France to invest €670 million euros for Genomics and Personalized Medicine

Government of France Announce plans to invest €670 million euros or ($760.8 million) for Genomics and Personalized Medicine which will see it establish 12 genome sequencing centers and two national centers for genomic expertise and data analysis. The program would initially focus on cancer, diabetes and rare diseases but after 2020 would expand to include common diseases.

This investment by France follows the release on Wednesday of a report by medical experts examining the possibility of France widening access to genetic medicine within 10 years. A key objective in the report for the first 10 years of the programme is to prepare for the integration of genomic medicine into the normal course of patient care in the country, which means sequencing about 235,000 genomes per year by 2020.

Health Minister Marisol Touraine said Investment in the five year initiative will also come from industry. He also expected Companies like Google, Amazon, Apple and Facebook are interested in the growing genomic medicine sector

Several European countries have already begun to integrate genomic medicine into their health systems and there are large scale genomic initiatives in the UK, US and China. China has even recently announced a Precision Medicine Cloud

 

 

Is bioinformatics still a viable career choice or a business model?

If you are on linkedin take a look at the question posted by Jake Chen, Founding Director at Indiana Center for Systems Biology and Personalized Medicine.

One area where bioinformatics havn’t experimented a lot is probably adopting SaaS (software as a service) methodology for growth. Software being developed for scientists is still not that user-friendly. Bioinformatics have evolved; but has it been hijacked by engineers?.

Though bioinformatics companies have lost the sheen, the growing need for data analysis is unmistakable , with more large genome projects being announced everyday.

1996-2002 was a period when bioinformatics was the darling of budding entrepreneurs and scientists the world over. Depending on your point of view the industry is now either passé or futuristic. The only ones that made money were the equipment companies and the those making reagents. Propelling the acquisitions phase that is still going on, transforming most of the erstwhile famous names from pure play bioinformatics to drug discovery/development services companies.

The future is there as a CEO puts it “We’re just at the tip of the iceberg of addressing the real problem — helping scientists understand how to use software to make a discovery,”

surprisingly given below is a quote I found in the website of the Stanford University Center for Molecular and Genetic Medicine , for the class on introduction to bioinformatics for fall-quarter 2007. here is the actual link . I hope am not going to be denied an admission there for posting this. But I agree with it completely, and its time for the industry to take note

“There are a wide variety of companies trying to commercialize bioinformatics. Some of these businesses have been around for many years, but a lot of them are just jumping in with nothing but hype to sell, trying and gain some market share and position themselves as “leaders” in the new area of genomics, hoping to become profitable or get bought out before the venture capital funds dry up”.

Missing Evolutionary Link -how RNA progressed to share functions with proteins

Alan Lambowitz, director of The University of Texas at Austin’s Institute for Cellular and Molecular Biology and Senior researcher Paul Paukstelis and his team has found the missing links in evolution of life from the simple to the complex and involvement of RNA.

By crystallizing a fungus the team of researchers were able to visualize the process of moving from RNA to RNA and proteins and then to DNA.

The crystal structure provides a snapshot of how, during evolution, protein molecules came to assist RNA molecules in their biological functions and ultimately assumed roles previously played by RNA quoted by Purdue structural biologist Barbara Golden

The study is published at January edition of Nature

The Staphylococcus aureus microarray Database inching closer to Staph Infection Vaccine

MRSA the very name send shudders to any one working in a hospital setup, the aggressive Methicillin-resistant Staphylococcus aureus (MRSA) , is a bacterium responsible for some difficult-to-treat infections in humans.

The organism is often the cause of community-acquired MRSA (CA-MRSA) or hospital-acquired MRSA (HA-MRSA) depending upon the circumstances of acquiring disease,

University of Southern Mississippi biological science professor Dr. Mohamed Elasri and student Vijayaraj Nagarajan, a doctoral student have developed an online database that holds collected data on genes related to stap.The Staphylococcus aureus microarray meta-database, known as SAMMD

There are more than 400 SAMMD users from 23 countries with numbers increasing daily. As researchers work to find a vaccine for MRSA, Elasri said this program can cut a significant amount of time it takes to find information about staphylococcal genes

So Thats how Humans Evolved! – Now we can begin to answer the big question

Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates the question have been answered by a team of scientists from University of Washington School of Medicine and University of California, San Diego.The research published by Evan Eichler from the University of Washington School of Medicine provide the first evolutionary history of the duplications in the human genome that are partly responsible for both disease and recent genetic innovations.

Evan Eichler has analyzed segmental duplications in the human genome and have successfully pinpointed the ancestral origin of each and identified the newly named core duplicon.

The study presents a comprehensive global analysis of the evolution of segmental duplications in the human enome. The authors identify the origin of ancestral duplication loci, regions of clustered duplicons, and evidence upporting a punctuated model of evolution.

This work marks a significant step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are – in terms of susceptibility to disease-causing genetic mutations.

