to it as the coming "litigation conflagration."
What I'm thinking through at the moment are the implications: Specifically, how will investors react when a critical mass of them realize there are fewer than 50,000 genes -- and most of them are already spoken for?"
redux [04.26.00]
""The analogy that I would use is that of a minefield," said Bob Levy, senior VP of science and technology for American Home Products. "We are spending an incredible amount of time now, when we find exciting targets and begin to validate them, in trying to define who has rights to what. And we're finding, in almost every product that we look at, that someone has patented the protein, the gene, a fragment, a diagnostic test." Levy noted that untangling patent rights, and determining which patents are dominant, are increasingly time-consuming and expensive tasks. And patent-holders must be paid. "The royalties that will be involved soon in some of the products that we are bringing to market, they're already up into the ten, fourteen, fifteen percent [range]," said Levy. "And that may increase with time.""
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MIT Technology Review
Medicine Gets Personal"Now that the Human Genome Project is largely complete, academics and companies are shifting their emphasis to the study of how genes vary among people. The Human Genome Project involves decoding the sequence of one complete set of human genes, a kind of genetic Everyman. But that template won't describe everyone, since DNA varies slightly from person to person. And those minute variations in the DNA, scientists believe, may determine which patients will benefit most from particular drugs—as well as which subgroups may be harmed by them."
"In the future, says Chase, "it is likely that we will know from a drop of blood that a patient has 14 of 19 genes for high blood pressure, and we have 172 drugs that will interact with that. Only a computer will be able to organize this information." Your doctor will become a middleman, Chase suggests, mediating between you, various genomic and information technology systems that will be the backbone of the health care system, and the pharmaceutical treatments that the computer prescribes."
redux [12.05.00]
"The backlash against gene patenting is heating up, and not a moment too soon. The U.S. Patent and Trademark Office has already granted more than 1,000 patents on human genes or their fragments, with over 20,000 pending. The patent office plans to issue new guidelines by the end of the year: Researchers will now have to indicate a gene's function--its "specific and substantial credible utility"--and its chemical code to get a patent. (The industry successfully lobbied against applicants' having to show they could actually make something with the gene.) Though the patent office's revised guidelines represent a minor improvement over the previous open-door policy, they won't do much to slow what Francis Collins, the head of the government-run Human Genome Project, ruefully compares to a gold rush."
"But many public researchers worry that they will have to secure dozens of licenses from private firms before they can conduct their studies. Many independent scientists are sounding alarms about the impact gene patenting will have on research. The red tape will discourage independent biomedical research or at least slow it way down. Besides, it's going to take decades to unravel the complicated biochemical processes encoded by genes, and it is unclear how useful that information will be. Many credible observers of genetic research argue that the medical hoopla surrounding completion of the Human Genome Project--the decade-long, government-funded effort to map the three billion-plus base pairs of human genes--was mostly biohype. "It is very unlikely that a simple and directly causal link between genes and most common diseases will ever be found," Richard Horton, editor of the British medical journal The Lancet, wrote recently in The New York Review of Books. "This message is not one that many scientists want the public to hear; continued political support for funding genetic research depends on persistent public credulity."redux [11.16.00]
"Basic science came to be dominated by molecular genetics. The discovery of DNA spawned new technologies that led to research into genetic engineering, genetic screening, and gene therapy. Naive investors, often ignorant about the wafer-thin credibility of the research they were paying for, poured millions into biotechnology companies. The result, according to Le Fanu, has been that "the impression of progress has not been vindicated by anything resembling the practical benefits originally anticipated."
Worse, gene therapy has largely turned out to be "not only expensive but useless." Why has the new genetics so far failed medicine? Le Fanu answers that "genetics is not a particularly significant factor in human disease." And, in any case, genes are "complex," "unpredictable," and "perverse." They are not amenable to easy understanding. Their involvement in disease is largely "incomprehensible.""
