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.

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. Copyright © 2007, Oracle Corporation and/or its affiliates. All rights reserved.

The IBM Clinical Genomics for targeted clinical research

THe Haifa Lab of IBM provides the Technlogy for Clinicalgenomics and leads the research in lifesciences fieds.

The Clinica, Genomics division plans to provide technology to integrate clinial genomics data and HL7 and other complaince protocls followed in clinical research and clinia, trial and integrate them to provide better and focused clinical trials

Clinical genomics for biopharmaceuticals from IBM

the main advatages as per IBM website is that

• Encapsulate raw genomic data into an HL7 Clinical Genomics message, including transformation services of proprietary data formats to standardized formats like MAGE and BSML
• Access patient’s clinical history stored in an enterprise EHR system
• Access all major ontologies that provide genotype-phenotype relationships like OMIM, PharmGKB, etc.
• Parse the encapsulated raw genomic data and bubble-up selected genomic data items based on ontological knowledge as well as the patient clinical data
• Compare two Genotypes (the data model at the heart of the HL7 specs) in order to provide case-based reasoning services to decision support application that will use CGL7 as a specialized clinical genomics middleware
• Find a similar pedigree in case base of pedigrees in order to support risk assessment applications that base their assessment on family history

Hocus Locus Spins out of University of Albany

Hocus Locus, a bioinformatics company which is part of the $225 million Gen*NY*Sis   Programe (Generating Employment through New York State Science) is located at the Center for Excellence in Cancer Genomics in University of Albany, it makes products to help small drug discovery companies speed up development of new drugs.

Plants too recognise its kin

Now wonder,  research proves that even plants recognise their kins. Researchers from McMaster University have found that plants go competitive when forced to share their own environment like pot, with strangers of the same species, but they’re accommodating when potted with their siblings.

How they do it???

When a different plant of same species is potted with a growing plant they start growing more roots, which allows them to grab water and mineral nutrients before their neighbours get them. when they share a pot with family i.e the sibiling 1st or 2 nd generation they don’t increase their root growth. Because differences between groups of strangers and groups of siblings only occurred when they shared a pot, the root interactions may provide a cue for kin recognition. The following is the paper that is being published on the same.

Dudley, S. A. and A. L. File (2007). Kin recognition in an annual plant. Biology Letters, in press.

4th Dimension in Biology

4D imaging of different microorganisms was the first step of 4D in biology. Recently now from the University of Calgary, sun centre for excellence for visual genomics have created the 4D virtual human (CAVEman) with flesh, and muscles, a breakthrough step ahead in the medical informatics. This 4D virtual human can be used for many new pathways for surgical studies. It can be used also to see the disease and genetic changes virtually, allowing to assess the various morphological changes occuring during a diseased or genetically affected individual. You can download Demo verrsion so of the 4D demos of heart , human skelton and many more,

Future of High Throughput Genome Sequencing

In Bangalore Bio 2007 LabIndia has introduced  SOLiD: Sequencing by Oligonucleotide Ligation and Detection which is the Future of High Throughput Sequencing.

“This is useful for those who want to do full genome sequencing. Whole genome projects will be more cost effective with this new instrument than they are today,” said Dr. Anupama Gaur, Team Leader Application Support, Labindia Instruments, Pvt. Ltd.

HistoGenetics has come up with Sequence Based Typing which has many advantages such as identifying many rare and new alleles. “Nearly 2000 alleles have been identified so far and it has been launched in the US and UK as of now” said Dr. Cereb Nezih, M.D., President and co-founder, Histogenetics, Inc.

State law protects DNA of Minnesota wild rice

ST. PAUL — The DNA of Minnesota wild rice gets special protection under a new state law adopted this year with the backing of Indian tribes.

Genetic modifications to wild rice will be watched more closely, with environmental impact statements required and permits controlled by the Minnesota Environmental Quality Board.

Stein GAVE Bioinformatics Ten Years to Live

Its an old story but looking at whats happening in bioinformatics industry now i think this topics some what relevant. The industry has seen an unprecedented number of mergers and collaboration something unthinkable at the early stages of bioinformatics era.

Lincoln Stein’s keynote at the O’Reilly Bioinformatics Technology Conference was provocatively titled “Bioinformatics: Gone in 2012. it was proved to some level that all the compaies that sproute up are not going to be around for a long time. but it seems 2012 is defenitely not going to be the end of bioinformatics. personalized medicine, functional genomics and theranostics have given it a new lease of life and lot of steam to speed ahead

the old article is present at oreilynetwork 

DNA DATABASE TO HELP IDENTIFY DISAPPEARED

(May 23, 2007) The head of Chile’s Medical Legal Service (SML), Patricio Bustos, announced this week that his organization would create a DNA database that will be used to help identify the remains of those who were disappeared and murdered during the military regime led by Gen. Augusto Pinochet.

