The Four Types

September 24, 2012

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The Cancer Genome Atlas reports on four breast cancer subtypes, in Nature. The researchers examined tumor and germline DNA from 825 patients using a number of different approaches, including mRNA expression microarrays DNA methylation chips, and whole-exome sequencing, among others. From this profiling, the researchers found that mutations in only three genes, TP53, PIK3CA, and GATA3, occurred in more than 10 percent of breast tumors. But, they note, there are certain subtypes have specific mutations and enrichment of certain mutations. They write that "our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity." Those four subtypes are: HER2-enriched, luminal A, luminal B, and basal-like breast cancers.

The New York Times adds that such knowledge of breast cancer subtypes may lead to better treatments. "This is the road map for how we might cure breast cancer in the future," Matthew Ellis from Washington University tells the Times.

Our sister publication GenomeWeb Daily News has more on the TCGA study here.

On Massgenomics: Highlights

Submitted by dkoboldt on Mon, 09/24/2012 - 13:19.

On Massgenomics: Highlights of the atlas of breast cancer genomes by one of the authors

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

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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.

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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

Andrew Johnson

Investigator
National Heart, Lung, and Blood Institute

A Bridge Across the Gap

There can be a bit of a chasm between dry lab work and wet lab work. But NHLBI's Andrew Johnson aims to close that gap. "A lot of things that I attempt in terms of projects try to bridge those barriers between the dry lab, computational side of things and wet lab experiments that are two different worlds," he says.

Currently, Johnson's work focuses on developing tools. During the early days of genome-wide association studies, he noticed that it was difficult for researchers to compare results generated across various array platforms. In conjunction with scientists at the Broad Institute, he developed a tool called SNAP to do just that. "[It] was pretty successful in terms of allowing people to rapidly query for proxy markers, but also just to do basic annotation of SNPs, like chromosome position, gene, and also to do plotting for regional genetic association plots," he says.
Blog

Navigenics Founder Blasts Myriad's BRACAnalysis Pricing

David Agus calls for legislative action to prevent monopolies, such as Myriad's around BRCA 1 and BRCA 2 genes, that have life and death implications.

May 22, 2013

'Play Defense with the Facts'

Slate discusses the issue of nonpaternity and personal genome scans.

May 22, 2013

Oversight

The California Institute for Regenerative Medicine discloses a conflict of interest violation involving Lee Hood.

May 22, 2013

Federal Funds Boost Science, FASEB Argues

FASEB makes case for the role of NIH and NSF in medical, economic, and scientific gains.

May 22, 2013
Papers of Note

High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates
Dugar, Herbig, et al. PLOS Genetics

The University of Würzburg's Cynthia Sharma and colleagues undertook a transcriptomics-based analysis of the gastroenteritis-causing bacterial species Campylobacter jejuni. The team used its so-called differential RNA sequencing strategy to sequence and compare the transcriptomes of four C. jejuni isolates (three from humans and one from a chicken), applying a new method to automatically annotate transcription start sites in each. "Overall," they write, "our study provides new insights into strain-specific transcriptome organization and [small RNAs], and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level."

Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts
Hacquard, Kracher, et al. Proceedings of the National Academy of Sciences

The barley powdery mildew (Blumeria graminis f. sp. hordei) pathogen genome is comprised of chunks of sequence that are particularly rich or replete in polymorphisms, according to a study by researchers from the Max Planck Institute for Plant Breeding Research. The team sequenced the genomes of two Bgh isolates from Europe, comparing each to the barley powdery mildew reference genome. The newly sequenced isolates each contained distinct combinations of sequence blocks with high or low SNP concentrations — isolate-specific mosaic genomes that point to "exceptionally large standing genetic variation in the Bgh population," study authors say. Meanwhile, their transcriptome sequencing experiments offered a look at genes used by Bgh during attempted infiltration of barley or immunocompromised Arabidopsis.
People on the Move

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.

Hologic has appointed former Beckman Coulter head Scott Garrett to its board of directors, where he will serve on the corporate development committee.
Garrett currently is an operating partner with Water Street Healthcare Partners, a private equity firm. Garrett spent 10 years at Beckman Coulter, where he was chairman, president, and CEO.

Gina Costa is now senior director of genomic applications at Illumina. She joins Illumina from Life Technologies, where she was senior director of genetic analysis, working on development of the Ion Torrent and SOLiD sequencing technologies. She has also held positions at Agencourt Bioscience and Roche's 454 Life Sciences.

Bioinformatics firm Golden Helix has hired Andreas Scherer to be its new president and CEO. Scherer has managed large global software services businesses, and he started his executive career at AOL/Netscape. He will replace Former CEO Christophe Lambert, who will take on the new role of company chairman.
Upcoming Events

Conferences, Meetings & Deadlines

National Advisory Council for Human Genome Research meeting
May 20-21 / Rockville, Md.
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2013 ASCO Annual Meeting: Building Bridges to Conquer Cancer
May 31-Jun 4 / Chicago
American Society of Clinical Oncology

European Human Genetics Conference 2013
Jun 8-11 / Paris
European Society of Human Genetics

ASMS Conference on Mass Spectrometry
Jun 9-13 / Minneapolis
American Society for Mass Spectrometry

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

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Science
An international team has sequenced the genome of the carnivorous bladderwort plant, Utricularia gibba. Their findings suggest that the carnivorous plant has ditched virtually all its non-coding DNA, retaining a set of sequences that's almost exclusively genic. "What that says is that you can have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the ['junk' DNA]," said co-corresponding author Victor Albert.
Business
Agilent Technologies announced a restructuring program expected to reduce its headcount by about 450 employees and save the company $50 million annually in operating expenses. CEO Bill Sullivan said that the focus of the restructuring will be on Agilent's Electronic Measurement Group and that the company will explore opportunities "to streamline our organization around the world." The firm also announced that its Q2 revenues were flat year over year.
Funding
The US Department of Energy's Joint Genome Institute has funded six new initiatives to develop technologies that will help JGI and its users conduct their research efforts into microbiology, metagenomics, and plant genomics. The projects will be supported under the Emerging Technologies Opportunity Program with a total of around $3.5 million over the next two years. Among the researchers receiving funding are Stephen Quake and Jay Shendure.
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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