Sequencing Step Now 'Trivial' Part of Clinical Genomics Pipeline amid Analysis, Reimbursement Challenges

June 13, 2012

By Monica Heger

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Monica Heger tracks trends in next-generation sequencing for research and clinical applications for GenomeWeb's In Sequence and Clinical Sequencing News. E-mail Monica Heger or follow her GenomeWeb Twitter accounts at @InSequence and @ClinSeqNews.

In this issue of Clinical Sequencing News

GenomeWebinars

Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

Sponsor: EMD Millipore

Data presented in this webinar illustrates the value of live cell analysis at the single-cell level to identify differences in expression levels across populations of cells. The cells remain intact for downstream analysis. Our experts also discuss the use of SmartFlare RNA detection probes for the direct quantification of circulating miRNAs with rapid processing of blood plasma/serum, which is done without the use of enzymes. Using circulating miRNAs with established roles in cancer and quality control, we can accurately detect these miRNAs in plasma using a microplate fluorometer within an hour after plasma preparation.

On-demand recording is available here.

Optimization of NGS Library Preparation: Low Inputs and Fast, Streamlined Workflows

Sponsor: New England Biolabs

Library preparation methods continue to be challenged by the requirement for faster and more efficient protocols, using lower input amounts. In this online seminar, recorded Feb. 7, 2013, experts discuss new approaches to tackle these challenges, particularly for bacterial and exome sequencing.

Available here.
Young Investigator Profile

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.
Blog

Molecular Biology and the Court

In its decision, the US Supreme Court describes molecular biology.

Jerome Karle Dies

Jerome Karle, who won the Nobel Prize for work in crystallography, has died.

NIH of its Own

The Japanese government is considering its own version of the National Institutes of Health.

This Week in PLOS

In PLOS this week: fungal fish pathogen genome, admixture in the Quebec founder population, and more.
Papers of Note

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
McLean, Lombardo, et al. Proceedings of the National Academy of Sciences

Investigators with the J. Craig Venter Institute and other centers in the US and Russia describe the "mini-metagenome" approach they used sequence the genome sequence of a representative from the uncultivated bacterial phylum dubbed TM6. From swab samples collected from a biofilm in the sink of a hospital's public restroom, the team narrowed in on individual bacterial cells using fluorescence activated cell sorting and other techniques. After amplifying and sequencing DNA in individual bacteria cells, investigators put together an assembly comprised of reads from cells with shared 16S ribosomal RNA sequences, covering around 90 percent of the genome for a TM6 bug called TM6SC1.

Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits
Randall, Winkler, et al. PLOS Genetics

A PLOS Genetics study looks at genetic variants influencing traits such as height, weight, body fat, or waist and hip measurements that differ between men and women. Members of the international Genetic Investigation of Anthropometric Traits, or GIANT, consortium drew on data for 133,723 individuals for a meta-analysis aimed at finding sexually dimorphic genetic contributors to these and other anthropometric traits. That analysis, followed by a validation study involving more than 137,000 other individuals, led to variants at seven loci showing significant ties to waist-related traits in women but not men.
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.
Upcoming Events

Conferences, Meetings & Deadlines

International Meeting on Cell-Free DNA
June 20-21 / Copenhagen
Copenhagen University Hospital

Intelligent Systems for Molecular Biology
July 21-23 / Berlin
International Society for Computational Biology

2013 AACC Annual Meeting
July 28-August 1 / Houston
American Association for Clinical Chemistry

NGS for Drug Developers
July 31-August 2 / Boston
Wyss Institute

Cancer Cytogenomics Microarray Consortium meeting
August 5-7 / Chicago
Cancer Cytogenomics Microarray Consortium

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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.
GenomeWebinars
GenomeWebinar: Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

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.

On-demand recording available here.

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Sequencing Step Now 'Trivial' Part of Clinical Genomics Pipeline amid Analysis, Reimbursement Challenges

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