Tuesday, July 31, 2001

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""All happy families are more or less like one another: every unhappy family is unhappy in its own particular way." In his opening line to Anna Karenina, Tolstoy might well have been referring to breast cancer families. While two genes responsible for about 15% of hereditary breast cancer, BRCA1 and BRCA2, have been found, researchers have had little success finding a single gene that is responsible for the bulk of hereditary breast cancer. And prospects remain gloomy, according to Doug Easton, co-discoverer of BRCA2, speaking last week at the 25th Annual Meeting of the Human Genetics Society of Australasia in Cairns."

"In other words, the intrinsic problem may be akin to that which Tolstoy identified. Each different family may have a different collection of predisposing genes, and when family studies are combined, the separate findings merely obliterate each other."

"This line of thinking suggests family studies may not be able to yield more predisposition genes. An alternative approach is to sift through the genomes of huge numbers of breast cancer cases and controls, looking for those gene variants that clearly differ in the two populations. Gene variants under-represented in the cases might be protective; those over-represented could be risk genes."

redux [03.20.01]
BreastLink Both Genes and Environment Play Role in Causing Cancer

"The study?s analysis suggests that having a gene associated with a particular cancer does not mean that the individual carrying that gene will inevitably develop cancer. Even a person whose identical twin develops cancer has less than a 15 percent chance of having the same kind of cancer. This study thus introduces a much needed shot of reality into the media portrayal of fatalism and inevitability surrounding the issue of genetic heritage.

The study also points to a need for accelerated research into the extent to which genes interact with the environment to affect an individual?s susceptibility to disease. Most importantly, this and similar studies make it abundantly clear that the nature-versus-nurture argument is based on a false and arbitrary separation."

redux [05.26.00]
British Medical Journal Both Genes and Environment Play Role in Causing Cancer

"Research in disease aetiology has shifted towards investigating genetic causes, powered by the human genome project. Successful identification of genes for monogenic disease has led to interest in investigating the genetic component of diseases that are often termed complex, that is, they are known to aggregate in families but do not segregate in a mendelian fashion. Genetic epidemiology has permitted identification of genes affecting people's susceptibility to disease, although progress has been much slower than many people expected. While the role of genetic factors in diseases such as hypertension, asthma, and depression is being intensively studied, family studies and the large geographical and temporal variation in the occurrence of many diseases indicate a major role of the environment. Thus, it is necessary to consider findings about susceptibility genes in the context of a population and evaluate the role of genetic factors in relation to other aetiological factors. This article discusses some approaches used to resolve the genetic architecture of disease and to study the relation of genes to environmental factors in the population."

redux [11.16.00]
The Centers for Disease Control The Future of Genetic Studies of Complex Human Diseases: An Epidemiologic Perspective

"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."

Monday, July 30, 2001

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"Protein folding has been called one of the great unsolved mysteries of molecular biology, a process too complex and elusive to predict with accuracy. Recently, however, a team led by HHMI investigator David Baker at the University of Washington School of Medicine has begun making predictions that one admiring expert compares to a string of home runs."

"Baker has developed a computational technique, called Rosetta, that predicts the ways in which proteins, which start out as the string-like amino acid sequences that emerge from the protein-synthesis machinery, undergo a folding process that might be dubbed "extreme origami.""

redux [01.20.01]
Nature: Science Update Protein predictors need start to finish

"Figuring out the shape of the proteins encoded by the thousands of genes in every cell may have just got a little easier. Researchers in Switzerland have made a discovery which they say "pushes the simulation of protein folding processes within reach"1. It is all about knowing where to start."

"An unfolded or 'denatured' protein is not compacted into a well-organized shape. It is more like a loosely tangled ball floating in water. Attempts to model protein folding by computer often assumed that it doesn't matter much what denatured state you start with, since they are all more or less equally messy.

Not so, says van Gunsteren's team..."

Thursday, July 26, 2001

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"To enable its customers to quickly tie together the many strands of genomic and microarray data relevant to their experiments, Affymetrix announced Wednesday that it has launched NetAffx, an online genomic information resource."

"The website, www.netaffx.com , includes links to GenBank, UniGene, and other public genome databases, as well as proprietary information on protein-related annotations developed at Affymetrix. It is powered by a search engine from Affymetrix's collaborator, Lion Bioscience of Heidelberg, Germany"

Wednesday, July 25, 2001

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"Celera Genomics Corp. is launching an ambitious effort to identify the genetic variations responsible for human disease, a move the Rockville firm hopes will bolster its plans to develop new drugs and diagnostic tests."

The company that mapped the human genome plans to turn its scientific expertise toward finding the tiny genetic differences, known as SNPs, for single nucleotide polymorphisms, that make individuals unique. The project will focus on SNPs linked to disease and varying patient responses to medicine."

"The initiative is part of a broader strategy by Celera's parent company, Applera Corp. of Norwalk, Conn., to cash in on the vast amounts of genetic information generated by Celera's mapping of the human genome."

The Standard Celera Enters a New Genome Race

"Celera, which has one of the nation's largest civilian computer complex, could conceivably surge ahead of companies such as Orchid in the SNP race. But scientists say that when it comes to applying SNPs to drug development, the goals are much broader and vaguer than they were during the race to sequence the human genome.