"Neither we nor our critics defined a revolution in medicine. We mean a paradigm shift in theory or practice. Sotos and Rienhoff's plea for "precise diagnosis" epitomizes the current paradigm. In most of those who will have common disorders, the interaction of genetic, environmental, and behavioral factors makes the quest for precise diagnosis illusive. "
"The revolution in medicine will come with the recognition, based in part on genetic research, that the quest for single causes for common diseases will seldom be fruitful and that a new paradigm of a causal web must be adopted. Interventions must be directed at the most vulnerable points in the web. Sometimes this will involve biomedical interventions. At other times, it will involve modifying aspects of our social structure, lifestyle, or environment that increase the risk of disease."redux [11.02.00]
"On both sides of the Atlantic, revolutionary claims have been made about the ultimate impact of genetics on clinical medicine. John Bell at Oxford has asserted that "within the next decade genetic testing will be used widely for predictive testing in healthy people and for diagnosis and management of patients.... The excitement in the field has shifted to the elucidation of the genetic basis of the common diseases." (1) And in the United States the director of the National Human Genome Research Institute, Francis Collins, has stated that the good that would come from mapping the human genetic terrain "would include a new understanding of genetic contributions to human disease and the development of rational strategies for minimizing or preventing disease phenotypes altogether." (2)
Statements like these clothe medicine in a genetic mantle. The result of efforts to identify genes that have a role in common diseases suggests a different picture: the genetic mantle may prove to be like the emperor's new clothes. In this article we argue that the new genetics will not revolutionize the way in which common diseases are identified or prevented. Mapping and sequencing the human genome will lead to the identification of more genes causing mendelian disorders and to the development of diagnostic and predictive tests for them. The development of safe and effective treatments, however, will usually lag behind, (3) although occasionally a treatment does precede the discovery of the disease-causing allele, as was the case for hemochromatosis. (4) Furthermore, only a small proportion of the population has mendelian disorders, and this will limit the ultimate impact of the Human Genome Project.
Our doubts stem from the incomplete penetrance of genotypes for common diseases, the limited ability to tailor treatment to genotypes, and the low magnitude of risks conferred by various genotypes for the population at large. Consequently, most people will have little interest in learning their genotypes."
"With advances in the human genome project and the increasing availability of DNA markers scattered throughout the genome such as simple sequence polymorphisms, variable number tandem repeats, and short sequence repeat polymorphisms, it has become increasingly possible to search for the genetic basis of complex human diseases using genomic wide screening methods. Linkage analysis using LOD score analysis in large pedigrees has been the traditional tool to identify gene loci for human disorders both for single gene disorders (e.g. Huntington) and for complex chronic diseases (e.g. bipolar disease). Recently, Risch and Merikangas have argued that the future of genetic studies of complex human disease may depend, to a large extent, on applications of new "association" type methods to family-based data. The main method of interest is the transmission disequilibrium test (TDT) in which alleles at a given locus for a person with a specific disease are compared with parental non transmitted alleles, to look for evidence of deviation from expectations in the absence of linkage. The TDT has been shown to be a valid test of linkage in the presence of linkage disequilibrium (which creates associations with specific alleles). They showed that the TDT has more power than traditional linkage analysis for disease genes with weak to moderate effects on disease risks.
In this paper, we argue that the future of the genetic study of complex disorders will rely increasingly on the classical epidemiologic "association" paradigm. We show that on the long run, improvements in study designs and in adjusting for population stratification using interviews and genetics markers will lead to a new era of population-based incident case-control studies that could have more power and lead to more detailed information not only on the presence or absence of a disease susceptibility gene but define the magnitude of risks and gene-environment interaction- a crucial first step to disease prevention and health promotion."
"As a result of the revolution in the biological sciences following the development of recombinant DNA technology and the sequencing of most of the human genome, the role of genetics in the pathogenesis of human disease now dominates biomedical research. There is every sign that the rapidly evolving technology of the post genome era will unravel the function of the human genome and explain how the 50 000 to 100 000 genes interact with one another and the environment to make us what we are.
