Sequencing and Analysis of the Hydra Genome
Chapman, Kirkness et al., Nature
An international research collaboration reports their sequencing and analysis of the Hydra magnipapillata genome, and compare it to the genomes of several other organisms. "The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle," the authors write. They team suggests that comparisons of the Hydra genome to the reported sequences of other animals have helped them to elucidate the evolution of several of the organism's characteristics.
From his updated map of sequencers, Nick Loman says that Illumina machines are still dominant — making up 60 percent of his sample — but that the race for second place is close. Roche, he says, has just nudged out SOLiD by eight machines. (His Google map can be seen here.) To get a better estimate of what sequencers are out there, Loman is kicking off "the great high-throughput sequencing serial number challenge," taking inspiration from a statistical approach used by the British during World War II to estimate the number of German tanks through serial numbers. If those serial numbers are continuous, then a better guess at the number of tanks, or sequencers, can be made. At Genetic Future, Daniel MacArthur calls it a "fiendish plan." He adds: "There are certainly a number of ways in which such estimates can prove inaccurate — but as Loman says, it's still worth doing the experiment."
March 19, 2010
At Think Gene, Andrew Yates wonders how physicians are supposed use genetic information from tests, such as 23andMe's. He notes that 23andMe's terms of service agreement says that their tests are "for research and educational use only. …The services cannot be used for health ascertainment or disease purposes." In a follow-up post, he argues that "this contract is imposed by 23andMe to the public in bad faith because 23andMe actively promotes its users to violate this clause." For example, he says, one user tweeted that he shared his warfarin report with a cardiologist and the company replied to, and retweeted, that message, thus promoting the violation of that clause. Yates concludes that he is "supposed to 'ignore' that part of the contract."
March 19, 2010 / 1 comment
Adding More SNPs to Breast Cancer Risk Models Doesn't Help
In the New England Journal of Medicine, researchers from the National Cancer Institute say breast cancer risk assessment models don't perform any better when they include common inherited genetic variants linked to the disease. The study's senior investigator, Sholom Wacholder, says the improvement in the risk models wasn't enough to matter to a majority of women. Wacholder and his team combined data from five studies, altogether including 5,590 breast cancer patients and 5,998 healthy women. Then they examined the predictive accuracy of the Gail model – using information on a woman's personal health and reproductive history to estimate the risk of developing breast cancer within the next 5 years, or over a lifetime – and tested the accuracy of a model using SNPs and found they each worked as well as the other. An inclusive model using both SNPs and Gail factors performed only slightly better than either model alone.
March 19, 2010
NIH Creating Genetic Testing Registry
The National Institutes of Health is creating a genetic testing registry: a public database that researchers, consumers, healthcare providers and others can use to search for information submitted by genetic testing providers. The NIH says its aim is to improve access to information about the availability, validity and usefulness of the more than 1,600 genetic tests available to patients and consumers. Genomics Law Report's Dan Vorhaus says that since the registry is voluntary, that limits its usefulness as a regulatory tool, but he adds that "it has the potential to prove extremely valuable to personal genomics companies and consumers alike." DTC genetic testing company 23andMe has already indicated its willingness to participate in the project.
Blogger Daniel MacArthur writes at Genetic Future that the database will have the added benefit of "providing consumers with an easier way to distinguish between accurate, useful genetic tests and contemptible bottom-feeders."
March 19, 2010
In Science Signaling this week, researchers in Germany report on their loss-of-function RNAi screen which revealed Ras- and Raf-independent MEK-ERK signaling in human epithelial cells during Chlamydia trachmatis infection. Their study also identified 59 host factors that either positively or negatively influenceChlamydia replication; depletion of Ras or Raf in HeLa cells increased the pathogen's growth. "Together, these findings not only show that Chlamydia regulates components of an important host cell signaling pathway, but also provide mechanistic insights into how this is achieved," the authors write.
In Science Translational Medicine, an international research team presents evidence that mutations in fibrillin-1 cause Stiff Skin Syndrome, an autosomal dominant congenital form of scleroderma. The researchers found that mutations in the only Arg-Gly-Asp sequence-encoding domain of fibrillin-1 — wherein integrin binding is mediated — causes the condition, which involved fibrosis and hardening of the skin. "The observation of similar findings in systemic sclerosis, a more common acquired form of scleroderma, suggests broad pathogenic relevance," they write.