"Unlike the moon shot that the sequencing of the human genome represented, where there's such a well defined goal, the next age of value development of genetic diversity is going to be characterized by diversity itself," says Dale Pfost, the CEO of Orchid. "There's going to be a range of strategies.""

GenomeWeb Celera Diagnostics Begins to Find its Place Within Applera

"Celera Genomics may be responsible for generating the genomic data that will fuel Applera's new $75 million initiative to reach commercial success, but its sister company Applied Biosystems will initially benefit the most from Celera's genome and SNP mapping activities, executives for the companies said Tuesday."

""We figure that the ability of people to get useful information from studying a host of biological problems in a large number of individuals results in a much bigger experimental load that needs to be fed by a reagent stream, as well as instrument systems," said Hunkapiller. "We would see this as a really big opportunity for us.""

Tuesday, July 24, 2001

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"Compaq Computer and Edinburgh Biocomputing Systems said Monday they had successfully achieved one billion comparisons per second running the Smith-Waterman algorithm on a single 1 GHz Alpha processor."

In a demonstration at the International Conference on Intelligent Systems for Molecular Biology, EBS used its MPSRCH sequence analysis software to run a Smith-Waterman search on a 353-residue protein sequence in Swiss-Prot in 12.5 seconds. EBS CEO Shane Sturrock said the same search would have taken 17 times as long using a standard Smith-Waterman implementation such as S-Search on the same machine."

"Noting that "there has been some confusion" in the life sciences community about the Alpha phase-out that the company announced several weeks ago, Binns reiterated that the company plans to support the Alpha technology even as it moves toward implementation of the Intel Itanium platform."

redux [06.26.01]
Forbes IBM's Biotech Resurgence

"In 1998, biotech upstart Celera Genomics needed a supercomputer to help it map the human genome. It didn't turn to IBM , which built 204 of the 500 fastest supercomputers. Both Celera and its academic competition, the Human Genome Project, used machines built by Compaq Computer. Two years later, Compaq is the leading seller of supercomputers to biological researchers.

But IBM noticed that biologists now need microprocessors as much as microscopes. A year ago, it used $100 million to start a division that sells computers, software and services to biotechnology and drug companies. This life sciences division has had some success; pulling into second place behind Compaq, it must do better."

redux [05.21.01]
Business 2.0 Tech Giants Court The Genome Crowd

"According to scientists, decoding the human genome is the most complicated civilian computational problem ever tackled, and the data generated by genomics has been doubling every six months. Proteomics eventually will generate 100 times more data than genomics and require 1,000-times more computing power.

"We don't need an evolution in computing, we need a revolution . The normal increase in CPU power is just not enough," says Marshall Peterson, vice president of infrastructure development for Celera. "This is what we call Venter's law-it states that biology will outpace Moore's law. Fast makes the difference in the very beginning of a market, but we won't be at this stage for long.""

Monday, July 23, 2001

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"A haplotype is defined as the genetic constitution of a person with respect to one member of a pair of genes. Small differences in genes are known as single nucleotide polymorphisms (SNPs). Researchers analyzed 313 genes in 82 individuals with different ancestral backgrounds. They found that "the strength of the genetic association of pairs of SNPs (linkage disequilibrium), which is important in the identification of disease-related genes, could not be readily predicted from examining individual genes or genomic regions." It appears that haplotypes provide more information as genetic markers in a gene than do SNPs.

Reference: Stephens, J.C., Schneider, J.A., Tanguay, D.A. et al. 2001. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293(5529):489-493."

USA Today Genome guide is next goal

"Until recently, scientists had hoped to predict a person's response to medicines and find disease-causing genes by analyzing specific gene variations, called single nucleotide polymorphisms, or SNPs. But the vast number of SNPs in the human genome would make this costly and laborious.

But new research indicates that SNPs actually travel together from one generation to the next in strands called haplotypes, Collins says.

Creating a haplotype map, he says, would greatly simplify the process of analyzing an individual's risk of disease and response to certain drugs. "The whole Human Genome Project has been a prelude to this," says Eric Lander of MIT, a leader of the publicly funded project."

""Trust me, it's going to be a very powerful way to understand genetic disease," he said."

redux [07.18.01]
BioMedNet For haplotype mappers, deja vu all over again
[requires 'free' registration]

"A US government-centered effort to gain useful information from a map of single nucleotype polymorphisms (SNPs) might be late off the starting block, again chasing a private effort toward the same goal. That conclusion is emerging even as the National Human Genome Research Institute (NHGRI) convenes a two-day planning meeting here, involving the SNP consortium of pharmaceutical and biotechnology companies as well as academic leaders."

"Larry Thompson, chief of the communications and public liaison branch of NHGRI, told BioMedNet News that there is no Haplotype Project currently underway, and this week's meeting (which Brooks had billed as the "Haplotype Meeting") will examine the opportunities that the science presents. "This is a natural extension of efforts that are currently underway and which we believe will help identify genes and their relationship to disease," he said. "How this project will take shape is a big unknown at the moment.""

Wired News Geneticists Await Haplotype Map

"An effort called the SNP Consortium is also underway to identify and interpret individual variations. Looking at SNPs individually can help determine predisposition to disease and potential reactions to drugs."

""It's like the differences between buses and cars," Venter explained."