The central question for the medical sciences is the extent to which it will be possible to relate events at the molecular level with the clinical findings or phenotypes of patients with particular diseases. This problem will permeate every aspect of medical research and practice in the future. It will dominate predictive genetics and genetic counselling. It will also be of major importance for clinical decision making as new and novel approaches to the treatment of disease become available, particularly those involving genetic manipulation. Further exploration of the genome may also provide information on some of the common killers of Western society, such as heart disease, stroke, diabetes, and psychiatric disease, leading to a new form of pharmacology in which drugs are tailored to an individual's genetic make up. Even more important, and certainly more complex, will be relating genotype to phenotype. Many of our most important diseases almost certainly reflect varying susceptibility, due to the action of many different genes and a wide variety of environmental factors and to the ill understood biology of ageing."
"Is there any way of guessing the likely levels of complexity that will be encountered as the genetic basis of disease is explored with the new technology?"
redux [07.13.00]
[requires 'free' registration]
"Genes may cause more than one-quarter of three major types of cancer, more than previously thought, a group of researchers says.
Scandinavian researchers concluded that genes account for 42 percent of the risk for prostate cancer, 35 percent for colorectal cancer and 27 percent for breast cancer.
The rest of the cases are caused by what people do, such as smoking and diet, or what happens to them, such as on-the-job hazards or viral infections, the researchers said."
"...the conclusion runs contrary to the widespread belief that scientists "will find solutions or cures to all diseases in the genes," Dr. Lichtenstein said. "That won't be the case."
redux [10.05.00]
"Simple genetic diseases, such as cystic fibrosis and thalassaemia are just that — simple. A single gene underlies them. Finding it is like climbing a steep hill — hard work but straightforward. Complex disorders, such as asthma and type 2 diabetes, by contrast, have many components, which makes finding a cause more like scaling Everest — far harder, requiring more specialist equipment and the strong possibility of failure.
In work published in the October issue of Nature Genetics, University of Chicago researchers have cleared a path to studying the genetic foundation of type 2, or non-insulin-dependent diabetes mellitus (NIDDM). In a study of a Mexican-American population and two white populations (Finns and Germans) they have found that small genetic variations, called single-nucleotide polymorphisms (SNPs), in a particular gene tend to occur more often in diabetics than in healthy relatives. Although finding a common genetic variation in family groups affected by simple genetic disorders is implicit, a gene implicated in a population with a complex disease could provide a potential new target for gene therapy. "Variation in this gene is associated with a threefold increased risk in the groups studied," explains lead researcher Graeme Bell. "
"The research does represent a shift in the landscape of genetic diseases. "Studies are not going to be easy," says Bell "but they are not impossible and each locus will present its own challenges." Kruglyak feels the path is clearer, if only because of the 'psychological factor' of showing it can succeed. How important it will be in the overall problem of diabetes, or how often this kind of success will occur in other diseases, will emerge in time. "
redux [08.31.00]
""Like any large construction project in the public domain, sequencing the human genome has been a subject of discussion and controversy. Major issues have been the cost of the project, its scientific merit, and the effects of the knowledge gained on human affairs. The concern about cost subsided as the project proved viable and attracted private funding. That leaves the other two questions: What will we learn from this sequence, and how will it affect our lives? With fame and fortune to be made in the genome business, one can only be skeptical of the wondrous claims made by the project's protagonists. The Triple Helix examines these questions from a critical and biologically informed angle."
"In Lewontin's triple helix, the genes are placed in their natural context, where history and geography shape the nature of organisms and the genes they contain. His differences with the most modern of molecular and cellular biologists are irreconcilable and reflect the ever-widening gulf between biologists who have an affinity for what goes on outside the laboratory and those for whom the differences between individuals and between species represent "an annoyance [to be] ignored whenever possible." In many laboratories, organisms are now studied under conditions in which genetic variation is eliminated and the environment held constant. It is only under these special conditions, where neither variation nor natural selection is tolerated, that the triple helix collapses into the double helix and genes appear to be paramount.""
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The New York Times
First Complete Plant Genetic Sequence Is Determined[requires 'free' registration]
"Scientists from the United States, Europe and Japan have determined the first complete genetic sequence of a plant, an accomplishment that should deepen understanding of plant biology and provide new ways to genetically engineer crops to increase food production and improve nutrition.
The plant, Arabidopsis thaliana, is a diminutive weed that is related to the mustard plant and is worthless as a crop. But it is quickly becoming the laboratory mouse of the plant world, studied for insights that can be applied to virtually all other plants."