Source Santigao times

Errors in DNA database

The exciting news of google or its benefactor investing in genomics companya and google founders earlier enthusiasm to offer its billion dollar power for genomics indutsry, has produced a mixed responses. I agree with Hsiens post that we should welcome the move

I guess its worthwhile to know why its better if google does so , The UK’s national DNA database, which houses 4.1 million records pertaining to evidence of crimes collected by police, has been found to have upwards of 100,000 incorrect records. 

According to theregister.co.uk, the complex relationship between the country’s police force, its National DNA Database Unit and the forensic service along with a lack of checks and balances has left its DNA database with the large amount of corrupted records, causing 26,200 load problems alone

“There’s in the order of 100,000 unreconciled records now,” claims The Register’s source.

Realated posts

GeneticsandHealth

ScienceDirect

NEWS

DNA file on 100,000 innocent children

This day in genetics history

I thought of adding anadditional catagory to my blogs called “This day in genetics history”  so today May14 is an important day because in

May 14 1796 1st smallpox inoculation administered, by Edward Jenner  marking his first experimental vaccination against the disease

Video in Laboratory

I had mentioned earlier a number websites, that offer scientific videos

though many researchers have their own restriants when it comes to using technology whetehr it is open source or peer reviewd journal or blogs itself. Perhaps groups was the only social content driven concept that got off the ground when it comes to science and especially life science

but that certainly doesnt seem to deter more people coming up with new site that offer more web2.0 services to scientists

this time the new kid on the blck is http://www.labaction.com another science video sharing website
for more information on similar services and technology see my earlier posts

Gene splicing, SNP, Jumping genes, Transposons

I was looking for an easy way to explain DNA, Gene splicing, SNP, Jumping genes, Transposons and such to a non biologist without using too much technical jargons. And then I came across a study by University of Cambridge about how human mind reacts and learns written text , JUst see if you can read the following text, They are sure not spelling mistkes but made by rearranging text  in word by retaining the first and last letter in such a way that your mind still can read it

 

*I CAN READ IT! CAN YOU*

 

Cna yuo raed tihs? fi yuo cna raed tihs, yuo hvae a mnid to udrtsand DNA and why it is poisbssle for DNA to Evovle.

 

i cdnuolt blveiee taht I cluod aulaclty uesdnatnrd waht I was rdanieg. The phaonmneal pweor of the hmuan mnid, aoccdrnig to a rscheearch at Cmabrigde inervtisy, it dseno’t mtaetr in waht oerdr the ltteres in a wrod are, the lny iproamtnt tihng is taht the frsit and lsat ltteer be in the rghit pclae. The rset can be a taotl mses and you can sitll raed it whotuit a pboerlm. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. Azanmig huh? yaeh and I awlyas tghuhot slpeling was ipmorantt! now you can raed tihs

Did you read the text and were you able to understand the meaning and the message it contained, If so think about it if you can read the message even when the order at which it is written is changed, Our DNA is also evolving in a similar fashion,now go on read about Gene splicing, SNP, Jumping genes, Transposons you would understand them better.

I guess perhaps we can use the same to explain to students or non biologists many other features of DNA especially how it is possible for HSP genes to create different proteins from different structural arrangement or how more than one DNA can code for one protein

Theranostics-Genetics Testing for Clinical Diagnostics for Personalized Medicine

Theranostics is the term used to describe the proposed process of diagnostic therapy for individual patients – to test them for possible reaction to taking a new medication and to tailor a treatment for them based on the test results or in plain english Personalized Medicine.

Personalized medicine is the use of detailed information about a patient’s genotype or level of gene expression and a patient’s clinical data in order to select a medication, therapy or preventative measure that is particularly suited to that patient at the time of administration

The test results are used to tailor treatment, usually with a drug that targets a particular gene or protein.

Seen the movie Gattaca it shows glipses of the what to come.

This method is looked as the possible end result of new advances made in Pharmacogenomics, Drug Discovery using Genetics, Molecular Biology and Microarray chips technology

The technology is set to grow by leaps as new companies are introducing new microarray chip which are getting cheaper day by day

Already there are microarraychips approved by FDA for clinical diagnostics