In an advance, online publication of Science this week, investigators in Japan and the US report that inactivation of the dcr-1 gene in Caenorhabditis elegans "compromises apoptosis and blocks apoptotic chromosome fragmentation." Their studies show that DCR-1 fragments chromosomal DNA during apoptosis — in addition to processing small RNAs — and undergoes a "protease-mediated conversion from a ribonuclease to a deoxyribonuclease."
A report in Science this week describes CKAMP44 as a brain-specific type I transmembrane protein that modulates short-term plasticity at specific excitatory synapses. Using a proteomic approach, researchers found that CKAMP44 expressed in Xenopus oocytes "reduced GluA1- and A2-mediated steady-state currents, but did not affect kainate- or N-methyl- D-aspartate receptor-mediated currents." In a mouse model, hippocampal CA1 pyramidal neurons expressed CKAMP44 at low abundance; dentate gyrus granule cells exhibited strong CKAMP 44 expression.
March 19, 2010
SBS and ALA Announce Proposed Merger
The Society for Biomolecular Sciences and the Association for Laboratory Automation have proposed a merger to create the Society for Laboratory Automation and Screening. The societies are waiting for approval from their members. SBS President Jeff Paslay says that despite serving different scientific niches, members of both societies have similar educational interests and member service priorities. If the merger is approved, SBS and ALA will become individual sections of SLAS, retaining their individual missions and also collectively addressing the overall SLAS mission, which is to provide forums for education and information exchange to encourage the study of lab automation and screening. Voting opens March 15 and closes May 5. If the members approve the merger, it will become official on July 1.
March 18, 2010
Francis Collins on Genetic Tests
In this video, Francis Collins speaks with the Washington Post's Fred Hiatt about the state of genetic testing. Collins says that the research linking genetic variants to disease is further along than he'd anticipated, but adds that most of the clinical payoffs are still to come:
March 18, 2010 / 1 comment
An Honor for Claire Fraser-Liggett
Claire Fraser-Liggett is to be inducted into the Maryland Women's Hall of Fame this evening along with five other women who have made contributions to the economics, politics, culture, or society of Maryland. "I am truly humbled to be part of this most prestigious tradition. Scientists often focus on the global impacts of our research, but to be successful, we need to be working in an environment that nurtures our work," she says in a statement. "I am very fortunate that our Institute is part of the University of Maryland School of Medicine, a place that encourages innovative thinking and fosters women's leadership." The other inductees include civil rights activist Irene Morgan Kirkaldy and Title IX champion Bernice Sandler.
March 18, 2010
Thieves Pull Off $75 Million Drug Heist
It's a scene out of "Mission: Impossible." The Wall Street Journal reports that thieves cut a hole in the roof of an Eli Lilly warehouse in Connecticut, disabled the alarm, climbed down ropes, and stole $75 million in antidepressants and antipsychotics. Police say the wooden crates full of prescription pills were loaded onto a tractor-trailer and driven away. The thieves didn't take any controlled substances like painkillers and narcotics, the company says. In the past, such stolen drugs have ended up on the black market or in Latin America or Asia. Even legitimate U.S. pharmacies sometimes buy them, the WSJ reports. Industry experts say theft of pharmaceuticals is on the rise, and there have been 10 pharma thefts valued at a total of $110 million this year alone. In 2009, there were 46 thefts, valued at a total of $184 million. In the meantime, Lilly says its pharmaceutical distribution on the east coast won't be disrupted, and the company is negotiating with its insurance company to cover the loss.
March 18, 2010 / 1 comment
'Government Sources' Confirm Varmus Will Head NCI
Science Insider and the Wall Street Journal's health blog are both speculating about the possibility that Nobel laureate Harold Varmus — former director of the National Institutes of Health — will soon be named director of the National Cancer Institute. Rumors that Varmus would soon head up NCI began shortly after he issued a public letter saying he had asked Memorial Sloan-Kettering Cancer Center's board to begin looking for his successor as president, according to the WSJ. According to D.C.-based newsletter The Cancer Letter, "multiple sources in the federal government and outside it confirmed that the announcement appears imminent." On March 7, Science ran a story in which Varmus denied that he would become director of the NCI, calling the rumors "far-fetched."