"These are difficult concepts for non-scientists to understand, but Collins said everyone has an interest in knowing about this type of research."

""Trust me, it's going to be a very powerful way to understand genetic disease," he said."

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""Biologists would rather share their toothbrush than share a gene name," says Michael Ashburner, joint head of the European Bioinformatics Institute (EBI) at Hinxton near Cambridge, and one of GO's founders. "Gene nomenclature is beyond redemption.""

"There is also a realization that genes may have several functions as they are expressed at different times during development or are transcribed in different ways - so names based on known functions may turn out to be misleading. "It'll be many years before we can agree on a set of names," says Mark Boguski, senior vice-president of research and development at Rosetta Inpharmatics, a company in Kirkland, Washington, that specializes in exploiting genomic information."

Sunday, July 22, 2001

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"Recognizing the growing importance of computational and information sciences to biology, the National Institutes of Health is establishing a new Center for Bioinformatics and Computational Biology (CBCB). The new center is designed to support research and training in areas that merge biology with computer sciences, engineering, mathematics, and physics.

"The future of the biological sciences will be driven by advances in bioinformatics and computational biology," says Marvin Cassman, director of the National Institute of General Medical Sciences (NIGMS)."

Friday, July 20, 2001

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"Scientists planning the next phase of the human genome project are being forced to confront a treacherous issue: the genetic differences between human races."

"With the decoding of the human genome largely complete, government scientists are beginning to construct a special kind of genetic map that would provide a shortcut to locating the variant human genes that predispose people to common diseases."

"The question the scientists face is whether that map should chart possible differences that may emerge among the principal population groups, those of Africans, Asians and Europeans."

redux [03.18.01]
The Atlantic Online The Genetic Archaeology of Race

"Genetics research is demonstrating that the differences in appearance among groups are profoundly incidental, but these differences do have a genetic basis. And although it's true that all people have inherited the same genetic legacy, the genetic differences among groups have important implications for our understanding of history and for biomedical research. These complications in an otherwise reassuring story have thoroughly spooked the leaders of the public and private genome efforts. The NIH has been collecting information about genetic variants from different ethnic groups in the United States, but it has refused to link specific variants with ethnicity. Celera has been sequencing DNA from an Asian, a Hispanic, a Caucasian, and an African-American, but it, too, declines to say which DNA is which.

This strategy of avoiding the issue is almost sure to backfire. It seems to imply that geneticists have something to hide. But the message emerging from laboratories around the world should be hailed, not muzzled. It is one of great hope and promise for our species."

redux [06.11.01]
The New York Times Do Races Differ? Not Really, DNA Shows
[requires 'free' registration]

"Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level.

But the more closely that researchers examine the human genome -- the complement of genetic material encased in the heart of almost every cell of the body -- the more most of them are convinced that the standard labels used to distinguish people by "race" have little or no biological meaning.""

"Through transglobal sampling of neutral genetic markers -- stretches of genetic material that do not help create the body's functioning proteins but instead are composed of so-called junk DNA -- researchers have found that, on average, 88 percent to 90 percent of the differences between people occur within their local populations, while only about 10 percent to 12 percent of the differences distinguish one population, or race, from another.

To put it another way, the citizens of any given village in the world, whether in Scotland or Tanzania, hold 90 percent of the genetic variability that humanity has to offer."

""Ethnicity is a broad concept that encompasses both genetics and culture," Dr. Anand said. "Thinking about ethnicity is a way to bring together questions of a person's biology, lifestyle, diet, rather than just focusing on race. Ethnicity is about phenotype and genotype, and, if you define the terms of your study, it allows you to look at differences between groups in a valid way."

redux [08.01.00]
GeneLetter Inequalities and individualized medicine

"Over the next few years a number of competing groups - my own company, Sequenom, among them -- will sort through the diverse genetic material of the human species to find those variations called single nucleotide polymorphisms (SNPs, pronounced SNIPS) that predispose individuals to major clinical disorders."

"At present the overwhelming bulk of the effort to identify these natural variations is in the private sector. This is inevitable because SNPs that associate with major diseases are patentable, by traditional standards."

"Whatever ensues, it is clear that the rate of discovery of medically important SNPs and their conversion into clinically useful tools will not progress equally fast or uniformly for all segments of mankind."

"It will be easier to discover medically important SNPs in geographically isolated and inbred populations in which good familial records and where migration has not introduced confounding genetic variation. Iceland and Finland are strong early candidates."

redux [03.12.01]
GeneLetter Drawing DNA lines of ethnicity

"The idea of using genetics to determine ethnic heritage has been growing in popularity over recent years. When Rick Kittles, a geneticist at Howard University, offered to trace tribal roots via a $350 DNA test, African Americans flooded his telephone line with requests.

"Even if an identifying marker shows up, the result isn't necessarily definitive. While certain markers may be more common to one ethnic group, most also can be found in other populations as well.

"Because of the tremendous genetic variation within populations, it would be biologically impossible to settle on a limited number of genetic markers that could define "Native Americans," says Morris Foster, an anthropologist at the University of Oklahoma who has wrestled with the risks faced by Indian tribes interested in genetic research.

Furthermore, Foster added in an e-mail interview with GeneLetter, "it is absurd to try to define what is essentially a social identity by using biological characteristics. This, though, is how racism has historically worked."

