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The Classroom Within

Students at a handful of institutions across the US turn to their own DNA to learn about their genetic risk and ancestry. This year, students in Stanford University School of Medicine's Genetics 210 class — which the Mercury News says is open to medical students, graduate students, and undergraduates — learned about their risk for Achilles tendon injuries and dementia, but also about how closely related they are to Neandertals or whether they had a different father than they'd thought.

"I am teaching something they need to know," says Stuart Kim, a Stanford professor and co-founder of the course. "These are future scientists who need to understand the underlying concepts behind this exploding field.

Similar courses are offered by Mount Sinai School of Medicine in New York, the University of Miami, Harvard Medical School, and others.

Two students in the Stanford class, twin brothers, are using what they learned to change how they exercise, the Mercury News says. Andrew and Thomas Roos, both graduate students and triathletes, learned that they have a higher risk of Achilles tendon injuries. Because of that, they changed their workout routine.

"Trying to use my own genetic information as a learning tool — that sounded like something I wanted," Thomas says.

May 24, 2013

Microbiome Battleground

Bacteriophages found in the mucus of a variety of organisms appear to be helping to fend off bacterial invasions of the host, a new study in the Proceedings of the National Academy of Sciences reports. Researchers led by Forest Rohwer at San Diego State University examined how phages adhere to the mucus and infect bacteria there.

The phage-to-bacteria ratio is increased near mucosal surface — in organisms ranging from cnidarians to humans — and cell culture studies indicate that increased numbers of phage in the mucus protects the underlying epithelium from infection, the researchers write. Further, metagenomic analysis, they add, found a number of phage Ig-like protein domains that bind glycan residues of the mucin portion of mucus.

From this, Rohwer and his colleagues suggest a model in which the phage and mucodsal surface have coevolved to promote phage adherence.

This relationship, The Economist notes, "helps the phages, because their bacterial prey also accumulate in mucus, which is thus a rich hunting ground. And it helps the animal host, be that host sea anemone, fish or human being, by stopping any particular bacterial species running out of control."

May 24, 2013

The DNA Sell

Miinome, Minneapolis-based startup, envisions a marketplace in which companies could advertise to people based upon their DNA sequences. The pitch, as MIT's Technology Review puts it, could be: "Do you carry the genetic variants associated with lactose intolerance? Here, Lactaid has a coupon for you."

Founders Paul Saarinen and Scott Fahrenkrug discussed this DNA-based marketing at South by Southwest last year. "The marketplace is getting close to making this a reality,” Fahrenkrug said at the time, according to Social Media Today. "You’re leaving DNA everywhere, since you shed one million cells every day."

They are, Tech Review says, envisioning this company as an opt-in service.

However, interpreting DNA sequences remains a challenge — going from a certain sequence to a propensity for buying garden gnomes (or enjoying spicy food, as Tech Review says) isn't quite within range yet.

But James Ostheimer, another Miinome cofounder, says it's coming. He envisions people linking up their genetic information to their Twitter or Facebook accounts, which could then be mined to find such associations.

"Scientifically, that sounds like a stretch. But commercially it might not be," Tech Review adds.

May 24, 2013

This Week in Science

In this week's Science, investigators from Cancer Research UK report the discovery that a protein known as MTBP that has been associated with breast and ovarian cancers in humans is also tied to DNA replication in plants and other animals. They found that MTBP interacts with Treslin/TICRR, the human ortholog of a yeast protein with a known role in DNA replication. The team then found that RNA interference-mediated inhibition of MTBP also suppresses DNA replication, indicating that the protein may be a promising cancer target.

Also in Science, scientists from the Max Planck Institute for Psycholinguistics and Radboud University propose that genomic changes may be the result of cultural evolution, and not the other way around. They argue that while it is assumed that "biological changes must precede cultural changes," this may not be true. For example, lactase-persistence mutations did not trigger dairy farming, but rather spread as a result of dairy consumption. They point to the recognition of "culture-driven gene evolution in the origins of modern humans" as a "powerful reminder of how easy it is to confuse cause and effect in science."

Meanwhile, in Science Translational Medicine, an international group of researchers publish details of a genetic test that may help identify aggressive lung cancers. Noting that in cancer normally latent genes often become active, they analyzed the gene expression patterns of 300 early-stage lung tumors and compared them to patients' outcomes. They then selected 26 abnormally active genes that, together, may indicate aggressive lung cancer and could be used clinically for tumor stratification.

GenomeWeb Daily News has more on this study here.

May 24, 2013

New Stem Cell Paper May Contain Errors

The recent Cell paper showing that human skin cells can be reprogrammed into embryonic stem cells is under review for possibly containing improperly manipulated images, Retraction Watch reports.

