Sunday, October 12, 2008

The DNA Network

The DNA Network

Breast Cancer Gene Tests Explained [deCODE You]

Posted: 12 Oct 2008 03:59 PM CDT

On October 8th MSNBC published an article by Arthur Caplan, Ph.D. on genetic tests for breast cancer.
The following is a response by Jeff Gulcher, M.D., Ph.D, Chief Scientific Officer at deCODE Genetics.

Arthur Caplan stresses caution in the application of the new genetic risk tests for common diseases and I certainly agree that genetic testing should be applied with care.  However, he goes too far when he says that the new deCODE BreastCancer genetic risk test is only useful for women who have two or more close relatives with breast cancer, is not based on large enough studies to be accurate, and is not regulated.

There are two major types of breast cancer: the rare, early onset form that occurs in certain families and for the detection (for which the Myriad Genetic test is well suited), and the common form which accounts for 95 percent of breast cancer. The vast majority of women who develop breast cancer do not have the conventional risk factors of family history, pregnancy history or breast density. Unfortunately, many of these women were likely considered to be of average risk before their cancer was found. Therefore, they were not even offered screening with breast MRI which detects two to three times more cancer at an earlier stage than mammography alone, or preventive measures such as tamoxifen treatment which can cut down cancer rates by 40 to 50%.
To date, the healthcare system has not been as good as it would like to be at predicting which women are at higher risk of the common forms of breast cancer: But we at deCODE and others have invested years of research and tens of millions of dollars to find other factors that can complement the conventional factors. Our efforts have paid off, because there are 7 genetic markers, easily and accurately measured from a cheek swab, that define most of the genetic risk for the common forms of breast cancer.  The test defines risk from 0.4-fold to 4-fold compared to the general population risk (the average woman of European ancestry in the US has a lifetime risk of 12%).  Based on this test alone, 10 percent of women have risks ranging from 1.4- to 4-fold, and would account for about 17 percent of breast cancer cases.  Five percent of women are at more than 2-fold average risk, and the 1 percent are at 3-fold risk, so the risk is substantial for a significant portion of the population.

This risk is independent of family history and other conventional risk factors and therefore may identify some women as having higher risk even if breast cancer does not appear to be in their families. So Arthur Caplan is fundamentally incorrect in stating that only women with a family history of breast cancer would benefit from genetic testing.  That may be true for traditional genetic diseases like Huntington's disease and the rare highly familial form of early breast cancer addressed by the Myriad test, but the new tests for common diseases define risk beyond family history.

Each of the genetic markers in this risk test have been replicated in between 5 and 30 different populations in studies by deCODE genetics, the National Cancer Institute, and UK Cancer Research. These studies have been published in the most prestigious, peer-reviewed journals, including Nature Genetics and the New England Journal of Medicine. Altogether almost 100,000 patients and controls have been studied to define the marker risks.  We made this test available for physicians to order for their patients through our reference laboratory which is regulated under CLIA by the US Federal government.

However, it is important to emphasize that the test does not diagnose breast cancer: it is simply a means of assessing personal risk of the disease, much more analogous to an LDL-cholesterol test for assessing heart disease risk than traditional genetic tests for purely genetic rare disorders like that for Huntington's disease.  That is, women at higher risk based on deCODE Breast Cancer are not destined to develop breast cancer. They may have a 20 to 36 percent lifetime risk for developing cancer (versus baseline risk of 12%).  Women at lower risk are not immune from breast cancer and therefore would still be regularly screened with mammography.  Women at higher risk above a certain threshold may benefit from more intensive screening using breast MRI on top of mammography, as recommended by the American Cancer Society.  Also, certain medications such as tamoxifen which blocks the estrogen stimulation of breast cancer cells are approved by FDA to reduce breast cancer risk for women at higher risk.

In summary, this test may reclassify as higher risk some women who were previously considered to be of average risk, contributing to earlier detection and more focused prevention strategies.   In fact, this test together with family history could define as higher risk the roughly 20% of women who may account for 35 to 40% of future breast cancers.

Looking at the big picture, about 5 percent of the health care budget is used for diagnostics and most of the rest is for therapeutics. Much money has been invested in the development and use of new expensive therapies for women with advanced cancer. But individual women and our healthcare system may both benefit from the increased use of risk diagnostics to help to focus on women at higher risk and thus diagnose cancers earlier rather than later, saving lives, suffering, and money.

Anyone who wants to hear some real stories from real people about how genetic tests like this may improve healthcare can find them on this blog.

Jeff Gulcher MD PhD
Chief Scientific Officer
deCODE Genetics

Sunday Science Book Club [adaptivecomplexity's column]

Posted: 12 Oct 2008 03:30 PM CDT

Only A Theory: Evolution and the Battle for America's Soul

Kenneth R. Miller, Viking 2008

Ken Miller is not preaching to the choir. Although he has a day job as an active research biologist at Brown University, Miller has spent more than two decades on the front lines of the battle over evolution as a writer, lecturer, and expert witness in court. During these two decades of culture war, he has come to realize that, although the stakes are high in this fight, sometimes the best tactic is the non-martial one: don't treat the American public as pawns in a propaganda war.

