Daily Archives: January 18, 2013

Visualize Affymetrix Probes in Genome Browser

By: OmicsoftCorporation

Follow this link:
Visualize Affymetrix Probes in Genome Browser - Video

Scouring information available to anyone with an Internet connection, a team of genetic sleuths deduced the names of dozens of supposedly anonymous people who had their DNA analyzed for scientific and medical research.

The snooping feat, which took advantage of genealogy websites that let people compare their DNA to search for relatives, was in full compliance with federal privacy regulations. Experts said it underscored a stark reality about genetic privacy in the age of social media: Don't count on it.

"Nobody can promise privacy," said Mildred Cho, who heads up Stanford University's Center for Integration of Research on Genetics and Ethics, and wasn't involved with the study.

Whitehead Institute geneticist Yaniv Erlich and his team, who described their work Thursday in the journal Science, didn't provide a complete recipe that would help others ferret out the identities of research volunteers. Nor did they divulge the names of the people they were able to unmask.

Since the first draft of the human genome was published in 2000, scientists have scrutinized its 3 billion pairs of DNA letters to try to find variants that cause disease, to understand human physiology, and to unravel the evolutionary history of our species.

Toward that end, academic efforts like the 1000 Genomes Project post complete genomes online for public use. The idea is that providing free access to the data will allow scientists to compare DNA from many people and help them discover connections between genes and traits, eventually leading to the development of personalized, targeted treatments for a wide range of disorders.

Keeping genomic data private has been a concern all along. Worries that health insurers or employers might use information about genetic health risks to drop benefits or discriminate against workers inspired the 2008 Genetic Information Nondiscrimination Act, which provides protection against abuse. Last year, the Presidential Commission for the Study of Bioethical Issues recommended a variety of additional measures to further secure genetic data.

Potentially complicating these efforts are the legions of amateur geneticists who want to learn their risk for diseases or gain clues about their ancestry. As sequencing costs have dropped, these enthusiasts have sent vials of saliva, swabs of cheek cells, circles of dried blood or other types of DNA samples to private sequencing companies. Often, they post their tests results online, for the world to see.

Erlich has been interested in privacy since he worked as a professional hacker breaking into corporate networks as a "vulnerability researcher" for a computer security company to help support himself in college. He started planning the current research after hearing about a 15-year-old boy who had part of his genome sequenced in 2005 in order to find his biological father, a sperm donor.

The boy compared a pattern of repeating DNA letters from his Y chromosome to the corresponding patterns of men who had posted their genetic data on a genealogy website. Finding several men whose pattern matched his led him to his father's last name. He then used other clues to make contact.

Read the original:
If your genome is public, so are you, researchers find

Researchers found they could tie peoples identities to supposedly anonymous genetic data by cross-referencing it with information available online.

If you contribute your genome sequence anonymously to a scientific study, that data might still be linked back to you, according to a study published today in the journal Science. The researchers behind the study found they could deanonymize genomic data using only publicly available Internet information and some clever detective work.

The study points to rising issues concerning genetic privacy and the need for better legal protection against genetic discrimination, experts say, since such a technique could reveal a persons propensity to a particular disease. The work also shows that study participants need to be better educated about the risks of joining genetic research efforts.

Open-access data sets of human genomic information are an important resource for researchers trying to uncover the genetic basis of human disease. The 1000 Genomes Project, for example, is a publicly available catalog of variation in humans that researchers can use to identify mutations that cause disease risk in certain populations (see The Future of the Human Genome). Researchers use this kind of open database much more often than controlled access sources, the National Institutes of Health said in a response to todays findings that was also published in Science.

Our last intention is to push these resources behind some firewall, says Yaniv Erlich, a geneticist at the Whitehead Institute for Biomedical Research and senior author on todays study. We are in favor of public data sharing, but we need to think about how it could be misused and describe that correctly to people.

While the Genetic Information Nondiscrimination Act of 2008 offers people some protection against employers or health insurers discriminating against them based on their genetics, life insurers and disability insurers are not prevented from using such information in their decisions.

We have no comprehensive genetic privacy law, says Jeremy Gruber, a lawyer and president of the Council for Responsible Genetics. People need to be much better informed of the lack of privacy protections we have for genetic information, says Gruber.

