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01.11.07
Posted in cancer, methylation, news links at 6:35 am by Trevor
BioCangen Inc. has announced the initial results of its clinical validation study of early cancer detection.
Among the blood samples from 102 patients with solid tumors including lung cancer, colon cancer, breast cancer and stomach cancer, 73 samples were correctly identified as the cancer, showing a 71.6% detection sensitivity. Among the 82 health individuals, only 3 samples were identified as the cancer, indicating a 96.3% specificity.
These results will be further validated with multi-center trials for submission to the FDA. Link
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01.10.07
Posted in cancer, methylation, news links at 6:14 pm by Trevor
Illumina Inc. (NASDAQ:ILMN) has announced that it has introduced a high-throughput DNA methylation profiling technology capable of surveying up to 1,536 methylation sites across 96 samples simultaneously. From Business Wire:
By pairing Illumina’s proven BeadArray platform with the GoldenGate(R) assay approach, researchers have the ability to perform genome-wide methylation profiling across multiple areas such as cancer and human embryonic stem cell research. The GoldenGate Methylation Cancer Panel I, the first standard panel, covers 1,505 methylation sites over 800 cancer genes. Custom-content methylation panels will soon be available to meet individual research needs.
Recently, the NCI and the National Human Genome Research Institute (NHGRI) announced two more components of The Cancer Genome Atlas (TCGA) Pilot Project, a three-year, $100 million collaboration established to test the feasibility of using large-scale genome analysis technologies to identify important genetic changes involved in cancer. As part of this project, the Sidney Kimmel Comprehensive Cancer Center of the Johns Hopkins University and the Norris Comprehensive Cancer Center of the University of Southern California were awarded funds to establish Cancer Genome Characterization Centers (CGCC). At these centers, researchers will utilize Illumina’s GoldenGate methylation technology to detect changes in methylation profiles associated with transcribed genes in cancer samples.
Link
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01.08.07
Posted in news links at 6:36 am by Trevor
In November 2006, the Secretary’s Advisory Committee on Genetics, Health, and Society (SACGHS) met to discuss and approve the final version of their report on policy issues associated with undertaking a large U.S. population cohort project on genes, environment, and disease. Our previous coverage of this project, including a brief summary of the project’s history and scope, can be found here.The task force that spearheaded work on the report was led by Dr. Huntington F. Willard, Director of the Institute for Genome Sciences & Policy at Duke University Medical Center. Dr. Willard began his presentation before the committee with a brief introduction regarding the project:
For those who are new to this, the issue at hand is to examine issues relevant to a possible United States large population study which we define in this report as an approach to learning more about relationships among genes, the environment, and common disease. And the goals of the studies, both ones ongoing and ones planned both in this country and elsewhere, are to determine mechanisms underlying common complex diseases to inform treatment and prevention strategies and ultimately, of course, to improve health in this country and elsewhere.
Following a half-day session discussing the fine details of the report, including suggested revisions to wording and substantial additions following review of public comments, the committee voted unanimously to approve the final report and send it to the Secretary of Health and Human Services on or around January 1, 2007. Transcripts and video webcasts of the committee’s 2-day meeting are available online. Link
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01.07.07
Posted in commentary, news links at 4:10 pm by Trevor
It’s Sunday afternoon, the roads are covered in a slick, slushy melting snow that doesn’t make for easy driving, and it seems like a good time to share links to some good science writing.
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01.06.07
Posted in cancer, environmental alterations, methylation, news links at 2:36 pm by Trevor
Discover Magazine has recognized several related discoveries in the field of epigenetics as the fifth top science story of 2006. The article details the research of Dr. Minoo Rassoulzadegan at the University of Nice:
Minoo Rassoulzadegan’s mice are unruly. In blatant violation of the laws of genetics—described a century ago by famed monk-scientist Gregor Mendel—they inherit their parents’ coloring without inheriting the genes that cause it.
Rassoulzadegan stumbled upon her rodent scofflaws after altering a gene in gray mice so that their feet and the tips of their tails turned white. The big surprise came in the next generation. Some offspring also had white spots, even though they didn’t inherit the mutated gene and so should have been all gray. When she looked for the cause, Rassoulzadegan found unusual amounts of RNA in the sperm of the mutant parents. She then injected RNA from the brains and sperm of those mice into ordinary gray mouse embryos. Many of the RNA-injected embryos likewise grew into white-tailed adults, regardless of the coloration written in their DNA.