""There's thousands of applications coming down the pipeline," said Chris Somerville, director of the department of plant biology at the Carnegie Institution, professor at Stanford University and an early organizer of the sequencing project. "Our goal — and I say we're going to reach it in the next decade — is to understand plants like little machines. And we're going to use it to do real engineering."
[requires 'free' registration]
"Corn geneticist Virginia Walbot of Stanford, who wrote the Nature News and Views, emphasized in an interview that the project was the second example of how well an international collaboration could function, the first being the C. elegans project.
"So now there are two models for doing Big Biology and Big Science in a collaborative, cooperative mode rather than the competitive mode," she said. Walbot also praised Cereon Genomics for its decision last summer to freely share its database of A. thaliana SNPs and other polymorphisms. "That's another model for how industry can derive proprietary information but also share data with academic scientists in order to speed things up.""
[requires 'free' registration]
"The genomes of yeast, worms, bacteria, fruit flies, and humans are complete or nearly complete. Now the plant Arabidopsis thaliana joins the list. This small member of the mustard family is a favorite of botanists. It has been used as a model organism for years. Knowledge of the plant’s complete genome will allow scientists to extend what they have learned about Arabidopsis to other plants. As with all genome projects, the next big step will be to figure out what the proteins encoded by the newly described genes do.
Reference: The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815."
redux [05.31.00]
"A group of plant scientists are calling for a project to understand the biological machinery of a plant in enough detail so that they could construct a 'virtual' plant. "
"The effort is called Project 2010 because by 2010 plant researchers hope to construct a complete "wiring diagram" of all the biological pathways of Arabidopsis.
Dr Chory said, "Ultimately, we hope to create a 'clickable plant.' We want to be able to go to our computers and click on a cell type and understand all the protein-protein interactions."
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Wired News
Estonia to Open Gene Bank"The Estonian parliament Wednesday passed a law allowing the creation of a nationwide gene bank that scientists say will be the world's biggest -- and a treasure trove for genetics-based health research.
The lawmakers adopted the Human Genes Research Act -- which puts tiny Estonia at the forefront of a global ethical and legal debate on the use of genetic material -- by a vote of 42-3 with one abstention."
"The act limits the use of the gene bank's data to scientific research sanctioned by a new nonprofit foundation, which will be established in the next few months, and imposes jail sentences for the misuse of genetic information.
The law requires that participation by gene donors must be voluntary and their identity kept secret. It forbids employers and insurance companies to collect genetic data on clients or workers, and it bans the use of the data as evidence in law courts."
redux [11.24.00]
"A biotechnology company has acquired the exclusive rights to research the genetic make-up of people living on the South Pacific island of Tonga.
Researchers at Melbourne-based Autogen want to study the remote community to trace the genes that cause particular diseases."
"The biotechnology wing of the Australian company will take DNA and blood samples from among Tonga's 108,000 inhabitants.
"It is not known how much, if anything, Autogen has paid the authorities in Tonga for the right to carry out the tests."redux [09.22.00]
[requires 'free' registration]
"Should genetic material be collected from individuals for the purpose of studying human disease in specific populations? The native genome of Iceland offers a powerful and rare resource in genomic research -- a relatively homogeneous population. In this setting, the proposed Icelandic Healthcare Database, which would integrate medical information with genealogy and molecular genetic data, has driven a number of issues -- both ethical and scientific -- to the fore."
"Leading geneticists scrutinized plans for a national gene bank Thursday, with advocates saying it could dramatically improve understanding of diseases and critics saying it's a waste of money in a country still struggling with basic health needs.
The government in this former Soviet republic recently OK'd the dlrs 200 million proposal to digitally store the genetic codes of at least two-thirds of the 1.4 million population and sent it to parliament, where it's expected to win easy approval."
""Estonia can be a follower of knowledge in the world or it can a leader,'' said Jaanus Pikani, chairman of the Genome Foundation, which drafted the project. "I want it to be one of the leaders.''"redux [06.15.00]
"KUCHING: The Chemistry Department will complete building the DNA (deoxyribonucleic acid) database for the Iban, Bidayuh and Melanau communities in Sarawak by December or early next year, said Science, Technology and Environment Minister Datuk Law Hieng Ding.