March 18, 2010
Dan Vorhaus at the Genomics Law Report considers what the Federal Communications Commission's National Broadband Plan could mean for genomics and personalized medicine. In Section 10.4, he says, the FCC conjures the value of data and the importance of consumer access. "In focusing on the value of data the FCC clearly indicates that it’s interested in liberating all types of healthcare data — patient and provider, administrative, research and clinical — from the 'proprietary siloed' systems that do not communicate with one another and therefore cannot be easily exchanged, aggregated or analyzed," Vorhaus writes. Further, the FCC acknowledges the merits of dispersing genomic data, as it "could help researchers better understand the interplay of genetics and the environment." As far as access is concerned, Vorhaus points out that the FCC recognizes the importance of "consumers" having access to their healthcare data. "With seamless access to their raw health data including lab data and prescriptions, consumers could plug the information into specialized applications of their choice and get personalized solutions for an untold number of conditions," the plan reads.
March 18, 2010
In an advance, online publication of Nature this week, an international research team reports their sequencing and analysis of the freshwater cnidarian Hydra magnipapillata genome, as compared to the genomes of the anthozoan Nematostella vectensis and other animals: "The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle," the authors write. They suggest that comparisons of the Hydra genome to those of other animals have helped them to elucidate the organism's evolution of epithelia, contractile tissues, and developmentally regulated transcription factors, among other things.
Also published online in advance, European researchers report their sequencing of the mRNA portion of the transcriptome in 60 HapMap individuals of European ancestry. The team quantified exon abundance based upon read depth and found that nearly "10 million reads of sequencing can provide access to the same dynamic range as arrays with better quantification of alternative and highly abundant transcripts." Additionally, correlation with SNPs led to a larger discovery of expression quantitative trait loci than with arrays, the researchers write. They suggest that high-throughput sequencing technologies are capable of illuminating the properties of genetic effects on the transcriptome.
In this week's issue of Nature, researchers in Spain and the US present their determination that compensatory evolution in mammalian mitochondrial tRNAs, wherein it effectively affixes two alleles that are individually deleterious, could be a common phenomenon. The team examined the "fitness landscapes traversed by switches" between nucleotide pairs at complimentary sites of mitochondrial tRNA in 83 species. Compensatory evolution must occur through rare intermediate variants that never reach fixation, the authors suggest.
In an advance, online publication of Nature Genetics this week, researchers present results from their genome-wide association study for ulcerative colitis, which identified risk loci at 7q22 and 22q13. Their analysis included 1,897,764 SNPs from 1,043 UC cases and 1,703 controls from Germany, and confirmed risk associations in six replication panels from different regions of Europe.
March 18, 2010
Last night, some 150 cancer researchers and people devoted to the field gathered at the Hilton New York to honor Peter Vogt of The Scripps Research Institute, winner of the 2010 Szent-Györgyi Prize for Progress in Cancer Research. The award was sponsored by the National Foundation for Cancer Research, which was cofounded by Albert Szent-Györgyi in 1973.
John Lechleiter, CEO of Eli Lilly and Company, gave a keynote speech at the award dinner. In it, he said that two main drivers in defeating cancer would be tailored therapies and increased collaboration among pharmas, academia, and more. Establishing those partnerships will necessitate figuring out what information is truly competitive and what can be shared, he said. "The next generation of cancer treatments must be more tailored," he added.
In accepting his award, Vogt's comments reminded attendees of why he's renowned both as a cancer researcher and as a principal investigator. Included in his list of people to thank were the people who have gone through his lab: "The character and quality of a lab are determined by its postdocs and grad students," he said. Vogt's work began with studies of Rous sarcoma virus, but he is best known for his research around P1 3-kinase and elucidating the protein-protein interaction of Myc and Max. Read more about the award in the official announcement.
March 17, 2010
