Daily Archives: January 25, 2013

Public genome data is a significant risk to individuals, according to research led out by Yaniv Elrich, a geneticist at the Whitehead Institute for Biomedical Research.

The team that Elrich led was able to de-anonymise genome data using only public information and careful Internet searches. A little chillingly, individuals could be associated with patrilineal genetic characteristics, even if they werent in the databases. A family members presence in the database can be enough, if theyre related in the male line and carry the same surname.

Working with data published in two public genomic databases, Ysearch and SMGF, Elrich demonstrated the privacy risk by matching chromosome data with 50 individuals, in a paper published in Science (abstract here, full paper available free with registration).

Among the genome data recorded in the databases is a genetic marker called short tandem repeats (for which genetic science hasnt yet identified a specific purpose), which are passed down the male line.

As the paper notes, it had been assumed that listing surnames in the databases didnt place individual identity at risk, since surnames could match thousands of individuals. However, the genome data has become a genealogy tool as well, in databases such as YBase.

DNA sequencing pioneer Dr Craig Venter volunteered as a test subject in the research. With only the relevant DNA sequence, Dr Venters age, and the US state where he lives, Erlich was able to retrieve just two possible records one of which was Dr Venter.

With a known surname, the searches become even more accurate: Combining the recovered surname with additional demographic data can narrow down the identity of the sample originator to just a few individuals, Erlich states in the paper.

Surname inference from personal genomes puts the privacy of current de-identified public data sets at risk, it continues.

In five surname recovery cases, we fully identified the CEU* individuals and their entire families with very high probabilities data release, even of a few markers, from one person can spread through deep genealogical ties and lead to the identification of another person who might have no acquaintance with the person who released his genetic data.

*CEU refers to a particular genetic dataset: multigenerational families of northern and western European ancestry in Utah who had originally had their samples collected by CEPH (Centre dEtude du Polymorphisme Humain).

Read more from the original source:
Public genome databases can leak identity

Jan. 23, 2013 A retrovirus called HERV-H, which inserted itself into the human genome millions of years ago, may play an important role in pluripotent stem cells, according to a new study published in the journal Retrovirology by scientists at UMass Medical School. Pluripotent stem cells are capable of generating all tissue types, including blood cells, brain cells and heart cells. The discovery, which may help explain how these cells maintain a state of pluripotency and are able to differentiate into many types of cells, could have profound implications for therapies that would use pluripotent stem cells to treat a range of human diseases.

"What we've observed is that a group of endogenous retroviruses called HERV-H is extremely busy in human embryonic stem cells," said Jeremy Luban, MD, the David L. Freelander Memorial Professor in HIV/AIDS Research, professor of molecular medicine and lead author of the study. "In fact, HERV-H is one of the most abundantly expressed genes in pluripotent stem cells and it isn't found in any other cell types."

In the study, Dr. Luban and colleagues describe how RNA from the HERV-H sequence makes up as much as 2 percent of the total RNA found in pluripotent stem cells. The HERV-H sequence is controlled by the same factors that are used to reprogram skin cells into induced pluripotent stem (iPS) cells, a discovery that garnered the 2012 Nobel Prize in Physiology or Medicine. "In other words, HERV-H is a new marker for pluripotency in humans that has the potential to aid in the development of iPS cells and transform current stem cell technology," said Luban.

When a retrovirus infects a cell, it inserts its own genes into the chromosomal DNA of the host cell. As a result, the host cell treats the viral genome as part of its own DNA sequence and begins making the proteins required to assemble new copies of the virus. And because the retrovirus is now part of the host cell's genome, when the cell divides, the virus is inherited by all daughter cells.

In rare cases, it's believed that retroviruses can infect human sperm or egg cells. If this happens, and if the resulting embryo survives, the retrovirus can become a permanent part of the human genome, and be passed down from generation to generation. Scientists estimate that as much as 8 percent of the human genome may be composed of extinct retroviruses left over from infections that occurred millions of years ago. Yet these sequences of fossilized retrovirus were thought to have no discernible functional value.

"The human genome is filled with retrovirus DNA thought to be no more than fossilized junk," said Luban. "Increasingly, there are indications that these sequences might not be junk. They might play a role in gene expression after all."

An expert in HIV and other retroviruses, Luban and his colleagues were seeking to understand if there was a rationale behind where, in the expansive human genome, retroviruses inserted themselves. Knowing where along the chromosomal DNA retroviruses might attack could potentially lead to the development of drugs that protect against infection; better gene therapy treatments; or novel biomarkers that would predict where a retrovirus would insert itself in the genome, said Luban.

Turning these same techniques on the retrovirus sequences already in the human genome, they discovered a sequence, HERV-H, that appeared to be active. "The sequences weren't making proteins because they had been so disrupted over millions of years, but they were making these long, noncoding RNAs," said Luban.

Specifically, the HERV-H sequence was making abundant amounts of RNA in human embryonic stem cells -- and only stem cells. In total, there are more than 1,000 HERV-H retrovirus genomes scattered throughout the human genome. The Luban lab also found high levels of HERV-H RNA in some iPS cells. Other iPS cells, perhaps those lines that were not sufficiently reprogrammed to pluripotency, had lower levels of the HERV-H RNA, another indication that HERV-H may be an important marker for pluripotency.

Interestingly, the HERV-H genes that were expressed in human pluripotent stem cells are only found in the human and chimpanzee genomes, indicating that HERV-H infected a relatively recent ancestor to humans, said Luban.

Here is the original post:
Retrovirus in the human genome is active in pluripotent stem cells

Using publicly available information, researchers found they could figure out the identities of 50 individuals who had loaned their genes to science. Karen Hopkin reports

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Since the first human genome sequence was published, thousands of people have submitted their DNA for scientific analysis. They made these donations anonymouslyor so they thought. Now, using publicly available information, researchers found they could figure out the identities of 50 individuals who had loaned their genes to science. Their results, although not the names of the people, are in the journal Science. [Melissa Gymrek et al., Identifying Personal Genomes by Surname Inference]

Biomedical research depends on the participation of human subjects, and issues of privacy have always been a concern. When scientists share genomic data, they first strip away identifying information, like the individuals name and date of birth. But is that really enough?

Researchers looked at a specific set of markers in genomes whose sequences were in a public database. And they found that by matching up these markers with sequences that people had submitted to genealogy web sites, they could identify some of the genome donors relatives and, with a bit more sleuthing, come up with their actual names.

Of course, many people now post online accounts of whats on their minds or even on their menus. But even those who are relatively relaxed about their privacy might think twice about their genomes going public.

Karen Hopkin

[The above text is a transcript of this podcast.]

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Genome Donators Can Be Sleuthed Out