He said a similar database for Sarawak's other minority sub-groups, like the Penans, Kayans and Bisaya, would be established next year.
The department relies on hospitals for the supply of blood from the various ethnic groups to build up the DNA database.”
"Law said the first to be established were the DNA database for the Malay, Chinese and Indian communities in the peninsula, which could also be used for Sabah and Sarawak.
Taib said the state government would set up a research council next year to coordinate research actitivities in the state."
"DNA molecules are entirely separate from medical records. In the future, however, the DNA molecule and the medical record are likely to merge into one when it becomes possible to sequence a person's entire genome and put that information on a computer chip or disk. This is not deCODE's current project, but we should not wait until this step is taken to explore its implications. The most important questions would then be who has the authority to make such a disk in the first place; who owns the disk; who controls the use of the disk; and whether the disk containing the genome should be treated as specially protected medical information, as is the case for psychiatric and drug-dependency records? In clinical settings, it seems reasonable to treat such a disk as containing particularly private and sensitive medical information. It also seems reasonable to permit patients to agree to have their entire genome scanned without detailing the tens of thousands of tests that would be run. This is akin to consent to a battery of tests during an annual physical examination.
On the other hand, in a research setting, or when a specific genetic disorder is suspected, the creation and use of an individual patient's genome disk should be subject to the informed consent of the patient. And since they can be both separated from the medical record and readily recreated, research subjects should retain the right to have the files containing their genetic information destroyed at any time.
Iceland's experience with deCODE provides a useful catalyst for formulating fair and ethical rules for research on genetic variation. The Icelandic experience demonstrates that people are concerned about how genetic research is done, that medical-records research and DNA-based research are not the same, that community consultation is necessary but not sufficient to justify DNA-based research ethically, that the probable benefits of such research should be spelled out as clearly as possible, and that international standards for consent to and withdrawal from research should apply directly to research on human genetic variation. Rules for such research will retain their relevance even after it becomes possible to transfer all the genetic-sequence information in a DNA molecule to a computer disk."
Science When an Entire Country Is a Cohort
[summary - can be viewed for free once registered]
"Denmark has gathered more data on its citizens than any other country. Now scientists are pushing to make this vast array of statistics even more useful by easing restrictions on the use of data coded by personal identification numbers. But government officials are reluctant to do so, citing privacy concerns."
redux [02.25.00]
[summary - can be viewed for free once registered]
"Following the examples of Iceland, Sweden, and Estonia, the United Kingdom is drawing up plans to create a national database linking the DNA of 500,000 of its citizens to their medical records and lifestyle details. Its main goal is to tease apart the genetic and environmental components of conditions such as cardiovascular disease and cancer and, eventually, to come up with new drugs to treat--or even prevent--these conditions. An expert panel is currently hammering out a strategy for setting up the database and is due to report its recommendations next month.”
redux [02.13.00]
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.
The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.
Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."
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Wired News
Genomics Gets a New Code: GEML"The Internet uses HTML, and soon perhaps genomics will use GEML.
At least that's what Rosetta Inpharmatics (RSTA), the creators of Genetic Expression Markup Language, or GEML, is hoping. The prestigious science journal Nature adopted the language on Monday, which should give a significant boost to its acceptance in the scientific community."
"According to Metcalfe's law, penned by 3Com founder Robert Metcalfe, the more people who use any system, the more valuable it becomes. And since researchers will now be required to submit papers using GEML, the value of the language should increase exponentially."
redux [10.30.00]
"Version 1.0 of Rosetta Inpharmatics’ Gene Expression Markup Language (GEML) Conductor tools is now available for downloading from the company website (http://www.rii.com.). This suite of applications, which employs an open-standard XML file format, enables researchers to visualize and exchange data between different gene expression databases and analysis systems.
The company refers to its GEML Conductor tool as a universal solution for visualizing and exchanging gene expression information produced by different technology platforms. It allows users to convert any well-formatted gene expression data file into a common, flexible data format.