Thursday, July 19, 2001

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"The first thing you see on the Icelandair video screen after takeoff on the flight from the United States to Keflavik International Airport isn't a sweeping tour of Iceland's famous glaciers, geysers, healing hot springs or vast lava fields. It isn't even an introduction to the country's lucrative fishing industry or its legendary Norse sagas. It's a three-minute presentation on Iceland's newest national treasure, DeCode Genetics."

It's not your average airplane fare, but DeCode is not your average company."

redux [02.17.01]
The Scientist Gene Pool Expeditions
[requires 'free' registration]

"A good gene pool, like love, is where you find it. Now genomics researchers have two new ones to swoon over: one from Estonia, a crossroads of Scandinavian cultures and the northernmost of the former Soviet Union's Baltic republics; and from Tonga, an island kingdom half a world away where a Polynesian people has lived in near-perfect isolation for close to 3,500 years. Tonga and Estonia laid final plans last November and December, respectively, for national gene pool exploration programs aimed at discovering disease-associated genes and developing therapies based on the discoveries.

They follow the trail blazed by Iceland, where for several years the gene pool of 275,000 Icelanders has been the fishing preserve of Reykjavik-based deCODE Genetics which is hunting for gene variants that affect serious, often chronic diseases by finding statistical links between Icelanders' genotypes and their inherited illnesses."

redux [06.15.00]
New England Journal Of Medicine Rules for Research on Human Genetic Variation -- Lessons from Iceland

"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."

Wednesday, July 18, 2001

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"A US government-centered effort to gain useful information from a map of single nucleotype polymorphisms (SNPs) might be late off the starting block, again chasing a private effort toward the same goal. That conclusion is emerging even as the National Human Genome Research Institute (NHGRI) convenes a two-day planning meeting here, involving the SNP consortium of pharmaceutical and biotechnology companies as well as academic leaders."

"Larry Thompson, chief of the communications and public liaison branch of NHGRI, told BioMedNet News that there is no Haplotype Project currently underway, and this week's meeting (which Brooks had billed as the "Haplotype Meeting") will examine the opportunities that the science presents. "This is a natural extension of efforts that are currently underway and which we believe will help identify genes and their relationship to disease," he said. "How this project will take shape is a big unknown at the moment.""

Wired News Geneticists Await Haplotype Map

"An effort called the SNP Consortium is also underway to identify and interpret individual variations. Looking at SNPs individually can help determine predisposition to disease and potential reactions to drugs."

""It's like the differences between buses and cars," Venter explained."

"These are difficult concepts for non-scientists to understand, but Collins said everyone has an interest in knowing about this type of research."

""Trust me, it's going to be a very powerful way to understand genetic disease," he said."

Tuesday, July 17, 2001

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"A court case in the UK that involved police gaining access to confidential medical records threatens to undermine a £20 million national database to study the role of genes in disease, senior government advisers have been told."

"The Human Genetics Commission, the Government's own watchdog on DNA research, said it was deeply concerned at the implications of the court case, in which supposedly private records of a medical project were used by police despite protests from scientists."

redux [03.01.01]
British Medical Journal Safeguards for research using large scale DNA collections

"Declining confidence in the governance of clinical practice has serious implications for medical research. Recent studies looking at public opposition to genetically modified foods and the social psychology of risk have shown that the level of trust in the institutions governing a particular activity is the key factor affecting public perceptions of risk in that area.2 The loss of confidence in the Ministry of Agriculture, Fisheries, and Food and the agencies responsible for food safety following the uproar over bovine spongiform encephalopathy laid the foundation for widespread public scepticism about the safety of genetically modified foods. If there continues to be erosion of trust in the medical profession there is a real danger that controversial areas of research, such as genetics, will provoke increasing levels of public opposition. It is in this context that the proposals for the creation of a very large collection of DNA samples for genetic research should be examined."

British Medical Journal Safeguards for research using large scale DNA collections

"Current and emerging technologies will allow rapid identification of mutations causing well described single gene disorders, single nucleotide polymorphism profiling, and genomic sequencing. These powerful technologies may enable the identification of predispositions to common, multifactorial disorders and predict individuals' responses to conventional therapeutic interventions. On the basis of discussions with general practitioners and practice nurses, and the findings of a recent informal survey among general practitioners in South Wales about attitudes and knowledge of genetics (unpublished data), I think that few professionals in primary care would be confident in explaining the nature of these techniques and the importance and implications of the data that would be generated. This would seriously limit the ability of professionals in primary care to obtain informed consent and answer questions that arise over the years of the study. The long term nature of the proposals reinforces the view that education and training in genetics, and particularly in the basic science that underpins the subject, are a priority for medical, nursing, and associated professions at the basic, specialist, and continuing education stages. The success of the proposed study and future population genetic studies are dependent on this educational need being immediately and effectively addressed."

redux [10.31.00]
Healthcare Informatics Truth AND Consequences

"Space has been called the last frontier. But now modern science has begun exploration of another new territory: the human genome. In mapping this instruction book of life, researchers are becoming able to pinpoint genes for a wide array of diseases and to guide creation of revolutionary new drug treatments.

