Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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...

Illumina today announced it signed a definitive agreement to acquire clinical software firm NextBio. NextBio, based in Santa Clara, Calif., provides platforms to aggregate and analyze large amounts of phenotypic and genomic data for research and clinical applications. It currently has customers at more than 50 commercial entities and academic institutions. By acquiring the firm, Illumina "will be able to offer customers enterprise-level bioinformatics solutions that accelerate the discovery of new associations between the human genome and disease, and ultimately, enable the application of those discoveries within healthcare," according to a company statement. NextBio's platform allows customers to compare experimental data against existing data sets using a correlation engine, enabling them to discover new associations. It uses "highly scalable" software-as-a-service enterprise technology and is capable of analyzing petabytes of data. Illumina plans ...

Qiagen has acquired CLC Bio, a privately held bioinformatics software company headquartered in Aarhus, Denmark. The news was first reported on AllSeq's blog . This is the second bioinformatics company that Qiagen has purchased this year. In May, it bought Ingenuity Systems for $105 million in cash to offer its life science and clinical customers a complete and integrated workflow for its PCR- and next-generation sequencing-based molecular testing solutions ( BI 5/3/2013 ). Qiagen has been making some interesting moves lately, slowly building an end to end sequencing solution. They’ve already established themselves as the market leaders in sample prep, but then they started acquiring the missing pieces. First they bought Intelligent BioSystems in June 2012, giving them access to a sequencing platform built with the clinical market in mind (fairly standard SBS chemistry, relatively fast runs and multiple flow cells to obviate the need for sample multiplexing). Then they ...

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...