20 year study on psychological impact of gene testing

In the background of the mounting negative publicity agianst consumer gene testing companies. Navigenics is teaming up with Scripps reseacrh institute to study how such tests affect patient behavior.

This is a long time study, over 20 years. with help from Affymetrix to Scan, Navigenics to interpret and offer life style guidance and the Microsoft HealthVault will be the place where participants can enter information and share it as they see fit with physicians

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Entire Genome Sequencing from Single Molecule DNA

Cambridge based Helicos Bioscience announced the publication of a report in Science Magazine demonstrating the first single molecule sequencing of an organism (M13 virus genome) examining more than 280,000 strands of captured DNA.

Helicos’ uses a proprietary form of sequencing-by-synthesis called True Single Molecule Sequencing(tSMS)™. Unlike other methods, the technique builds up the sequence of each strand of DNA one base at a time.

Searching Through DNA – Impact of new genetics technologies in American Life

One of the reader had posted a question about my earlier post on genetics of Transplant Organ Rejection so this post is a part answer to her comment, I choose the title american way of life as my first post in 2008 is not mine but an interesting article from Newyork Times

A good article about what can we expect from genomics in clinical decision making and therapeutics

Cryptography with DNA binary strands

Biotechnological methods can be used for cryptography. DNA binary strands can be used for steganography to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages.

I thought this as an interesting article since my last post was about DNA based security

http://www.cs.mun.ca/~banzhaf/molcomp.html

AUTHORS: Andre Leier, Christoph Richter, Wolfgang Banzhaf and Hilmar Rauhe

SOURCE: BioSystems, 57 (2000) 13 – 22,Extended Manuscript from 6th DIMACS Workshop on DNA Computing, Leiden, 2000

AUTHORS: Andre Leier, Christoph Richter, Wolfgang Banzhaf and Hilmar Rauhe

DNA-based security solutions to Prevent fraud and theft

Applied DNA Solutions is NewYork company that offers DNA-based security solutions to Prevent fraud and theft

Applied DNA Sciences’ technology has been utilized to successfully mark nearly 1 billion items including DVDs and CDs, fine art, prestige wine, luxury and personal care goods botanical DNA encryption, embedment and authentication solutions that can help protect companies, governments and consumers from counterfeiting, fraud, piracy, product diversion, identity theft, and unauthorized intrusion into physical locations and databases.

ADNAS uses DNA segments from one or more botanical sources, rearrange them into unique encrypted sequences, and then implement one or more layers of anti-counterfeit techniques

MIT team discovers new DNA modification in bacteria acting as DNA Bookmark

Researchers from MIT have discovered that bacterial genes, known as the dnd gene cluster, gives bacteria the ability to employ DNA modification by adding sulfur to the sugar-phosphate DNA backbone as a phosphorothioate,

The same method used in laboratories worldwide to modify synthetic oligonucleotide.Why would bacteria conserve this system which requires five enzymes, each with different co-factors?”

Peter Dedon says the modification system might serve as either protection against foreign (unmodified) DNA, or as a “bookmark” to assist with transcription or replication of DNA.

New Microarray technology replacing PCR and speed up HTS

Dr. Richard Gibbs, director of the Baylor College of Medicine Human Genome Sequencing Centre and his researchers along with the help of  NimbleGen Systems the  company recently acquired by Roche Applied Science has developed a new technique that combines gene chip technology with the latest generation of gene sequencing machines to allow fast and accurate sequencing of selected parts of the genome

 The technology, called “sequence capture,” enables fast and accurate enrichment of thousands of selected genomic regions, either contiguous or dispersed, such as segments of chromosomes or all genes or exons uses , The study had uses NimbleChip™ microarrays in preparation for a high-throughput 454 Sequencing™.

The study Direct Selection of Human Genomic Loci by Microarray Hybridization presented on October 10, 2007, at the J. Craig Venter Institute’s Genomes, Medicine, and the Environment (GME) conference, Roche NimbleGen and 454 Life Sciences, working with Dr. Richard , will create a whole-genome human exome (all exons) microarray, with the goal of resequencing the entire human exome faster and cheaper.