But this new age of discovery also is resurrecting old issues of privacy and discrimination. Medicine can now accurately predict who will contract certain illnesses, such as Huntington's disease, but it still cannot save patients from its debilitating effects. On the other hand, a woman might test positive for a gene predisposing her to breast cancer but nevertheless live a long, cancer-free life.

How can medical records be protected so patients are free to be tested for genetic defects without losing health insurance or being unfairly eliminated on job applications? Those who work with medical records--whether electronic or paper-based--will undoubtedly come face-to- face with such privacy considerations very soon, if they haven't already."

redux [07.18.00]
ComputerUser Medical Privacy Concerns Heightened by Genome Mapping

"Privacy advocates, still reeling from last year's passage of legislation that allows banks and insurance companies to share personal information, are bracing against a new threat to the confidentiality of medical and financial information: The Human Genome Project.

"Latanya Sweeney, professor of computer science and public policy at Carnegie Mellon University, said currently more than 40 US states have laws requiring hospitals to make available to insurance companies and researchers certain information about each visit they receive, including the diagnosis, birth date, ethnicity, gender and Zip code of all patients discharged.

While state regulations say such categories are sufficiently anonymous to conceal the identity of patients, Sweeney said companies can and do match such information with personally identifiable data, using just a few publicly available resources."

""It may surprise some to know that 87 percent of the US population is uniquely identifiable today by just their birthday, gender and zip code," Sweeney said."

"Sweeney said the stakes become much higher when genetic information comes into play. For instance, she said, gender can usually be identified using just the base of a person's DNA sequence. Using a larger chunk of DNA information, researchers can infer particular diseases by catalogued and known sequence patterns. Link those sequences to publicly available hospital data, and you have an undeniably complete picture of an individual's most private information, Sweeney said."

Monday, July 16, 2001

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"A year after the deciphering of the human genome boggled the world, investors are realizing that manipulating genes to fight disease is still in its infancy -- and far from profitable."

Nowhere is that more clear than in the industry for genetic information, or bioinformatics."

redux [06.01.01]
GenomeWeb Software Vendors Hungry for a Piece of the Burgeoning Bioinformatics Consulting Market

"Justin Saeks, an analyst with Frost & Sullivan, sees plenty of room for new players in the consulting market. "I think there is definitely a demand for this," said Saeks, "Maybe equal to or more than the software sales, depending on whether you include hardware with IT consulting."

A Frost & Sullivan study conducted for IBM predicted that life sciences companies would spend nearly $6.5 billion on IT services by 2004.

One reason for the surge of interest in the field is the maturation of data-generating technology, which has left biotech and pharma clients "struggling with the rate of change and the degree of integration on their shoulders," said Bob White, vice president of Accelrys' worldwide sales and consulting division."

redux [04.01.01]
BusinessWeek Bioinformatics

"The reason for this sudden feeding frenzy? Sales growth. Although analysts estimate that bioinformatics will grow into a $2 billion dollar industry in the next five years, most IT companies believe the payoffs will be much higher. An internal study commissioned by IBM, for instance, predicts that when the markets for high-performance computing, storage, and e-commerce combine with that of data management, the worldwide market for IT products and services in the life-sciences sector will swell to $43 billion by 2004. Looking at these kinds of numbers, "now is not the time to think small,'' says Caroline A. Kovac, vice-president of IBM's Global Life Sciences Business Unit."

redux [06.26.00]
Oscar Gruss & Son Trends in Commercial Bioinformatics

"The purpose of this document is to provide an overview of the rapidly emerging field of "commercial bioinformatics."

"For the purposes of this review, we define bioinformatics as the backbone computational tools and databases that support genomic and related research, which broadly encompasses the study of DNA structure/function, gene expression and protein production/structure/function."

Sunday, July 15, 2001

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"Last year, when Melissa Cline graduated from the Univeristy of California at Santa Cruz with a Ph.D. in computer science, she asked her adviser what she could do in bioinformatics, her chosen field of study. He responded by telling her about his visit to a university in Virgina where the faculty wanted to build up a large bioinformatics program. "They apparently wanted 20 or 25 people," Cline told me, beginning to chuckle. "And my adviser had to tell them that there probably weren't 25 qualified people in the whole country to staff such a program."

This scenario is typical in the growing field of bioinformatics -- also known as computational biology."

Saturday, July 14, 2001

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"You probably don't realize that the DNA you carry inside your body is patented by companies, universities and government agencies.

There were more than 25,000 DNA-based patents by the end of 2000, but you aren't allowed to look at some of your own DNA sequences because researchers keep the information private in order to stay ahead of the competition and to sell the information as a trade secret."

"Dr. Robert Cook-Deegan, director of the National Cancer Policy Board and the National Academy of Sciences Commission on Life Sciences, said keeping DNA data secret stops up the flow of information and slows the discovery of potential treatments for disease.

But biotech companies and the U.S. Patent and Trademark Office defend themselves by saying that without patents there would be no innovation."