Rosetta GEML Conductor tools' features include:
"The inability to analyze gene expression data from multiple technology platforms has long been hampered by software compatibility issues," stated Mark Boguski, senior vice president of research and development for Rosetta Inpharmatics. "By translating diverse data formats into a single common format, the Rosetta GEML Conductor tools enable users to share and visualize information across platforms, thus maximizing the value of gene expression data."
- File Conversion. Users can convert any gene expression data file, including Affymetrix GeneChip and BioDiscovery AutoGen, into the GEML format.
- Plot Viewer. Users can visualize and share data by turning any GEML profile into a plot. The Plot Viewer includes a Zoom feature, which allows magnification into or out of particular sections of a plot.
- Magic Lasso. Users can select specific plot areas for closer viewing.
- Intensity Plot Viewer. Users can measure the intensity of one channel of data against the intensity of another channel of data.
- Customizable Visualization. Users can customize groups, colors, and labels according to viewer preferences.
- InstaLink. Users can access built-in hotlinks to popular databases and information centers on the World Wide Web.
- Table Viewer. Users can convert GEML data into customizable tables with resizable and reorderable columns.
redux [10.13.00]
"Imagine that your co-worker in the next cubicle has some information you need for a report that's due soon. She e-mails it to you, but the data are from a spreadsheet program, and all you have is a word processor, so there's no possibility of your cutting and pasting it into your document. Instead you have to print it out and type it in all over again. That's roughly the situation facing biologists these days. Although databases of biological information abound--especially in this post-genome-sequencing era--many researchers are like sailors thirsting to death surrounded by an ocean: what they need is all around them, but it's not in a form they can readily use.
To solve the problem, various groups made up of academic scientists and researchers from biotechnology and pharmaceutical companies are coming together to try to devise computer standards for bioinformatics so that biologists can more easily share data and make the most of the glut of information resulting from the Human Genome Project. Their goal is to enable an investigator not only to float seamlessly between the enormous databases of DNA sequences and those of the three-dimensional protein structures encoded by that DNA. They also want a scientist to be able to search the databases more efficiently so that, to use an automobile metaphor, if someone typed in "Camaro," the results would include other cars as well because the system would be smart enough to know that a Camaro is another kind of car."
"Eric Neumann, a member of both the Bio-Ontologies and BioPathways consortia, is a neuroscientist who is now vice president for life science informatics at the consulting firm 3rd Millennium in Cambridge, Mass. (no relation to Millennium Pharmaceuticals). He says Extensible Markup Language (XML) is shaping up to be the standard computer language for bioinformatics."
redux [05.10.00]
The XML Cover Pages XML and Semantic Transparency
"We may rehearse this fundamental axiom of descriptive markup in terms of a classical SGML polemic: the doubly-delimited information objects in an SGML/XML document are described by markup in a meaningful, self-documenting way through the use of names which are carefully selected by domain experts for element type names, attribute names, and attribute values. This is true of XML in 1998, was true of SGML in 1986, and was true of Brian Reid's Scribe system in 1976. However, of itself, descriptive markup proves to be of limited relevance as a mechanism to enable information interchange at the level of the machine.As enchanting as it is to contemplate the apparent 'semantic' clarity, flexibility, and extensibility of XML vis-à-vis HTML (e.g., how wonderfully perspicuous XML <bookTitle> seems when compared to HTML <i>), we must reckon with the cold fact that XML does not of itself enable blind interchange or information reuse. XML may help humans predict what information might lie "between the tags" in the case of <trunk> </trunk>, but XML can only help. For an XML processor, <trunk> and <i> and <booktitle> are all equally (and totally) meaningless. Yes, meaningless.
Just like its parent metalanguage (SGML), XML has no formal mechanism to support the declaration of semantic integrity constraints, and XML processors have no means of validating object semantics even if these are declared informally in an XML DTD. XML processors will have no inherent understanding of document object semantics because XML (meta-)markup languages have no predefined application-level processing semantics. XML thus formally governs syntax only - not semantics."
redux [09.15.00]
"With XML has come a proliferation of consortia from every industry imagineable to populate structured material with standard terms (see Appendix B). By one estimate, a new industry consortium is founded every week, perhaps one in four of which can collect serious membership dues. Rising in concert are intermediary groups to provide a consistent dictionary in cyberspace, in which each consortium's words are registered and catalogued.
