siRNA Libraries

"Sometimes the first step to learning a gene’s role is to disable it and see what happens. Now researchers at the Stanford University School of Medicine have devised a new way of halting gene expression that is both fast and cheap enough to make the technique practical for widespread use. This work will accelerate efforts to find genes that are involved in cancer and the fate of stem cells, or to find genes that make good targets for therapeutic drugs."

Press Release, Gene-Disabling Technique Simplified by Stanford Team. Jan 13 2004.  This group has developed a method for creating siRNA libraries.  Here is a flash animation showing a mechanism for RNA interference or RNAi.  In the animation, the little red pieces labeled "guide sequeces" are short interfering RNA or siRNA.

$24 million toward $1000 genome

According to the GenomeWeb, the National Human Genome Research Institute announced a commitment of $24 million for FY2004-FY2005 "aimed at reducing the costs of sequencing a single, full-length mammalian genome to $1,000 - down from current average costs of $10 to $50 million per genome - by the end of a 10-year time frame."  See article here (free registration required).

Which mammal has the smallest genome you wonder? T. Ryan Gregory, the scientist for whom size matters, has an answer for you in his Animal Genome Size Database.

UPDATE: The full text of the RFA is now online

Emerging Technologies: Personal Genomics

This month’s Technology Review features a roundup of the "10 Emerging Technologies that will change your world."  (free registration required) Personal genomics comes in at number 10.  The article on personal genomics focuses on the work of David Cox of Perlegen Sciences.  Other listed as leaders in the field are Richard Begley of 454 Life Sciences, Daniel Branton of Harvard University, Eugene Chan of U.S. Genomics, and George Church of Harvard University.


Prospective Care

Laura Landro, Preventive Medicine Gets More Aggressive; The ‘Health Coach’, WSJ Feb 12 2004. (subscribers only)

"The new approach is called "prospective" rather than "preventive" medicine. It uses patient medical histories to identify people at the greatest risk of developing specific diseases, and takes steps to intervene early to prevent their onset. The key is getting the patient far more involved. It’s really prevention plus personalization: Every patient gets a health risk assessment, a personalized health plan and direct involvement in setting his or her own health goals. One pioneering program even provides "health coaches" and support groups to help carry them out…"

A couple insightful quotes from members of the medical community in the article:

"We have to find a way to raise the value of preventive self-care so people can set priorities for their own health," says Michael Johns, executive vice president for health affairs and director of the Robert W. Woodruff Health Sciences Center at Emory University…"

… "What we are trying to do is be on the leading edge of a change in how health care will be delivered in the next five years," says Ralph Snyderman, Duke’s chancellor for health affairs. "We want to get beyond disease management into a focused, realistic way to have early detection and early intervention — not with a cookie cutter approach to every patient but by tailoring it to the individual."

Several organizations pioneering prospective medicine that are mentioned in the article are Duke University’s Prospective Health Program and the Seattle-based Group Health Cooperative.

Landro also mentions a recent paper by two researchers at the Yale School of Medicine, Mary Tinetti and Terri Fried.  She summarizes their argument as thus, "doctors must shift their focus from treating disease alone to tailoring treatments to individual patient needs."  The article is for subscribers only (or for those willing to shell out a hefty $30), but the abstract is free online.  Here is the info: 

Mary Tinetti and Terri Fried, The End of the Disease Era.  American Journal of Medicine. 116(3):179-185.


"The time has come to abandon disease as the focus of medical care. The changed spectrum of health, the complex interplay of biological and nonbiological factors, the aging population, and the interindividual variability in health priorities render medical care that is centered on the diagnosis and treatment of individual diseases at best out of date and at worst harmful. A primary focus on disease may inadvertently lead to undertreatment, overtreatment, or mistreatment. The numerous strategies that have evolved to address the limitations of the disease model, although laudable, are offered only to a select subset of persons and often further fragment care. Clinical decision making for all patients should be predicated on the attainment of individual goals and the identification and treatment of all modifiable biological and nonbiological factors, rather than solely on the diagnosis, treatment, or prevention of individual diseases. Anticipated arguments against a more integrated and individualized approach range from concerns about medicalization of life problems to “this is nothing new” and “resources would be better spent determining the underlying biological mechanisms.” The perception that the disease model is “truth” rather than a previously useful model will be a barrier as well. Notwithstanding these barriers, medical care must evolve to meet the health care needs of patients in the 21st century."



Press Release, Nano-Origami: Scientists at Scripps Research Create Single, Clonable Strand of DNA That Folds into an Octahedron. Feb 11 2004.