Miller starts with the assumption that most people will be fairly open-minded about evolution and intelligent design. Before they make a firm judgment on the role of evolution in our public schools, people genuinely want to know what the scientific status of evolution is, and whether intelligent design is truly a scientific challenger. Many previous books debunking evolution have missed people like this. Such books typically fall into two categories: necessary but dense, technical works that provide, in detail, the scientific community's best response to the claims of intelligent design advocates, and scathing, hard-hitting attacks that fire up those who already accept evolution, but turn off readers who are trying hard to understand this issue without being strongly biased either way. Only A Theory is a genuine attempt at persuasion, and its approach is a result of Dr. Miller's years of practice speaking to audiences who want to give both sides a fair shot.

Don't be fooled, however, into thinking that Miller is trying to find some mutually satisfactory middle ground. For those who want to know whether evolution really is good science, his answer is unambiguous - evolution is one of the most successful and important theories we have in biology. And what about intelligent design? Its advocates have not even attempted to make this a real scientific discipline; evolution is the only scientific game in town.


1000 Posts! [ScienceRoll]

Posted: 12 Oct 2008 11:48 AM CDT

Just a short announcement. This is the 1000th post of Scienceroll. In 690 days’ time, it’s not that bad.

I hope you will follow me for at least another 1000 posts…

Source: Flickr by *schnauzer*


Gene Genie 38: Back in action! [ScienceRoll]

Posted: 12 Oct 2008 11:30 AM CDT

Gene Genie is the blog carnival of clinical genetics and personalized medicine. Enjoy the numerous posts and articles focusing on these interesting fields of medicine. We dedicate this carnival edition to genetic testing, SNP watch and DNA.


Many thanks to Ricardo Vidal for the logo!

Genetic Testing:

Grace Ibay at Genetics & Health analysed whether genetic testing would motivate us to healthier life.

Edward Farmer at DecodeYou posted about deCODE BreastCancer™, a genetic test to screen for risk of the most common forms of breast cancer. Edward Weinman introduced Jack Doughery, a deCODEme customer, to us.

The Paternity Blog also covered this important topic.

Lisa E. Lee at DNA Direct Talk had 3 great posts. Stool DNA testing; FDA Recommends Genetic Test Before Taking HIV/AIDS Drug; and some thoughts about about Down screening.

Retinoblastoma video:

Personalized Genetics and SNP:

Yann Klimentidis posted about genes that can predict hair color.

Hsien-Hsien Lei at Eye on DNA interviewed Terry Carmichael, VP of Marketing & Sales at Consumer Genetics.

The Spittoon blog presented a genetic link between obesity and colorectal cancer.

Blaine Bettinger at The Genetic Genealogist informed us when we can have the first $1,000 genome.

Barbara Duck at The Medical Quack wrote in details about the group of Scripps, Navigenics, Affymetrix and Microsoft that may change personalized medicine.

Gene-ography from ScienCentral:

DNA and clinical genetics:

The PHG Foundation let us know about a potential new treatment for cystic fibrosis.

Sandra Porter at Discovering Biology in a Digital World analysed why a mutation in Google-cofounder, Sergey Brin, would cause Parkinson’s disease.

According to Wired Science, Gene Therapy Restores Sight as two people who once were blind now can see.

Larry Moran at Sandwalk focused again on junk DNA and discussed the issue with an Adaptationist.

Walter Jessen at Highlight Health had a detailed and well-referenced article about the Cancer Genome Atlas and the molecular characterization of brain tumors.

History of genetics video:

If you want to host the 39th issue of Gene Genie, let me know (berci.mesko [at] Don't forget to submit your articles via the official page.

And also check the Gene Genie official blog out!


Of microbes and centralization [business|bytes|genes|molecules]

Posted: 11 Oct 2008 09:33 PM CDT

The National Institutes of Health this week awarded more than $14 million to informatics projects intended to support the Human Microbiome Project, which aims to take a genomic tally of microbes that live in the body and on the skin.


It’s good to see our friendly little symbiotes get some informatics attention. A big chunk of the money goes to a data analysis and coordination center. I am getting increasingly disillusioned by such centers. It’s one think to have centers to generate data, but data analysis and coordination? I think we need to think about distributed work more, and let centers come up organically. The analogy that comes to mind is git (distributed version control) and github (organic centralized repository which makes it easy to move code around).

Your thoughts?

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Quick Quiz: Are you competent to understand genomic tests? [Think Gene]

Posted: 10 Oct 2008 07:16 AM CDT

Solve this simple math question.

Statistics and disease risks are invented for this exercise!

1% of people will have Hubbub Disease by age 70. Up to 80% of people with Disease will get positive HEBOT mutation tests.  9.6% of people without Hubbub Disease will also get positive HEBOT mutation tests.  A patient had a positive HEBOT mutation test in genomic screening.  What is the probability that patient will have Hubbub Disease by age 70?

The correct answer is about 68.1%. If you got this, good job, you’re qualified, click here.

If you got a different answer or need an explanation, click here.

note: updated to be even more nonsensical to avoid confusion. Thanks, neandrothal.

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