Science Celera human genome data not Wellcome
[summary - can be viewed for free once registered]

"In this policy forum, Cook-Deegan and McCormack urge that DNA sequence information contained in patents be made publicly available soon after patent applications are filed. This will speed access to valuable data without undermining investment in subsequent development of DNA-based inventions. The authors further suggest that federal agencies and nonprofit funds consider adopting this policy as a condition of accepting their funders; private firms could adopt it as a norm to reduce duplication of effort and to accelerate innovation."

redux [02.27.01]
The Financial Times Opinion: No price should be placed on the book of life

"Let me be frank here: my view is, and always has been, that the information in the genome is our genetic heritage and should not be profited from directly. It is not for sale. This is a pro partnership, not an anti-business, stance. We want to ensure that the entire world has equal access to the data, so that the potential health benefits are reaped by the many, rather than the few.

As Prime Minister Blair said: "The knowledge contained in the map of the human genome has the power to touch the lives of everyone on the planet." It is for precisely this reason that our commitment should be for the entire world to use this data so the benefits can be realised by all, and major killers such as malaria, tuberculosis, river blindness and leprosy will not be neglected."

The Economist Science and profit

"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner?s safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not?must not?mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."

"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome?has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."

Friday, July 13, 2001

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"Ambuj Goyal, IBM Research's general manager for software, solutions, and strategy, was more ambitious than that. Why not build a machine to model molecular dynamics using general-purpose chips rather than specialized ones? That way you'd produce a prototype for a whole new family of supercomputers. Not only would it be great technology development, it would be great marketing, too. Whereas the Department of Energy has the greatest interest in top-end supercomputing - with its need to understand how nuclear weapons work - focusing on the life sciences rather than the death sciences could make supercomputing more widely appealing. What's more, a biology program would be a way of telling one of the newest markets for big iron - the post-genome biotech world - that IBM took its interests seriously. "We believe that the life sciences are going to be a rapidly growing area," says Blue Gene project manager Bill Pulleyblank, "a huge growth area for IBM."

Scientific American The Do-It-Yourself Supercomputer

"Our solution was to construct a computing cluster using obsolete PCs that ORNL would have otherwise discarded. Dubbed the Stone SouperComputer because it was built essentially at no cost, our cluster of PCs was powerful enough to produce ecoregion maps of unprecedented detail. Other research groups have devised even more capable clusters that rival the performance of the world's best supercomputers at a mere fraction of their cost. This advantageous price-to-performance ratio has already attracted the attention of some corporations, which plan to use the clusters for such complex tasks as deciphering the human genome. In fact, the cluster concept promises to revolutionize the computing field by offering tremendous processing power to any research group, school or business that wants it."

"Above all, the Beowulf concept is an empowering force. It wrests high-level computing away from the privileged few and makes low-cost parallel-processing systems available to those with modest resources. Research groups, high schools, colleges or small businesses can build or buy their own Beowulf clusters, realizing the promise of a supercomputer in every basement. Should you decide to join the parallel-processing proletariat, please contact us through our Web site (http://extremelinux.esd.ornl.gov/) and tell us about your Beowulf-building experiences."

Thursday, July 12, 2001

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"The new deal is similar to one Celera signed earlier with a national research body in Australia. It sets out standard terms under which researchers at the cancer institute can secure access to Celera's databases, which include maps of the genetic material of humans, laboratory mice, fruit flies, and other organisms. Between 300 and 400 cancer researchers are potentially eligible, though it's unclear how many will sign up."

"It was always frustrating for me and some of my colleagues that originally came out of NIH to be listed as competing and battling with NIH," said J. Craig Venter, Celera's president and chief scientific officer. "We'd much rather be working with them than against them. This is a wonderful step in that direction."

GenomeWeb The NCI Subscription Deal with Celera

""I?m ecstatic, I want to see what?s there," said an NCI scientist who asked for anonymity. "My collaborators and competitors, Howard Hughes, Johns Hopkins, and others, have access to that information," the source added, anticipating the opportunity to soon review the data. "I?m sure there?s data there not in the public domain," especially with SNPs and the mouse genome. "To me, it?s worth the approximate $15,000 to $20,000" for access.

"How much these agreements and any subscriptions stemming from them may be worth to Celera, besides possibly bragging rights, is a matter of speculation, however."

redux [03.24.01]
BioMedNet Celera human genome data not Wellcome
[requires 'free' registration]

"The Wellcome Trust has told its grantees that they may not use Wellcome money to subscribe to the Celera Genomics human genome database. Since Wellcome helped provide funding for the public Human Genome Project, it wants researchers to use the free public databases. Celera says no problem; scientists can still access the free portion of the company's data. A Wellcome official says that the policy is just a way of getting value for its money, because there's no evidence that the private database is better than the public one.

Reference: Adam, D. 2001. No Wellcome money for Celera. Nature 410(6827):397."

Wednesday, July 11, 2001

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"Their bold proclamation has raised a few eyebrows in the scientific community. "It's easy to say that you'll complete a comprehensive proteome map," notes Marc Vidal of the Dana-Farber Cancer Institute in Boston. "But none of us knows what that means." There may be only one genome, but when it comes to the proteome, different proteins can be more or less active in different cells at different times during development, under different physiological conditions or in different disease states. The proteome's nature "makes it hard to define what we're doing--not just Myriad, but all of us," remarks Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School. "There's no such thing as a human proteome," adds Keith L. Williams, CEO of Proteome Systems, headquartered in Sydney, Australia. Look at the liver, for example, he says: "After a glass of red wine, you'll have a different proteome."

redux [06.20.01]
Forbes Proteins Are Back To Confuse Investors

"Scientists thought about trying to catalogue all the proteins in the body a decade ago.