Till now researchers relied upon PCR for selection of specific genomic regions for resequencing

Limitations of PCR  meant the length of sequence it can amplify was small, is difficult to scale or multiplex for the enrichment of thousands of fragments, and has limited performance in the repetitive regions typical of complex genomes, such as human.

The sequence capture microarray technology bridges the gap between next-generation DNA sequencing technology and current sample preparation methods by providing an adaptable, massively parallel method for selective enrichment of genomic regions of interest.

The new process is simpler, more accurate and efficient than the multiplex PCR . In one experiment, more than 6,400 exons (the part of the genetic code that carries the instructions for making proteins), were analyzed. Using the old technology this would have taken at least six months.

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

A new strain of virus named after Washington University

A new strain of virus has been identified by the medical school and named the “WU” virus after Washington University.

The virus, a type known as a polyomavirus, is closely related to two others, JC and BK, which attack the nervous system of HIV patients and cause kidney transplants to fail, respectively.

The virus has been reported in such geographically disparate countries as the United States, Australia, Germany and Korea, according to Gardner.

In fact, the first samples of the then-unknown WU virus came from the University of Queensland in Australia.

The samples were sent to the University because the school has ViroChip, a sophisticated pan-viral DNA microarray. This tool allows scientists to quickly screen viral samples and compare their structure to more than 22,000 known viruses. It was instrumental in distinguishing SARS from known viruses during the 2003 outbreak

David Wang, a University professor who leads the research team, states that the WU virus has unique properties unlike either of the others and he questions if it even is a human pathogen.

The scientific article is published at PLOS Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections

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.

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Microsoft Research, HIV, SPAM – MS anti-spam techniques help research HIV vaccines

Ever heard of the Teiresias algorithm, for spam detection developed by Chung-Kwei at IBM – the algorithm was developed in the bioinformatics group of IBM to detect patterns in DNA

This algorithm is tested for SPAM detection- discussed in my  my earlier bioinformatics post

So you may be wodering whats thats got to do with this post, OK I am coming to it- 

Microsoft is helping  David Heckerman a Physician with a PhD in computers with spam-blocking team at Microsoft Research, to find drugs for HIV, by learning from how Anti SPAM softwares works

An e-mail featuring “Viagra,” for example, was a good bet to be spam–but things got complicated in a hurry.

if spammers saw that “Viagra” messages were getting zapped, they switched to V1agra, or Vi agra. It was almost as if spam, like a living thing, were mutating

This parallel between spam and biology got the attention of David Heckerman

Bill Gates, the company chairman “got really excited,” Heckerman says. Well versed on HIV from his philanthropy work, Gates lined up Heckerman with AIDS researchers at Massachusetts General Hospital, the University of Washington, and elsewhere.

Since then, the 50-year-old Heckerman and two colleagues have created their own biology niche at Microsoft, where they build HIV-detecting software. These are research tools to spot infected cells and correlate the viral mutations with the individual’s genetic profile. Heckerman’s team runs mountains of data through enormous clusters of 320 computers, operating in parallel. Thanks to smarter algorithms and more powerful machines, they’re sifting through the data 480 times faster than a year ago. In June, the team released its first batch of tools for free on the Internet.

watch the video to learn more about the work

DNA test results in three days, or Money Back

IDENTIGENE Becomes First DNA Testing Lab to Promise Fast Results with a Money-Back Guarantee . The company now Now Offers the Industry’s First Money-Back Guarantee, together with a Three-Day Turnaround on Results

the website says IDENTIGENE is the only DNA testing lab with a money-back guarantee

 

 

 

 

 

Transplant Patients Could Live Free of Anti-Rejection Drugs

Scientists from the Lucile Packard Children’s Hospital and the Stanford University School of Medicine have identified a pattern of gene expression shared by a small group of patients who beat the odds and remained healthy for years without medication, after undergoing Organ transplant.