The article also highlights the research of Dr. Vicki Chandler of the University of Arizona at Tucson and Dr. Michael Skinner of Washington State University. Link
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01.05.07
Posted in commentary at 9:35 am by Trevor
Some of our highly observant readers may have noticed that I’ve added a “currently reading” section to the sidebar showing the covers of — you guessed it — books that I’m currently reading. Right now those books happen to be Next by Michael Crichton and Stiff: The Curious Lives of Human Cadavers by Mary Roach. My wife ended up getting me Next for Christmas after I showed some slight interest in the book during a walk through Costco in November. She showed her exceptional brilliance by splurging for the CD audio version, so I can listen to it 25 minutes at a time on my way to and from work/school.
Our lab manager at work gave me a Barnes & Noble gift certificate for the holiday (thank you!), and after browsing through a number of different topic areas, I came across this weird book about human cadavers that had been recommended by a professor named Raymond Lee at WSU when I took his introductory biology course as a freshman. Stiff: The Curious Lives of Human Cadavers has been a very interesting read, but I haven’t gotten very far due to all of the holiday fanfare and lots of projects requiring my attention at work during the winter break. Spring semester starts up again on Monday, so I can only imagine that Stiff will take a back seat to textbook reading in the very near future.
With any luck, I’ll finish these books and offer my comments for those that may be interested.
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01.02.07
Posted in cancer, methylation, research articles at 10:51 am by Trevor
Nature Genetics has published a brief communication from Marth et. al on the epigenetic stem cell signature in cancer:
Embryonic stem cells rely on Polycomb group proteins to reversibly repress genes required for differentiation. We report that stem cell Polycomb group targets are up to 12-fold more likely to have cancer-specific promoter DNA hypermethylation than non-targets, supporting a stem cell origin of cancer in which reversible gene repression is replaced by permanent silencing, locking the cell into a perpetual state of self-renewal and thereby predisposing to subsequent malignant transformation.
Link
Update: There are great summaries and reactions to this letter available at Migrations and Pure Pedantry.
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Posted in environmental alterations, methylation, news links at 7:18 am by Trevor
The Focus article in the December issue of Environmental Health Perspective covers a term that should be very familiar to anyone following epigenetics: biomarker. While the term “biomarker” can be used to mean many different things, there are actually clear definitions for biomarkers that have been designated by scientists:
In 1987, the National Research Council convened a committee to investigate how biomarkers were being developed and used in the environmental health sciences. The conclusions were documented in a seminal paper published in the October 1987 issue of EHP, which described the four basic biomarker groupings still in use today: exposure biomarkers (which include markers of external exposure and of internal dose); biomarkers of biologically effective dose; effect biomarkers (which include markers of health impairment or recognized disease, early disease precursors, or peripheral events that predict health impairment); and susceptibility biomarkers (which include intrinsic genetic or other characteristics or preexisting diseases that result in an increase in internal dose, biologically effective dose, or target tissue response).
One of the common ways that epigenetic researchers aim to identify a biomarker for a particular disease or phenotype is by measuring DNA methylation on specific gene promoters of interest — whether it be hypermethylation (an increase in DNA methylation) or hypomethylation (a decrease in DNA methylation). However, as the mechanism for linking a change in DNA methylation with disease susceptibility are not understood, there seems to be no clearly defined method for identifying an epigenetic biomarker using DNA methylation. Some researchers use a method that measures the percentage of methylated CG sites within a particular loci, while others examine specific CG sites and determine if any specific CG site’s methylation status is changed. These differing approaches, while both potentially useful in identifying changes in methylation pattern, may be a source of conflicting results in epigenetics research and could lead to a loss of confidence in using DNA methylation as a means of identifying clinically important biomarkers for disease. Link
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01.01.07
Posted in commentary at 2:40 pm by Trevor
I would like to wish all the readers of Epigenetics News a happy and safe New Year. You can look forward to much more epigenetics news in 2007.
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