Italian Team Shows LNA-Modified qPCR Method Outperforms Sanger Sequencing for KRAS, BRAF Mutations

May 17, 2012

By Molika Ashford

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Molika Ashford is a GenomeWeb contributing editor and covers personalized medicine and molecular diagnostics. E-mail Molika Ashford.

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Lei Xie

Associate Professor
City University of New York

Changing Approaches in Drug Development

After finishing his postdoc, Lei Xie started working at a pharmaceutical company where he saw firsthand the weaknesses of the one-drug-one-gene-one disease approach. Upon leaving industry, Xie returned to academia, set upon finding ways to improve the success rate of investigational treatments through so-called polypharmacology, an approach that aims to advance drugs that target disease-causing networks instead of inhibiting individual receptors.

In his research at CUNY's computational systems biology, molecular modeling, and bioinformatics lab, Xie aims to identify the targets of drugs across the whole genome and then map them into biological pathways and networks.
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Difficulties After the Freeze

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Now the Fastest

The current fastest supercomputer is China's Tianhe-2, Top500 says.
Papers of Note

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us
El Baidouri, Diancourt, et al. PLOS Neglected Tropical Diseases

Through a multilocus sequence analysis of 222 African and Eurasian Leishmania isolates, French researchers identified seven genetic clusters of Leishmania in the regions tested. For the most part, those clusters corresponded to existing Leishmania classification schemes, the study authors note, though their analysis suggests genetic distinctions are somewhat hazier for three Leishmania species implicated in visceral forms of leishmaniasis. "Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles," they say, "they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago."

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna
Nakamura, Mori, et al. Proceedings of the National Academy of Sciences

AJapanese team describes findings from a genome sequencing study focused on the Pacific bluefin tuna, Thunnus orientalis. An analysis of the genome revealed more than 26,400 predicted protein-coding genes, including genes coding for rhodopsin and opsin pigments poised to pick up blue, green, red, and UV light. Within genes coding for the color-sensing proteins, researchers found substitutions and duplications suspected of helping bluefish tuna differentiate between blue and green. If so, that could confer an evolutionary advantage in the fish's ocean environment, they say, perhaps explaining some aspects of the tuna's predatory proficiency.
People on the Move

Direct-to-consumer genetic testing firm 23andMe has appointed Andy Page as its president, a newly created post. Page, who has served as a member of 23andMe's board of directors for the past year, will report to CEO and co-founder Anne Wojcicki. He was previously president of the Gilt Groupe, an online luxury shopping website, and chief operating and financial officer at PlayPhone.

The Ludwig Institute for Cancer Research has appointed David Lane to be its new scientific director, effective June 1. He succeeds Andrew Simpson, who was scientific director for five years, from 2007 to 2012. Lane is chief scientist at Singapore's Agency for Science, Technology, and Research, and he will retain that post in addition to his new role at Ludwig.

Kevin Hrusovsky is resigning his post at PerkinElmer as senior VP and president of the Life Science and Technology division. Hrusovsky will serve as a consultant to the company for up to one year, beginning in June. He joined PerkinElmer through the company's acquisition of Caliper Life Sciences, where he was CEO and president.
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Science
An international research team has uncovered unexpected genetic diversity in the miniscule marine algae Emiliania huxleyi, a species now known to have the type of variable 'pan genome' previously described in some bacterial species. They detected an array of genes and repetitive sequences that are present in some E. huxleyi strains but not in others, varying with each strain's habitat, physical features, and metabolic capabilities, among others.
Business
The US Supreme Court unanimously ruled that human genes are not patentable, but synthetic DNA, or cDNA, is patent eligible because it does not occur naturally. Its decision had broad implications for the biotech industry and for Myriad Genetics, in particular, whose patents on the BRCA1 and BRCA2 genes were at the center of the case. The ruling runs counter to the US Patent and Trademark Office's policy of granting patents on isolated gene sequences.
Funding
The US investment in the Human Genome Project and the ensuing federal funding for genome science has reaped massive economic benefits, according to a new study from Battelle. It found that genomics-related fields from biomedicine to energy and agriculture have had a $965 billion impact on the US economy, stemming from a total of $14.5 billion in federal investments between 1988 and 2012. Genomics-related funding has yielded a $65 return on every $1 invested.
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Sponsor: EMD Millipore

GenomeWeb and EMD Millipore invite you to view an archived webinar discussing new approaches to detect RNA at the single-cell level as well as new probes for the direct quantification of circulating miRNAs. In this free online seminar, recorded April 25, 2013, our expert panel shares protocols for improved RNA and miRNA detection.

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Italian Team Shows LNA-Modified qPCR Method Outperforms Sanger Sequencing for KRAS, BRAF Mutations

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