A New Base for Bone Cancer

November 2011

By Ciara Curtin

Researchers are collaborating to take advantage of new and archived samples to study why people develop bone cancers and to track how patients respond to therapy.

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From the Deep

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Fluidigm Developing Cellular Sample Prep Platform for Single-Cell Gene Expression, NGS Studies

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As Novartis Prenatal Pact Ends, Fluidigm Offers IP to Others, Continues Single-Cell Genomics Push

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A Conversation with CeGaT's Saskia Biskup

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A Tour of Illumina's CLIA Lab

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Young Investigator Profile

James Noonan

Assistant Professor
Yale University

Development Deciphered

The Noonan lab is studying changes in developmental gene regulation during human evolution on multiple levels. They are refining statistical methods to quantify the rate of human-specific sequence change in noncoding DNA, in order to identify regulatory elements that changed rapidly in human evolution. In addition, the lab is also characterizing individual cis-regulatory elements with human-specific developmental functions by reverse genetic analysis in mouse models.
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A New and Improved Database

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This Week in the Journal of Clinical Pathology

In the Journal of Clinical Pathology this week: NF1 isoforms in sporadic breast cancer, more.

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Papers of Note

Melanoma Genome Sequence Shows PREX2 as a Significantly Mutated Gene
Berger, Hodis et al., Nature
A team led by investigators at the Broad Institute reports having sequenced the genomes of 25 metastatic melanomas and matched germline DNA, through which it identified a "wide range of point mutation rates," and PREX2 as a significantly mutated gene in melanomas.

Developmental Milestones in the Caenorhabditis Embryo
Levin, Hashimshony et al., Developmental Cell
Technion Israel Institute of Technology's Itai Yanai and his colleagues report that "embryonic development in five Caenorhabditis species proceeds through two distinct milestones, in which the transcriptome is resistant to differences in species-specific developmental timings." Comparing the complete protein-coding transcriptomes of individually timed embryos across ten morphological markers, Yanai et al. found that these milestones "can be characterized by their expression dynamics and activation of key developmental regulators."
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Science
Researchers from Duke University and the University of Michigan successfully diagnosed around half of the individuals that they tested during a pilot study on the use of clinical exome sequencing. The investigators did whole-exome sequencing on individuals from a dozen parent-child trios for the study and pinned down likely causal mutations in six of the individuals, including new mutations in genes linked to Mendelian diseases.
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Fluidigm and the Broad Institute launched a new center, housed at the Broad's Cambridge, Mass.-based headquarters, aimed at developing new methods and discoveries in mammalian single-cell genomics. The center intends to develop novel single-cell, microfluidic methods for gene expression profiling, RNA/DNA sequencing, and epigenetic analysis with an aim at making single-cell research accessible to the greater research community.
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Launching what will be the maiden initiative for the months-old National Center for Advancing Translational Sciences, NIH Director Francis Collins unveiled a program that will support researchers using biomarker-based studies and other approaches to repurpose compounds owned by three of the world's largest drug developers. NCATS will provide up to $20 million in 2013 through two types of cooperative agreements to fuel the new projects.
Genome Technology Magazine
While whole-genome sequencing is useful for studying disease, it is less likely to be useful in predicting whether a healthy individual will develop a disease, a study recently published in Science Translational Medicine says. At the American Association for Cancer Research meeting in Chicago, study author Bert Vogelstein from the Johns Hopkins Kimmel Cancer Center spoke about the work, saying that, for cancer, predictive whole-genome sequencing is not better for ensuring health than conventional risk-management strategies like regular check-ups and an overall healthy lifestyle.

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