Bio Saga Blog - A Chronicle of Life Sciences & Informatics

This is really getting interesting, BioSaga is making history as we keep blogging! The  GATTACA SAGA ! is coming to an reality! The Race has just begun! today for  Olympian Genes; tomorrow may be for a pianist with pair of hands with 6 fingers each!  There is now no limt to the human imagination there could be a new profession  as GENE ARCHITECT or a GENOME SCULPTOR!  Beginning in 2015, Uzbekistan says it will incorporate genetic testing into its search for Olympic athletes, the Atlantic reports. Rustam Muhamedov from Uzbekistan's Institute of Bioorganic Chemistry's genetics laboratory notes that he and his colleagues have been studying the genes of Uzbek athletes and are working on developing a set of 50 genes to determine what sport a child is best suited for. "Developed countries throughout the world like the United States, China, and European countries are researching the human genome and have discovered genes that define a...

O ne more story in our very own GATTACA SAGA ! Patient advocacy groups Global Genes and Swan USA announced on Tuesday a program to provide whole-exome sequencing to patients with rare diseases who cannot afford such services. Beginning March 1, Global Genes and Swan USA will provide funding for the whole-exome sequencing of about 30 undiagnosed patients in order to identify the genetic bases of their ailments. Parabase Genomics and the UCLA Clinical Genomics Center were selected as the first clinical genomic sequencing providers for the pilot project. Global Genes is a rare and genetic disease patient advocacy group, and Swan USA provides support to families of children living with diseases and syndromes that have yet to be named. According to them, a genomic test costs between $3,500 and $5,000. The financing for the program was raised through a donor-directed fund launched in September, and additional funding is underway in order to expand the program to include more undia...

GATTACA has always been one of my favorites; every now and then I have used it as a reference in many of my posts, this one being the recent! Genome From Birth - Dawn of the GATTACA era! This is what Senator Rand Paul (R-Ky.) says in his latest public address; Speaking at a Liberty University event in Virginia, Senator Rand Paul (R-Ky.) warned that genetic testing could lead to eugenics à la the 1997 movie Gattaca , reports the Associated Press . "In your lifetime, much of your potential — or lack thereof — can be known simply by swabbing the inside of your cheek," Paul said. "Are we prepared to select out the imperfect among us?" He was campaigning in Virginia for gubernatorial candidate Ken Cuccinelli. Other aspects of Paul's speech referring to the dystopian movie, though, resembled the Wikipedia entry on the movie, Rachel Maddow pointed out on her show on Monday. USA Today notes that Paul has not responded to those accusations. Paul added tha...

Following Roche's disclosure last week that it will shut down 454 Life Sciences and stop supporting 454 sequencing instruments by 2016, customers are making plans to move their sequencing over to other platforms, if they have not done so already. While Illumina, Life Tech's Ion Torrent, and Pacific Biosciences are eager to step in to fill the void, some customers say aspects of 454's technology cannot be replaced by other platforms at this point. Also, those customers who have started to use 454 for routine clinical applications need to revalidate their assays on a new platform. Roche said last week that it will close down 454, which is based in Branford, Conn., and lay off about 100 employees over the next three years ( GWDN 10/15/2013 ). By mid-2016, it will stop supporting the 454 sequencing platforms, the GS FLX+ and the GS Junior. Roche's decision to pull the plug on 454 came to light less than a month after the company announced a deal with Pacific Bios...

Dawn of the GATTACA era! this was one of my old post. AND now this is what we hear from Robert Green The idea of sequencing someone's genome at birth has been "has been around for a long time in a pie-in-the-sky way," Robert Green from Brigham and Women’s Hospital tells Carl Zimmer at Slate . But it is becoming more of a reality, Zimmer adds. Green's BabySeq project recently received funding from the US National Institutes of Health to study how sequencing the genomes of some 240 healthy and ill infants affects their lives. They will be compared to a similar cohort of infants whose genomes will not be sequenced. As the study is small, Zimmer notes that rare, deleterious mutations may not crop up. The project will, though, make the discussion of ethics in genomic medicine more concrete, he says. “We’ll be grappling with them in real life, with real babies and real families and real clinicians and real laboratory results,” Green adds.

By considering sequence data for individuals assessed through the 1000 Genomes Project, a team led by researchers from Yale University and Wellcome Trust Sanger Institute came up with a computational method for prioritizing potential disease culprits — including those in non-protein-coding parts of the genome. As they reported online today in Science , the researchers sifted through SNP profiles in coding and non-coding sequences in 1,092 genomes, focusing on functionally annotated areas. With the help of information from the ENCODE project, mutation databases, and other data sources, they narrowed in on sequences that seem especially sensitive to change. The group tapped these mutation-sensitive sites to develop an approach called FunSeq, which proved useful for uncovering new apparent driver mutations using sequences from around 90 cancer genomes. These included almost 100 driver candidates in non-coding sequences, according to study authors, who noted that FunSeq is expected...

