PacBio Says 'Strobe Sequencing' Increases Effective Read Length of Single-Molecule Sequencer

May 12, 2009

By Julia Karow

At last week's Biology of Genomes meeting at Cold Spring Harbor Laboratory, the company showed that by turning the system's lasers off and on during a run it can generate longer reads with gaps that could be useful for sorting out complex repeat regions in the genome.

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In this issue of In Sequence

Young Investigator Profile

Cedric Blanpain

Université Libre de Bruxelles
Interdisciplinary Research Institute
Principal Investigator

Studying Stem Cells

The Blanpain lab is using various models to study how multipotent progenitors are specified during embryonic development, the mechanisms that control the differentiation of embryonic progenitors into the different cell lineages that composed adult tissue, and how tissue maintenance is ensured during homeostasis.
They are also using novel genetic approach to identify the cell lineage at the origin of the most frequent epithelial cancers in humans and understand the mechanisms regulating cancer stem cell function during tumor growth and relapse after therapy.
Blog

GPUs in the Cloud

More and more, cloud and on-demand computing providers are offering GPUs.

September 10, 2010

LabCorp to Use Sysmex's Automated Hematology Systems for Five Years

The instruments comprise Sysmex's XE-Series automated hematology analyzers, its SP-1000i automated slidemaker/stainers, and Sysmex-distributed CellaVision DM96 automated digital cell-morphology systems.

September 10, 2010

Want to See More PGx Testing? Train More Pharmacists as Well as Clinicians

Pharmacogenetic testing could be a "potential positive contribution" to health care in the US, so long as clinicians and pharmacists receive more training in the discipline," according to a recent paper in a pharmacy journal.

September 10, 2010

Stem Cell Research Gets a Reprieve

An appeals court has ruled that stem cell research funding will continue while appeals on the recent ban are considered.

September 10, 2010
Papers of Note

IRF7 Regulates an Antiviral Expression Network and T1D Risk
Heinig, Petretto et al., Nature
An international research team reports that "a trans-acting locus regulates an antiviral expression network and type 1 diabetes risk." Specifically, using integrated genome-wide approaches across rat tissues, the team found an "interferon regulatory factor 7-driven inflammatory network enriched for viral response genes, which represents a molecular biomarker for macrophages and which was regulated in multiple tissues by a locus on rat chromosome 15q25." The human locus that controls the IRF7-driven inflammatory network is "associated with the risk of T1D at single nucleotide polymorphism rs9585056," the team writes.

Protein Composition of Mitotic Chromosomes via Combinatorial Proteomics
Ohta, Bukowski-Wills et al., Cell
A research team led by the Wellcome Trust Centre for Cell Biology's Shinya Ohta has determined the protein composition of mitotic chromosomes using multi-classifier combinatorial proteomics. Ohta et al. describe their approach, which "integrated quantitative proteomics with bioinformatic analysis to generate a series of independent classifiers that describe the [approximately] 4,000 proteins identified in isolated mitotic chromosomes." In their subsequent whole-chromosome proteome analysis, the team found — via Ska3/Rama1 genetic knockouts — "that the APC/C and RanBP2/RanGAP1 complexes depend on the Ska complex for stable association with chromosomes." The authors predict that they've yet to discover up to 97 novel centromere-associated proteins using their data set.
People on the Move

The National Human Genome Research Institute said this week that it has chosen Daniel Kastner to be its new scientific director. Kastner, who will join NHGRI in October, currently is clinical director and director of translational research at the National Institute of Arthritis and Musculoskeletal and Skin Diseases.

Former Genome Canada President and CEO Martin Godbout has been appointed chairman of MethylGene's board of directors. Godbout, who held the top post at Genome Canada between 2000 and 2009, has served as a member of MethylGene's board since 2002. He also has been senior VP of BioCapital and president and GM of Société Innovatech Québec.

Emergent Biosolutions has appointed former National Cancer Institute Director John Niederhuber to serve on its board of directors.

Niederhuber was director at NCI from 2005 to 2010, and he recently joined Inova Health System as executive VP and CEO of the Inova Institute for Translational Research and Personalized Medicine. He also still works as an adjunct investigator at NCI’s Center for Cancer Research.
Upcoming Events

Conferences, Meetings & Deadlines

4th CPTC Annual Meeting: Establishing the Standards in Clinical Proteomics
Sep. 8-9 / Bethesda, MD
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Quantitative and Systems Pharmacology Workshop II
Sep. 9-10 / Bethesda, MD
NIGMS

Global Biomarker Conference
Sep. 10 / Vancouver, Canada
GBC

Personal Genomes
Sep. 10-12 / Cold Spring Harbor, NY
CSHL

50th Interscience Conference on Antimicrobial Agents and Chemotherapy Meeting
Sep. 12-15 / Boston, MA
American Society for Microbiology

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Science
Members of the International HapMap 3 Consortium reported that they have genetically characterized individuals from 11 different populations, genotyping nearly 1,200 individuals and re-sequencing specific genomic regions in almost 700 individuals from 10 of the populations, comparing SNP and copy number variation patterns across the populations tested.
Business
Roche announced a cost-cutting initiative, dubbed a "Group-wide Operational Excellence initiative," that will be implemented in 2011-2012. It said that the initiative, which "aims to adapt cost structures and accelerate productivity improvements Group-wide," is in response to "mounting pressures to curb healthcare costs," particularly in the US and Europe.
Funding
The NIH will provide $161.3 million in funding to expand a nationwide effort to advance personalized medicine through the use of pharmacogenomics. The Pharmacogenomics Research Network program will support research into genetic variants linked to responses to a range of medicines for cancer, heart disease, asthma, and addiction.
Genome Technology Magazine
Whether you left the lab to raise children or to follow another passion, going back to the workforce is a daunting challenge. In this month's Careers column, Matthew Dublin looks into ways to ease your return to the bench.

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PacBio Says 'Strobe Sequencing' Increases Effective Read Length of Single-Molecule Sequencer

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