But it seemed impossible, and was therefore impossible to fund. Researchers moved on to the much simpler job of sequencing the human genome.

They were right to do so. Cataloguing proteins turns out to be downright confusing. Lately, more and more biotech companies are entering a field they call "proteomics," an ugly word searching for a focus group."

redux [03.31.01]
The Scientist Is a Human Proteome Project Next?
[requires 'free' registration]

"A commonly expressed opinion is that a single Human Proteome Project can never match HGP's success. Eric S. Lander , director of the Whitehead Center for Genome Research in Cambridge, Mass., notes that biologists simply don't know how to characterize the proteome "from end to end, nailing every protein. The tools are not ready. And it's not clear that [such a project] makes sense." He contrasts proteomics to HGP where "there is a certain fixed number of base pairs--about three billion--and we were going to get them all. And so it had a beginning and an end to it."

redux [01.31.01]
GenomeWeb Proteomics Effort Shouldn't Mimic Genome Project, Experts Say

"Can sequencing do for the proteome what it did for the genome?

On Wednesday, a number of world-renowned researchers in the field of proteomics issued a resounding " no."

Instead of devoting their efforts to decoding the human proteome, proteomics researchers should focus on developing a larger picture of protein structure, function, and pathways within cells and organisms, panelists said at a New York Academy of Sciences briefing entitled "The Promise of Proteomics."

"When a company has phenomenal success with strategy A, you want to do strategy A on the next subject," said John Richards, a professor of organic and biochemistry at California Institute of Technology, referring to current corporate attempts to map the proteome.

"This doesn't work," he said."

Tuesday, July 10, 2001

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"DoubleTwist, Inc. today announced that the genomic annotation XML format used to create its annotated human genome database is now freely available as an open standard to the life sciences community. AGAVE (Architecture for Genomic Annotation, Visualization and Exchange) allows users to manage, visualize and share annotations of genomic sequences using the document type definition (DTD) and associated tools available through www.agavexml.org."

"AGAVE was originally developed as part of DoubleTwist's bioinformatics architecture for high-throughput analysis of the human genome, which relies heavily on XML and Java technologies and tools. Central to AGAVE is a Java Object Model and a corresponding XML Document Type Definition (DTD) that facilitate data exchange, data integration and data transformation between components."

Agave.Org Introduction

"The design goals of AGAVE are to provide a comprehensive, extensible, open and readable markup language for genomic annotation. AGAVE is comprehensive because it can represent all the relevant biological data in public databases such as NCBI's GenBank, including the full sequence location format. It is extensible because it uses generic elements for computational results that can easily be used to capture results from new sequence annotation algorithms. Because AGAVE is XML-based, it is easy to use as an open standard for data storage and exchange. You can write programs to manipulate and extract genomic data using standard XML libraries, and you can easily transform data in the AGAVE format from and to other XML-based formats using tools such as XSLT (eXtensible Style Language Transformation). For example, you can easily transform data in GAME format to AGAVE format using XSLT templates. To aid readability, AGAVE focuses on biological data and uses standard biological terminology with a minimum of abbreviation."

GenomeWeb Incyte Outsources Genomics Knowledge Platform to Secant Technologies

"Recognizing that its Genomics Knowledge Platform has capabilities that exceed its own in-house research needs, Incyte Genomics awarded Secant Technologies an exclusive license to develop and market the data integration software platform, company officials said Monday."

"The platform, launched last November, provides tools for researchers to integrate and analyze a wide range of data, from gene sequence, expression, polymorphism, proteomic, and other functional data. The object model-based platform currently uses IBM's DiscoveryLink data integration software to integrate, or "federate," Incyte's multiple databases to make them appear to the user as a single source."

Yahoo! Finance Biomax Informatics AG Licenses the BioRS Integration and Retrieval Plus System to Millennium Pharmaceuticals, Inc

"Biomax Informatics AG announced today that Millennium Pharmaceuticals, Inc. (Nasdaq: MLNM - news) has licensed the BioRS(TM) Integration and Retrieval Plus System (version 4.0)"

""Millennium's unique approach to drug discovery and development is at the forefront of the industry," said Tim Clark, vice president, informatics at Millennium. "As a result, we are continuously evaluating software and technology products, and services that will help us enhance our productivity. We performed an extensive analysis of the BioRS system over several months and it proved to be a stable, comprehensive and efficient system. The speed and agility with which we assess drug targets in our gene-to-patient platform requires a system that can handle a broad spectrum of user scenarios for large data volumes. The BioRS system has the potential to meet our aggressive needs."

redux [03.22.01]
ZDNet IBM Experiments With XML

"Besides the proposed query language, IBM has built an experimental "dataless" database system that gets the user the information needed from a variety of sources by breaking down a query into its parts. Each part is addressed to the database system or repository that can supply an answer, even though the data may reside in radically different systems and formats. When the results come back, they are assembled as one report or assembled view to the user."

"The system will be a "virtual database" or a federation of heterogeneous databases, and a pilot Discovery Link system has been in use for several months by pharmaceutical companies trying to research and manufacture new drugs."