A contributor to PubPeer, a post-publication peer discussion site, notes what could be a number of instances of image re-use. For example, the contributor points out some images that allegedly are cropped versions of other ones. The contributor also notes the short time frame between the submission of the paper and when it was accepted and when it was published.

Cell tells Retraction Watch that "[o]ur editorial team is currently assessing the allegations brought up in the PubPeer piece."

Lead author Shoukhrat Mitalipov from Oregon Health and Science University tells Nature that the paper contains honest errors and that he and his colleagues plan to discuss an erratum with Cell. He says that there may have been a rush to publish — he tells Nature that he wanted to present his results at a stem cell meeting next month.

"I personally made the cell[s] and, with Masahito [Tachibaba, the first author], I saw them grow into colonies," Mitalipov adds.

May 23, 2013

Use it Well

The European Society of Human Genetics has issued guidelines for the use of genome sequencing in healthcare. The recommendations, published in the European Journal of Human Genetics, focus on unsolicited findings and informed consent as well as on the interpretation of genetic findings.

The society recommends targeted sequencing and filtering of results to limit the analysis to specific genes and to genes whose variants can be readily interpreted. "It is preferable to use sequencing or analysis specifically targeted at a particular health problem to avoid unsolicited findings, or those that cannot yet be interpreted, which can cause considerable anxiety to patients and their families," says Martina Cornel, the chair of ESHG's professional and public policy committee, in a statement.

The recommendations also highlight the need for genetic education for doctors and lay people, as well as for collaborations to enable better interpretation of genetic data.

"Whole-genome sequencing has given the scientific community the ability to look at all of a person's genetic information. Given this new ability, we now need to interpret this information and counsel the family on the significance — both expected and unexpected," Debra Han, a genetic counselor in California, tells Medscape Medical News. "Overall, we need to remember, 'first, do no harm,'"

May 23, 2013 / 2 comments

Really Open Access

Open access articles are meant to be shared, of course, but according to a story published this week in The Scientist, a pair of journals have taken this idea a bit too far.

The journals Science Reuters, which is not affiliated with the Reuters news organization, and Insight Biomedical Science have plagiarized papers originally published in journals including PLOS One and the African Journal of Biochemistry Research, reports Kerry Grens.

Contacted by Grens for comment, a support liaison at Insight Knowledge, publisher of Insight Biomedical Research, says that the publisher "reproduced mentioned articles in the journal just to circulate it around the world. Because these papers are published on the basis of Open Access."

PLOS, however, isn't exactly thrilled with Insight's circulating of its papers and has contacted the company to express its displeasure, Grens writes.

She notes as well that a number of the researchers whose work was plagiarized had no idea of the two journals' existence. More than that, several members of the journals' editorial boards weren't aware of their existence either.

"Thank you for alerting me to the fact that a journal I was not aware of has my name on their website as a member of the editorial board,” said Rosemary Bass, senior lecturer at Northumbria University, upon being notified by The Scientist of her apparent position with Insight Biomedical Science. "I will be instructing them to remove my name."

May 23, 2013

Rotted in the Ground

Genomic analysis of Phytophthora infestans, which causes potato late blight, indicates that one particular strain contributed to the Great Famine in Ireland in the 1840s. An international team of researchers performed shotgun sequencing of 11 herbarium samples of infected potato and tomato leaves that were collected in continental Europe, Great Britain, Ireland, and North America between 1845 and 1896 that they then compared to 15 modern strains of P. infestans.

As the researchers report in a forthcoming eLife paper available at arXiv, their analysis implicated the HERB-1 genotype in the epidemic. That strain, they add, appears to have gone extinct, possibly due to increased resistance breeding in the plants. Previously, the US-1 strain had been thought to be behind the blight epidemic. The two strains, the researchers tell NPR, are closely related.

NPR adds that this work wasn't only an exercise in historical curiosity. "Potato blight is still a huge problem worldwide," Sophien Kamoun from the Sainsbury Laboratory in the UK tells NPR. "[It's] the third most important food crop in the world, and potato blight is the major constraint for growing potatoes."

May 23, 2013

This Week in Nature

In Nature this week, Umea University researchers report the draft assembly of the Norway spruce genome sequence, marking the first such milestone for any gymnosperm. Despite the size of its genome, the number of well-supported genes of the tree is similar to the much smaller genome of Arabidopsis thaliana, and they found no evidence of recent whole-genome duplication in the gymnosperm lineage. "Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism," the investigators write. They also discovered that the expression of small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants.

GenomeWeb Daily News has more on the spruce genome here.

Also in Nature, University of London investigators publish data contradicting the prevailing hypothesis that rare genetic variants account for much of the heritability of autoimmune disease. They looked for protein-coding regions of genes known to confer risk of autoimmune disorders in a large group of patients with specific autoimmune conditions, and discovered that rare coding-region variants at known loci have a negligible role in susceptibility to common autoimmune diseases.

