Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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...

Initiating sequencing of a set of 60 closely related human genomes to identify novel genetic information relevant to cancer, metabolic and neurological disorders. Through this project, Avesthagen intends to establish a direct link between genes, genetics and the disorders themselves.  The study, led by Avesthagen, a life sciences company based in Bangalore, is being carried out in partnership with Genome Enterprise Limited, a subsidiary of The Genome Analysis Centre (TGAC) on the Norwich Research Park..   The TGAC team, specialists in DNA sequencing and bioinformatics, will use the SOLiD™ 4 next generation sequencing platform from Applied Biosystems, part of Life Technologies, to generate draft sequence, and will collaborate with the Avesthagen’s own bioinformatics experts to analyze and interpret the sequence data It is known that many genes on the human chromosomes may be involved during the manifestation of the above disorders. However, the power of present technologies to...

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...

A team of UK researchers, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), has publicly released the first sequence coverage of the wheat genome. The release is a step towards a fully annotated genome and makes a significant contribution to efforts to support global food security and to increase the competitiveness of UK farming. The genome sequences released comprise five read-throughs of a reference variety of wheat and give scientists and breeders access to 95% of all wheat genes. This is among the largest genome projects undertaken, and the rapid public release of the data is expected to accelerate significantly the use of the information by wheat breeding companies. The team involved Prof Neil Hall and Dr Anthony Hall at the University of Liverpool, Prof Keith Edwards and Dr Gary Barker at the University of Bristol and Prof Mike Bevan at the John Innes Centre, a BBSRC-funded Institute. The genome data released are in a 'raw' format, comprisin...

The first effort to sequence a complete cancer genome has underscored the power of second-generation sequencing while further establishing the lack of a “killer software app” in the field. In the study, published this week in Nature , a team of 48 scientists at the Genome Center of Washington University and elsewhere sequenced a female patient’s acute myeloid leukemia genome and compared it to the genome of her biopsied skin as well as reference genomes to uncover 10 cancer-associated mutations — eight of which were previously unknown. The team used two high-throughput sequencing platforms — the Illumina Genome Analyzer and the Roche/454 FLX platform — and software tools such as Maq, Cross_Match, BLAT, and Decision Tree analysis. The team also did its own scripting and algorithm development in the course of the project, Rick Wilson, director of the Genome Sequencing Center at Washington University School of Medicine, said. The AML sequencing team applied several established soft...

Complete Genomics emerged from stealth mode today brandishing an audacious service model for wholesale next-generation sequencing, with its first human genome already assembled and the CEO’s pledge to reach the magical “$1000 genome” price point as early as spring 2009. Based in Mountain View, Calif., Complete Genomics has raised $46 million in three rounds of financing since its incorporation in 2006. Unlike its commercial next-gen sequencing rivals – Roche/454, Illumina, Applied Biosystems (ABI) and Helicos – Complete Genomics will not be selling individual instruments, but rather offer a service aimed initially at big pharma and major genome institutes. “Our mission is to be the global leader in complete human genome sequencing,” chairman, president and CEO Clifford Reid in a briefing last week. “We are setting out to completely change the economics of genome sequencing so that we can do diagnostic quality human genome sequencing at a medically affordable price. Essentially, [we’ll...

It's the technology. Watson's genome was sequenced using one of the next generation sequencing technologies (454), which allows much more sequencing bang for the buck. This isn't a $1000 genome , but it's a step in that direction. The real value of Watson's genome sequence is a proof of principle. This project was completed at a low cost (relative to the previous methods of sequencing genome), but with high quality. They were able to identify not only sequence variation between Watson and the reference genomes, but also structural variation. To truly realize the potentials of personal genomics, we need many more of these genomes, with the phenotypic data on the individuals. Along with the article, Nature has published a News and Views piece on the Watson genome paper . The article takes many steps to point out that, while we are at the cusp of an era of personal genomics, there are many limitations as to what we can do with these data. Given our current knowledge, w...