"Pharmaceutical companies have the highest pain point" in trying to assemble diverse data, noted Jim Kleewein, developer of DataJoiner, an IBM predecessor product that extracts data from known sources. The drug companies are trying to combine information gleaned from the human genome, bio-informatic databases where human responses to chemical compounds are stored and new chemical interaction databases."

redux [03.11.01]
Health Informatics Europe Data warehouse deployment in pharmaceuticals increasing by 36% a year

"Research by Silico Research concludes that the deployment of data warehousing technology is widespread in the pharmaceutical, biotechnology and genomic sectors, with 77% of companies surveyed currently deploying at least one data warehouse somewhere in the R&D pipeline. Virtually all those who are not deploying data warehousing technology today expect to be doing so by 2004. This implementational build-out will combine with the fact that individual biopharmaceutical companies are deploying more warehouses across more functions to increase the number of warehouses in the sector by 36% a year and by 150% over the next three to four years."

"Today, data warehouse deployment is focused at the departmental level. "Companies believe, as a article of faith, that they should link scientists and researchers across the enterprise. How they go about doing this is another matter. We're seeing a lot of testing of federated and virtual warehouses and other middleware solutions but no clear answers so far", continued Emmett Power."

Monday, July 09, 2001

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"Earlier this year, researchers mapping the human genome estimated that human DNA contains about 30,000 genes. Now, based on the first-ever look at comparable sections of human and mouse DNA, a team of Walnut Creek-based Joint Genome Institute (JGI) scientists has confirmed that estimate as roughly accurate."

""There had been speculation that aligning the human and mouse DNA sequence might reveal many more genes," Stubbs said. "However, if chromosome 19 is indicative of other chromosomes, the estimate of 30,000 genes is fairly accurate.""

BBC Dispute over number of human genes

"Two rival teams that cracked the human genome may have underestimated the number of human genes, according to a new computer analysis."

Scientists in the United States claim humans are built from 66,000 genes, nearly twice as many as the current consensus."

"But the new analysis, published on the website of the journal Genome Biology, has been dismissed by the Sanger Centre, in Cambridgeshire, UK, which was responsible for about a third of the human genome sequencing effort."

""The experimental evidence actually points to 30-40,000 genes," Dr Hubbard told BBC News Online. "I don't believe the argument in this paper that there are a lot more genes. This is an entirely computational paper and I don't think it's very credible.""

redux [06.08.01]
Red Herring Genomics offers an odd proposition

"Research on the human genome may well pay fat dividends in 10 or 20 years, but you can make money on it now, the old-fashioned way: by gambling. Find out how on the Web site of Project Ensembl, a European organization that develops genome-related software."

At the May 2000 Annual Meeting on Genome Sequencing and Biology at the Cold Spring Harbor Laboratory in Long Island, New York, Ewan Birney, team leader of Project Ensembl, proposed GeneSweep, a betting pool to guess the total number of human genes. All bets must be entered by hand, in person, in ink, in a book kept at the Cold Spring Harbor Laboratory. The winner of the pool, which now stands at a whopping $348, will be announced at the 2003 genome meeting."

redux [02.11.01]
USA Today Human genome makes mind-boggling reading

"The first close reading of the "The Book of Life" ?the 3 billion letters that make up the human genetic code ? reveals that it's packed with more mysteries and surprises than a pulp thriller. Perhaps the biggest surprise since the code was deciphered in June is that it takes just 30,000 to 40,000 genes to make, maintain and repair a human. That's far fewer than the 140,000 genes some had predicted and not many more than an earthworm or a common weed. "If you're judging the complexity of an organism by the number of genes it has, we've just taken a big hit in the pride department," says National Genome Research Institute's director Francis Collins, who also heads the U.S. arm of the international Human Genome Project (HGP)."

redux [05.13.00]
Wired News Amped Geneticists Bet on Genome

"Well, they weren't all men, but mostly. The betting in the pub continued, the lowest bet being 29,800 genes placed by Pat Tome and the highest number coming from John Quackenbush at 118,259.

The pool was organized by Erwin Birney, a team leader at the European Bioinformatics Institute. He tried to convince the bartender to oversee the betting, but was told in no uncertain terms that no gambling was allowed in the Cold Spring bar.

Guesses on the number of genes in the human genome have lowered considerably since the mapping of chromosome 21, which researchers found to contain only 225 genes, far fewer than previously predicted. The researchers on the chromosome 21 study predicted their results could mean that there are as few as 40,000 genes in the entire human genome.

"Someone from Incyte will probably show up and bet 150,000," one gambler said."

Sunday, July 08, 2001

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"Patents are undoubtedly a hot topic in biotech and pharmaceuticals. A company's intellectual property strategy is often more important than its core technology in the race to win market dominance. This, of course, is not only they case with the brass ring at the end of the pipeline - the drugs themselves - but almost every component of the drug development process, from gene sequence to chemical compounds and to the enabling technologies that make discovery possible."

"But while some areas of the biotech landscape are embroiled in perpetual patent litigation, this is not the case in bioinformatics for a very simple reason: A dearth of patents."

redux [08.26.00]
MIT Technology Review One-Clicking the Genome

"One entrepreneur, who requested anonymity, described a "silent gold rush" as firms move to file patents staking out methods for sharing and manipulating the enormous quantity of genetic data being put online. Such approaches will be increasingly important to genomics, as scientists begin to "annotate"