“A group of scientists at The Scripps Research Institute has designed, constructed, and imaged a single strand of DNA that spontaneously folds into a highly rigid, nanoscale octahedron… [T]he structure can be amplified with the standard tools of molecular biology and can easily be cloned, replicated, amplified, evolved, and adapted for various applications. This process also has the potential to be scaled up so that large amounts of uniform DNA nanomaterials can be produced. These octahedra are potential building blocks for future projects, from new tools for basic biomedical science to the tiny computers of tomorrow.”

Leroy Hood on Future of Pharma

John Russell, Catching Up with Leroy Hood, Bio-IT World, Jan 30 2004.

"Big Pharma is going to be a dinosaur. I think the whole industry is going to be restructured and they’ll never be able to get systems biology, so they’ll be out of the discovery business. Big Pharma is the worst of silos, even worse than medical schools."

See also Snowdeal’s redux articles on the pharma/systems biology relationship.

DNA Discrimination Legislation Needed?

Sharon Begley, Bill Seeking to Ban DNA Discrimination Isn’t Really Necessary, Wall Street Journal, Feb 6 2004. (available only to subscribers)

Last October the Senate unanimously passed (S. 1053) the Genetics Information NonDiscrimination Act (see my post). Sharon Begley, columnist for the WSJ, picks up the story today by noting that the House of Representatives has so far “shown no interest in bringing [the bill] to a vote.” In the house, the bill is called (H.R. 3636) the Genetic Privacy and Nondiscrimination Act of 2003.

She argues that the threat of genetic discrimination is “grossly overstated.” She is not alone in this view. For example, Mark Hall and Stephen Rich of Wake Forest recently looked at the prevalence of requests for genetic information by health insurance companies, in states with genetic privacy laws on the books and those without them. They found “that there are almost no well-documented cases of health insurers either asking for or using presymptomatic genetic test results in their underwriting decisions, either (a) before or after these laws have been enacted or (b) in states with or without these laws.”

She challenges the symbolic value of the bill, “…to allay the fears of people who reject genetic tests in the belief that a positive result could make them uninsurable and unemployable” because “[b]y enshrining genetic status in federal law, we reinforce the widespread and pernicious belief that DNA is destiny. It isn’t…”

She concludes with the following maxims: “Supporters of the genetic discrimination bill should make clear that what they want to guard against is no more than a theoretical risk. They should make equally clear that the risk genes they’re so worried about are not all they’re cracked up to be.”

First Genetic Trust Awarded Patent

First Genetic Trust Gets Patent for Banking System, GenomeWeb, Feb 3 2004. (free registration required)

"First Genetic Trust has received a patent for an electronic genetic banking system, the company said today.  The patent, US patent No. 6,460,211 B1, covers methods, processes, and electronic systems for securely storing, analyzing, and managing genetic data.  First Genetic Trust, headquartered in Chicago, is aiming to develop and commercialize genetic banking and research management applications for biomedical research."

Genomic Harvest

Malorye Branca, Pharma’s Genomic Harvest, Bio-IT World, Jan-March 2004.

"The pharmaceutical industry has been anxiously awaiting signs that the much-anticipated genomics revolution is on its way, transforming medicine and speeding drug discovery and development. In this exclusive new online series from Bio·IT World, senior informatics editor Malorye A. Branca explores how genomics technologies are transforming drug discovery, based on in-depth interviews with genomics executives at the world’s leading pharmaceutical companies."

The first of ten articles in this series is based on an interview with Philip Vickers, Executive Director of Genomic and Proteomic Sciences, Pfizer Global R&D.

Biosapiens Network of Excellence

Press Release, European Virtual Institute for Genome Annotation receives 12 million Euro. EurekaAlert, Jan 26 2004.

The press release details the creation of a multinational virtual institute in Europe for the pursuit of bioinformatics.  One paragraph seemed particularly un-press-release-like for its shrewd generality:


"Data overload is reaching epidemic proportions among molecular biologists. As genome-sequencing efforts continue apace and are being supplemented by new types of information from microarray, proteomics and structural genomics projects, biologists are literally drowning in a sea of data. Bioinformatics - the science of storing, retrieving and analysing large amounts of biological information - is struggling to keep up and is also contributing to the information overload by generating large numbers of predictions about the biochemical functions of gene products. These predictions need to be tested in the lab, but the infrastructure to "complete the circle" between computational biologists and experimentalists needs to be improved. This will have to change if we are to fulfil the ultimate promise of genomics: better quality of life."


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