The findings made by Minnie Sarwal, MD, PhD, a pediatric nephrologist at Packard Children’s is a major advantage in organ transplantation treatment. Transplant recipients who share the same pattern of genes but are still on conventional medication may be able to reduce or eliminate their lifelong dependence on immunosuppressive drugs. The study may also help physicians determine how best to induce acceptance, or tolerance, of donor organs in all transplant patients, regardless of their gene expression profiles.

Although the anti-rejection medications, known as immunosuppressants, tamp down the immune system enough to permit lifesaving organ transplants, their benefits come at a price. They also quash the body’s natural response to dangerous invaders, such as bacteria and viruses, and to rogue cancer cells. Transplant physicians prescribing immunosuppressants to their patients walk a fine line between avoiding organ rejection and increasing the risk of infection and cancer

The researchers used microarray, or gene chip, technology to compare gene expression patterns in blood samples from 16 healthy volunteers with those from three groups of adult kidney transplant recipients from the United States, Canada and France

Microsoft accelerates free access to journals

Information technology company Microsoft will give technical assistance to enhance access to online research for scientists, thats when most of the publishers of scientific journals are fighting against Open Access journals. Take a look at the blog  on the subject by  Greg at nodalpoint

Announced at a meeting in Washington in July Representatives from the World Health Organization, the Food and Agriculture Organization, the UN Environmental Programme, and leading science and technology publishers, together with representatives from Cornell and Yale Universities met to officially extend their free access to peer-reviewed journals for many developing world scientists to 2015, in line with the UN’s Millennium Development Goals.

Microsoft will provide new software called the Intelligent Application Gateway 2007 (formally Whale) that will meet increased demand for access to heavily trafficked portals and perform at the standards of today’s most heavily trafficked websites. The system will also enhance security through authentication of users when they log on.

The website that benefit includes open access websites such as   HINARI  Cochrane Library   AGORA and Online Access to Research in the Environment (OARE),  

Microsoft life science

Well every one is writing about google and its foray into biology and life science, so what is going on with Other companies .

Microsoft started its BioIT alliance During 2006 and guss what Bill Gates said during the launch “Advances in our understanding of the human genome promise to revolutionize medicine and open the door to therapies that are tailored to individuals”,  means they have bigger plans. just like google entered 23andME

Founding members of the alliance include Accelrys Software, Affymetrix, Amylin Pharmaceuticals, Applied Biosystems and The Scripps Research Institute, among more than a dozen other life sciences and IT companies.

and the last month Microsoft has released Microsoft Computational Biology Web Tools as open-source some code for analysis of antiviral immunity

Hmm interestingly I found the project details hosted in Codeplex the open source project hosting the details are on at MSCompBio

And then there is Stochastic Pi-Machine the programming language to model and simulate biological systems- a research funded as part of the European Science Initiative

And then there is the webpage at Microsoft research for bioinformatics

But my favourite is this

Towards 2020 Science microsoft

to define and produce a new vision and roadmap of the evolution, challenges and potential of computer science and computing in scientific research in the next fifteen years.

and this beautiful image from the microsft website

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

Girls Really Do Prefer Pink? Yes Owe to evolutionary influences

Ok I did laugh a bit at that story, but interesting ha. according to a study outlined in a report in the Aug. 21 issue of the journal Current Biology Females do have a preference for pinkish colors that males don’t.

So whats the evolutionary reason , well the same old story females used to collect food, the study says Females were the ones who gathered red fruit against a green background,” she said. “Red is healthy in faces and in fruits

so intrigued read on at USNEWS website

Google Health -health information storage

interestingly I found this image from an earlier post of Bertalan at scienceroll

The story according to the blog Google Blogoscoped, Google’s nascent Google Health product, codenamed “Weaver”, will offer consumers the opportunity to create a central repository for their health records, including medications, history, test results and allergies. The blog has a number of screenshots of the program in development.

Well google certainly has more up its sleeve, doubt it, chek the google labs page,

Passionate about these topics? You should work at Google. among others listed is interest in genetic algorithms

multipathogen- and chemical-detection Microarray.

CombiMatrix announced that the DoD has awarded a one-year, $2.2 mln contract to CombiMatrix for further development of its microarray technologies for a multipathogen- and chemical-detection system.