Apart from the above study  the recently completed (check previous blogs) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences the study helps to explain the evolutionary origins of human DNA and the role played by transposons

Genomes can duplicate long stretches of DNA from one chromosome and insert the duplication in another area of the genome. The resulting segments of DNA are called segmental duplications.  They are important because they hold evolutionary secrets

Finding answers to questions such as, Which set came first? What changes were innovated, when and why? What was sacrificed when an innovation took effect? What is the connection between disease and innovations within segmental duplications?, are important because researchers can then design specific medical treatments and can lead to ket discoveries in  Pharmacogenomics research

Download the Research Article

Transposon insertion site profiling chip (TIP-chip)

Transposon insertion site profiling chip (TIP-chip) was invented by Researchers at the Johns Hopkins’ High Throughput Biology Center. Tip-chip can be used to help identify otherwise elusive disease-causing mutations in the 97 percent of the genome long believed to be “junk.”

TIP-chip (transposable element insertion point) can locate in the genome where so-called jumping genes have landed and disrupted normal gene function. This chip is described n the Proceedings of the National Academy of Sciences. the article titled Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposon insertion site profiling chip (TIP-chip

The most commonly used gene chips are glass slides that have arrayed on them neat grids of tiny dots containing small sequences of only hand-selected non-junk DNA. TIP-chips contains all DNA sequences. Because each chip can hold thousands of these dots – even a whole genome’s worth of information – scientists in the future may be able to rapidly and efficiently identify, by comparing a DNA sample from a patient with the DNA on the chip, exactly where mutations lie.

Jef Boeke, Ph.D., Sc.D, professor of molecular biology and genetics and director of the HiT (High Throughput Biology Center), who spearheaded both studies at the Institute of Basic Biomedical Sciences at Hopkins, and his team have focused particularly on transposable elements, segments of DNA that hop around from chromosome to chromosome.

These elements can, depending on where they land, wrongly turn on or off nearby genes, interrupt a gene by lodging in the middle of it, or cause chromosomes to break. Transposable elements long have been suspected of playing a role vital to disease-causing mutations in people. Boeke hopes that the TIP-chip eventually can be used to look for such mutations in people.

The new TIP-chip contains evenly sized fragments of the yeast genome arrayed in dots left to right in the same order as they appear on the chromosome. Boeke’s team used the one-celled yeast genome as starting material because, unlike the human genome, which contains hundreds of thousands of transposable elements of which perhaps a few hundred are actively moving around, the yeast genome contains only a few dozen copies.

Like a word-find puzzle, where words are hidden in a jumbled grid of letters, the TIP-chip highlights exactly where along the DNA sequence these elements have landed. By chopping up the DNA, amplifying the DNA next to the transposable elements and then applying these amplified copies to the TIP chip, the researchers were able to map more than 94 percent of the transposable elements to their exact chromosome locations.

double-tiled DNA chip 

Standard chips contain one layer of DNA dots that read from left to right, like the across section of a crossword puzzle. Boeke’s new double-capacity chips hold two layers of dots, a bottom layer that reads across and a top layer that reads down, again using the crossword analogy. So if their experiment lights up a horizontal row of dots, the researchers learn that the data maps to the region of the genome contained in the bottom layer; likewise, if the experiment highlights a vertical row, the data correspond to the top layer.

Says Boeke, “It’s so easy to differentiate the top and bottom layers. Next we’re going to try adding another layer reading diagonally” to triple the amount of genomic information packed onto the tiny chips.

Authors of the TIP-chip and double-tiled DNA chip papers are Sarah Wheelan, a new faculty member in the Department of Oncology, Lisa Scheifele, Francisco Martinez-Murillo, Rafael Irizarry and Boeke, all of Hopkins.

Oracle Openworld 2007- Personalized Genomics session

Its the time -Personalized Genomics

Advances in genetic information and laboratory technologies mean new ways to diagnose disease and determine patient risk. The wealth of genetic information makes it harder to provide meaningful information. During Oracle OpenWorld 2007 Oracle is presenting how laboratory information systems principles and Oracle customer relationship management and enterprise resource planning applications weave together, using Oracle Fusion Middleware to create a unique platform for translational medicine.


Click here to register now.

Oracle OpenWorld

Experience Innovation. November 11-15, 2007, San Francisco, Moscone Center.

As the Life Sciences industry continues to grow and change, Oracle is there to help you learn, adapt, and succeed.

Please join us this fall in San Francisco as we address some of the biggest challenges facing the Life Sciences industry and how Oracle is prepared to meet those challenges.

Session highlights include:

  • Product Lifecycle Management—At this session, learn how Oracle’s Agile product lifecycle management solutions for Life Sciences improve new product introduction cycle times, reduce direct material and operating costs, and enable cost-effective compliance.
  • A Cure for Clinical Trials: From Data Capture to Submission—Approximately 80,000 clinical trials are being conducted in the United States at any given time. More than half of them are behind schedule by one to six months. Clinical trial sponsors hope to reduce this and other costly delays through the use of IT. Hear how the latest enhancements in Oracle’s industry-leading Life Sciences applications are streamlining the process of data capture, management, analysis, and reporting.
  • Enabling Personalized Medicine in Research and Development—The sequencing of the human genome is yielding exciting new tools to help physicians tailor treatments to individuals and their diseases. This powerful new capability, called personalized medicine, holds great potential to improve patient health. Learn how Oracle’s technology is enabling personalized medicine and improving efficiencies and outcomes in clinical development.

Click here for a full list of Life Sciences sessions.

Registration is now open for the most exciting technology and business conference of the year.
Registration fees go up soon So don’t wait—act now to save $900.

Click here to register now. To receive your special discount, select a registration category and enter keyword: ORF at the bottom of step 2 of the registration process.

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