In the long run, says Erlich, it is better for these potential breaches to be demonstrated by a friendly investigator rather than someone who really wants to exploit the data. That would really undermine the public trust, he says.

This isnt the first time privacy risks have been highlighted for public genome databases. Different groups have shown that with a second DNA sample, an individuals genetic information could be pulled out of what was thought to be anonymous pooled genomic data or gene activity databases. But Erlichs team used only knowledge of genetic markers and Internet detective work to identify nearly 50 people in public genomic data sets.

Erlich, a former computer security researcher, was once hired by banks and other businesses to test their computer systems. For the DNA sleuthing, Erlich and his team used free genealogical databases that link surnames with genetic markers, called short tandem repeats, on the Y chromosome. There is no known biological function for these repeats, but the length and number are commonly used in ancestry research because, like surnames, those patterns are typically passed from father to son.

More here:
Study Highlights the Risk of Handing Over Your Genome

See Inside

Unborn children will soon have their genes mapped. Without proper guidance for parents, the tests could prove calamitous

Image: Shannon Freshwater

In a few years you will be able to order a transcript of your entire genetic code for less than $1,000. Adults cannot do much to alter their biological lot, but what if parents could examine their unborn child's genome? Without proper guidance, they might decide to take drastic measureseven to end the pregnancybased on a misguided reading of the genetic tea leaves.

Two different university laboratories have developed tests that will reveal the entirety of a fetus's genetic code using just a blood sample from the mother (or that sample plus a drop of saliva from the father). Prenatal whole-genome sequencing will provide volumes of information beyond the currently available tests for genetic disorders such as Down's syndrome or Tay-Sachs diseaseassays that parents now use to decide how to respond to a pregnancy. The three billion units of code furnished in the new tests will also dwarf the relative trickle of information provided by consumer gene-testing services such as 23andMe, which currently look (postnatally) only at perhaps about one million locations in the genome.

Any woman who undergoes such a test will quickly learn that there is no such thing as a perfect baby. Parents will encounter hundreds and, as the science progresses, thousands of instances in which a particular variant of a gene may statistically suggest (but not guarantee) their child's future. Will the child-to-be one day suffer from melanoma or diabetes? What about obsessive-compulsive disorder? Moreover, clues will emerge in whole-genome scans about not only health prospects but personality as wellwhether she is likely to become an introvert or be able to carry a tune or star in high school sports. Whole-genome scans will tell parents a story about a particular future for their childa future that those parents may not be rooting for.

A compelling example of the angst-provoking uncertainties involved has been raised by bioethicist and Scientific American advisory board member Arthur Caplan. What if a test picks up the gene for albinism? Being an albino is not a disabling medical condition, but it can be a social burden. Might that be enough for some parents to consider ending the pregnancy?

Attitudes toward child rearing might also change, as parents wonder whether their kid is just being bad or whether that tantrum is an example of a dysfunctional serotonin transporter gene. Without careful planning, moreover, the new prenatal genetics might rob a child of the freedom to make decisions best left until adulthoodwhether or not to learn, for instance, if a mutation predicts the inevitability of Huntington's disease 20 years hence.

A customer of 23andMe can receive information via the Internet about a multifold greater risk of breast cancer or Alzheimer's disease without conferring with a genetics counselor. A similar laissez-faire approach to prenatal whole-genome testing, which might involve the decision to abort a pregnancy based on a personal and possibly inaccurate interpretation of dense and confusing genetic data, could portend tragedy.

Ultimately the U.S. Food and Drug Administration, genome-testing companies and professional societies such as the American Society of Human Genetics will need to develop a comprehensive policy on prenatal whole-genome testing. One option is to require that parents receive a filtered set of information from a genetics counselor. Bioethics scholars affiliated with the National Institutes of Health wrote an analysis last summer that calls on the medical community to develop a guide to the most relevant genomic data for future parents (life-threatening disease risk obviously tops the list). The report also recommends safeguarding the future child's right not to be told about later-in-life disease risk until adulthood.

Read the original post:
Fetal Genome Screening Could Prove Tragic