Microbial Genomes Curator @ Computercraft Corporation--Maryland (US).  Submitted by Computercraft Corporation; posted on Saturday, March 17, 2012 RESPONSIBILITIES: Computercraft seeks a microbiologist to work with a team of software developers and biologists on microbial genome analysis including pan-genome, protein clusters, phylogenetic tree and more. This is a technically challenging position requiring experience in genome sequencing and annotation. A background in comparative genome analysis such as alignments and tree building is a plus. Our scientists work with genomic experts at the NIH's National Center for Biotechnology Information (NCBI) to create and enhance a suite of databases and tools available to researchers worldwide. Teamwork interaction and excellent organizational skills are essential for this detail-oriented position, as is scientific problem-solving with a results-oriented focus. REQUIREMENTS: * PhD in molecular biology, microbiology, or related field * ...

7 - 19 May, 2012 | Naples | Italy The course topics will include theoretical and practical aspects in: Large-scale genome comparisons Evolutionary analyses Sequence and genome alignments Orthologs prediction and classification Genome data visualization & Next Generation Sequencing tools & analysis Theoretical presentations will be followed by practical sessions, so that the same speaker will ensure links between theory and practice. Reviews on each suggested topic will include their corresponding research perspectives, aiming at helping young scientists to gain insights into ongoing research in this domain. Practical sessions in a Linux environment will involve Unix shell and Perl scripting. Students are assumed to be familiar with this environment. Do you wish to know more?

The Centre for Applied Genomics (TCAG) at the Hospital for Sick Children in Toronto has reeled in C$5.1 million (US$5 million) from the Ontario Genomics Institute to support its operations, OGI said today. TCAG provides a range of core services including gene and genome sequencing; microarrays and genotyping; cytogenomics and biobanking; and statistical and informational services. The two years of funding was awarded under the Genome Canada Science and Technology Innovation Centre Competition. TCAG was founded in 1998 and it provides research support to labs involved in a wide array of genomic disciplines including human health, agriculture, and plant and animal studies.

Inching toward the  Dawn of the GATTACA era ! , making up history as we went along.  A group of researchers will use a $2.5 million federal grant to study the ethical and legal implications of providing genetic research results to the relatives of people who donated samples to biobanks, Mayo Clinic said today. The grant from the National Cancer Institute and the National Human Genome Research Institute will fund researchers at Mayo, the University of California, San Francisco, and the University of Minnesota who will study what families prefer, will analyze the legal and ethical issues, and propose recommendations for best practices policies. "Substantial debate surrounds the question of whether researchers have an ethical obligation to return individual research results to genetic relatives of patients, especially when the patient has died, and incidental findings have potential health or reproductive importance for kin," Gloria Petersen, the Purvis and Roberta ...

Kevin McKernan's company Medicinal Genomics announced that it has a draft assembly of the marijuana genome , reports Bloomberg. The data is to be posted to the Amazon EC2 cloud. According to Nature's News blog , the Cannabis sativa genome is estimated to be about 400 million bases, or three times that of Arabidopsis thaliana . McKernan, who was previously at Life Technologies, started Medicinal Genomics "to find ways to maximize the cannabis plant's therapeutic benefits and minimize its psychoactive effects," Bloomberg says. "This is the beginning of a more scientific approach to the genetics of the species," adds Richard Gibbs from Baylor College of Medicine. "This is not really about marijuana; it's about pharmacology." And, as Nature's News blog notes, the pot samples were prepared for sequencing at a lab in Amsterdam.

To design cells to spec, researchers still need better tools. MONDAY, JUNE 20, 2011 BY KATHERINE BOURZAC Last July , scientists created the first " synthetic cell ," an organism that's controlled by a chemically synthesized genome edited on a computer and stitched together in the lab. One year later, biologists at the  Fifth Annual Synthetic Biology  conference at Stanford University are still struggling to take the next step in the field. Holding them back are the vagaries of biology itself, and the expense and time needed to get from idea to engineered organism. While the creation of the synthetic cell, at the J. Craig Venter Institute , hints at a future in which synthetic biologists can redesign living cells to perform whatever tasks they dream up, that goal is still distant. Most research has focused on coaxing microbes to perform tasks that are similar to what they already do, such as transforming sugar into fuels using processes and materials that resemble the on...

A thorough discussion about personal genomics — what it means for the average consumer, the health care system, and the research community often raises more questions than it answers. While the public discourse on genetic privacy can be traced back to the days of the Human Genome Project, only recently has a new era been ushered in thanks to the steady decrease in the cost of DNA sequencing with promises of a tailor-made approach to medical treatment and new discoveries from rich genetic data sets. Depending on whom you ask, personal genetic information should either be protected at all costs as personal property or is merely information fit to published online for the whole world to see and contains nothing more revealing about health than, say, the knowledge that someone smokes. That there is such concern over whether genetic information is more vulnerable to attack or misuse than traditional personal health care records may be an unintended consequence of the hype that touted perso...