Having come so far with a syntactic standard, XML, will E-commerce and knowledge organization stall out in semantic confusion?"
"How are semantic standards to come about?"
"There is an increasing demand for formalized knowledge on the Web. Several communities (e.g. in bioinformatics and educational media) are getting ready to offer semiformal or formal Web content. XML-based markup languages provide a 'universal' storage and interchange format for such Web-distributed knowledge representation. This tutorial introduces techniques for knowledge markup: we show how to map AI representations (e.g., logics and frames) to XML (incl. RDF and RDF Schema), discuss how to specify XML DTDs and RDF (Schema) descriptions for various representations, survey existing XML extensions for knowledge bases/ontologies, deal with the acquisition and processing of such representations, and detail selected applications. After the tutorial, participants will have absorbed the theoretical foundation and practical use of knowledge markup and will be able to assess XML applications and extensions for AI. Besides bringing to bear existing AI techniques for a Web-based knowledge markup scenario, the tutorial will identify new AI research directions for further developing this scenario."
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Sean Eddy and Ewan Birney
An Open Letter to Bioinformatics Researchers"Dear fellow bioinformatics developers:
By now you have probably heard that Celera Genomics has submitted their human genome paper to the journal Science. Science and Celera have agreed to special terms for the release of the human genome sequence data. It will be made available through the Celera website, and will not be submitted to the international DNA database consortium (GenBank, EMBL and DDBJ). Science's statement regarding the agreement is at: http://www.sciencemag.org/feature/data/announcement/genomesequenceplan.shl
All major journals, including Science, have a policy of deposition of sequence data with the "appropriate data bank". The accepted community standard is submission to GenBank/EMBL/DDBJ. The reason for this deposition is to make the results of the work openly available for future research. This principle was specifically mentioned in the Clinton/Blair statement on human genome sequencing - http://www.usinfo.state.gov/topical/global/biotech/00031401.htm - who strongly upheld the view that "unencumbered access" to genome data was critical.
The terms of the Celera/Science agreement will give us access to the genome sequence, but not unencumbered access. Celera is suggesting publishing their data under a MTA (Material Transfer Agreement) which would prevent large scale downloads and incorporation of this data into GenBank/EMBL/DDBJ. In order to download the data, you and your institution will have to sign a contract guaranteeing that you will not "redistribute" the Celera data.
Science believes that the deal is an adequate compromise because it provides us the right to download the data and publish our results. We believe Science is thinking in terms of single gene biology, not large scale bioinformatics. It is probably not hard for you to imagine scenarios in bioinformatics in which "publication" and "redistribution" are virtually the same thing; we cannot imagine Celera allowing us to incorporate data into Pfam, for example, nor into Ensembl.
We are asking for your support in writing to Science to politely insist that genome sequence papers should be accompanied by unencumbered deposition to GenBank/EMBL/DDBJ. Please note that we have no issue with Celera either keeping this data unpublished for commercial reasons, nor with them combining their data with freely available data from the public genome projects. We would defend their right to do either. Our view is simply that the genome community has established a clear principle that published genome data must be deposited in the international databases, that bioinformatics is fueled by this principle, and that Science therefore threatens to set a precedent that undermines our research.
We encourage you to express your views on this matter to Donald Kennedy (kennedyd@kennedyd.pobox.stanford.edu), the Editor-in-Chief of Science, and/or to Barbara Jasny (bjasny@aaas.org), the managing editor in charge of genomics papers at Science."
[via bioinformatics.org]
"Two leading bioinformaticists have issued a call to arms to their colleagues in response to Science’s decision to allow Celera to submit its genome data under special circumstances.
“Agitate. Let Science know you care,” write the letter’s authors, Ewan Birney of the European Bioinformatics Institute and Sean Eddy of the Howard Hughes Medical Institute and Washington University. “Even if we can’t ch