Cognizant, a leading provider of consulting, technology, and business process outsourcing services, and Eagle Genomics Ltd., a bioinformatics software company specializing in genomic data management and integration, has announced they are working with the Pistoia Alliance, Inc., a nonprofit, precompetitive alliance of life science companies and vendors, as one of the groups engaged to develop a conceptual cloud-based platform to facilitate access to public and proprietary sources of gene sequence data. The Pistoia Alliance’s sequence services working group aims to define and document an externally hosted service for securely storing and mining both proprietary derived gene/sequence information and public domain gene databases. This conceptual platform developed by Cognizant and Eagle Genomics, as part of this piloting stage, will enable working group companies to securely share their bioinformatics resources among simultaneous, registered users in a secure, encrypted environment, while...

Avesthagen launches commercial Whole Genome Scanning Bringing Personalized Genomics to your doorstep. Avesthagen will use Affymetrix technology to decipher the association between single nucleotide polymorphisms (SNPs)/ mutation and predisposition to the disease. The DNA chip used by Avesthagen for whole genome scanning features more than 1.8 million markers of genetic variation that include SNPs as well as probes for copy number variation (CNV). A whole genome scan of an individual would provide information to understand his/her own genetic make-up that would lead to an increased awareness about the predisposition to a disease(s). The diseases, which are offered by Avesthagen, include major types of cancer, cardiovascular diseases, diabetes, schizophrenia, Alzheimer’s, asthma, anemia, arthritis and others. The technology platform at Avesthagen is able to interrogate the genetic markers (SNPs and CNVs) across an individual’s genome...

DNA sequencing’s first attempt at a personal-computer-like console is about to get a whole lot faster. The Ion Torrent Personal Genome Machine (PGM), launched with much fanfare (and  a Forbes cover ) in December, will be 100 times more powerful than it was at launch by the third quarter, according to Life Technologies, the $3 billion life sciences company that makes it. Life Technologies' Personal Genome Machine That means that the PGM will be able to sequence 1 billion letters of DNA code in two hours, making it much more competitive with a rival machine, the MiSeq, developed by Illumina, which now dominates the sequencing business. Perhaps more importantly, this leap would fulfill the promise made by Ion Torrent founder Jonathan Rothberg, who has promised that because his device relies on the same kind of semiconductor factories used to make Xboxes and iPods its performance will be able to improve 10-fold every six months. As he told me last year: “There isn’t a technology that w...

Using genome sequencing and other strategies, researchers from Pennsylvania State University and elsewhere are finding genetic clues that they say may be useful for selecting Tasmanian devils for breeding programs aimed at saving the animals from extinction. The team used Roche 454 technology to do  de novo  sequencing of two Tasmanian devil genomes, Penn State biochemistry and molecular biology researcher Stephan Schuster said during Roche Applied Science workshop at the Plant and Animal Genomes conference this week. By looking at SNP data in the nuclear and mitochondrial genomes of Tasmanian devils, he explained, the team is tracking down informative markers that they believe may be useful for gauging genetic diversity and managing Tasmanian devil populations through more tailored breeding programs. Do you wish to know more?

Researchers from the International Citrus Genomics Consortium announced this weekend at the Plant and Animal Genome (PAG) XIX conference in San Diego, California the availability of the sequence assembly and annotation of the first citrus genomes, the sweet orange ( Citrus sinensis ) and the Clementine mandarin ( Citrus clementina ). The sweet orange genome was sequenced and analyzed in joint collaboration between the University of Florida, DOE Joint Genome Institute, the Georgia Institute of Technology and  454 Life Sciences , a Roche Company, using the high-throughput  GS FLX System . Funded in part by the Florida Citrus Production Research Advisory Council, a citrus grower industry organization, the project is expected to assist geneticists and breeders improve these important fruit crops. The assembled and annotated genomes have been added to the publicly available database Phytozome.net, a project of the DOE JGI and the Center for Integrative Genomes. Grown in more than...

Direct-to-consumer genetics testing firm 23andMe has moved to a subscription-based pricing plan that now includes a one year contract and an additional charge of $5 per month. Along with the change in pricing, the company has done away with its separate Ancestry Edition and Health Edition products, which are now part of one service, called Complete Edition, that the firm offers. The base price for the testing service remains at $499 . The Ancestry and Health Edition products were launched a year ago by 23andMe. The changes took effect on Nov. 22. After the initial year expires, the contract will go to a month-to-month model, and customers will be able to cancel their contract at any time, a spokeswoman for Mountain View, Calif.-based 23andMe said. In an e-mail, she said the new monthly charge is based on the company's need to update its test and customers' test results as new genetic discoveries are made. The company's scientific team continually evaluates the latest scien...

A team of researchers from the J. Craig Venter Institute has created the first synthetic organellar genome, using a method called isothermal DNA assembly to construct a synthetic mouse mitochondrial genome from hundreds of overlapping oligonucleotides. The work, published online yesterday in   Nature Methods , is the latest in a series of synthetic biology achievements by the group. JCVI researchers reported in  Science  in 2008  that they had put together four Mycoplasma genitalium  quarter genomes in  Escherichia coli  and yeast to create the first synthetic genome, dubbed  M. genitalium  JCVI-1.0. They later tweaked this process, showing that they could assemble the  synthetic  M. genitalium  genome in a single step in yeast. And earlier this year the team took another step toward synthetic life when they made a synthetic  M. mycoides  genome, transplanted it into another bacterial species,  M. capricolum , ...