May 23, 2013

Navigenics Founder Blasts Myriad's BRACAnalysis Pricing

On the heels of Angelina Jolie's revelation that she underwent a preventive double mastectomy, a Navigenics founder is taking aim at Myriad Genetics' price for its BRACAnalysis test.

In an op-ed piece appearing in the New York Times, David Agus also calls for legislative changes to bar healthcare companies from having monopolies on technologies that have life and death implications.

In addition to being one of the founders of consumer genetics testing firm Navigenics, which is now part of Life Technologies, Agus is a professor of medicine and engineering at the University of Southern California.

In his op-ed, Agus compares the nearly $4,000 charged by Myriad for BRACAnalysis to other tests and procedures — including the sequencing of a person's genes for about $1,000; 23andMe's $99 test, which can detect a variety of diseases such as Tay-Sachs, cystic fibrosis, and sickle cell; and DNA tests for human papillomavirus that cost less than $100 — and says that the reason for BRACAnalysis' high price is that there's nothing to stop Myriad from charging as it pleases.

While Myriad says that the average patient who has health insurance pays about $100 or less out of pocket for the BRCA test, Agus points out that, ultimately, consumers pay for the high cost of BRACAnalysis in the form of higher insurance premiums, co-payments, deductibles, and taxes.

"I'm all for innovation and the right to protect intellectual property, but when there is a clear monopoly and human lives are at stake, we need legislative action for rational and appropriate pricing," Agus argues. "We don’t make vaccines prohibitively expensive so only the rich can protect themselves. Nor should we let other preventive measures that can save thousands of lives be priced at levels far above what normal 'market conditions' would suggest."

He highlights an idea from Dana Goldman, a health economist at USC, to allow technologies to be licensed and made available to the masses. Under such a model, Agus says, an insurance company can pay for the IP around a diagnostic test, buy a license "on behalf of customers (you and me), and then make sure as many at-risk individuals as possible were tested."

Myriad's patents around the BRCA genes are the subject of a lawsuit filed in 2009 by the American Civil Liberties Union and others, as GenomeWeb Daily News reported at the time. The US Supreme Court last month heard oral arguments for the case and is expected to render a decision in late June.

May 22, 2013 / 2 comments

'Play Defense with the Facts'

Like other tests that delve into medical history, personal genome scans like those from 23andMe can reveal unexpected news. Slate tells the story of "Jackie" and her brother "Alex." (Slate changed their names.) Jackie, who works in a biomedical research lab, decided to get the 23andMe scan to learn about her disease risk, but she also found out that Alex, who also was tested, was her half-brother, and the man she thought was her father was not.

Previously, doctors could determine such instances of nonpaternity — the exact rate of which is unknown, but Slate says is thought to be about 2 percent or 3 percent for overall population — through blood type testing.

Such information can now, though, be gained through not only blood typing or more focused, specific paternity tests, but through other not-so-specific tests that people might be pursuing for other reasons.

23andMe, Slate notes, has two layers of consent to go through before it will show familial relationships. "This quirky system shows the difficulties that arise in managing genomic data," Slate adds. "It used to be that people chose to learn about themselves or not, and doctors helped determine which bits of information were appropriate for each of us to know. Now we're heading for a place where secrets flow more freely, where wise consumers must play defense with the facts."

May 22, 2013

Oversight

Leroy Hood, the head of the Institute for Systems Biology in Seattle, violated a conflict of interest rule when he reviewed a friend's California Institute for Regenerative Medicine grant application, the Nature News Blog reports. Hood and the applicant, Stanford University's Irv Weissman, own vacation property together.

CIRM disclosed the conflict in a letter to the California legislature leadership, the California Stem Cell Report blog adds. The letter notes that Hood had not previously been part of the agency's grant review process and was not aware of its conflict policy regarding personal relationships. CIRM adds that Hood "agreed that there was a conflict of interest that he had overlooked."

The grant, a $24 million proposal for a genomics data center and research projects, was not funded, the Nature News Blog adds.

This, CIRM spokesman Kevin McCormack tells the California Stem Cell Report blog was "clearly a case of a new reviewer making an innocent error."

May 22, 2013 / 1 comment

Federal Funds Boost Science, FASEB Argues

The Federation of American Societies for Experimental Biology, the advocacy group that has been working hard to press the US Congress to maintain funding at the National Institutes of Health and National Science Foundation, has issued a new fact-sheet to highlight its case that federally funded support biomedical research is necessary.

Improved health, new technology innovations and industries, and a stronger economy are among the benefits that spring from federally funded science, and in particular from the kinds of basic research that the private sector depends on but is unlikely to conduct on its own, FASEB says.

Because of the uncertain and risky nature of basic research, FASEB says, and because the time-frame for basic science projects can, in some cases, be measured in decades, the private sector is far less likely to take the risk of long-term science efforts like the Human Genome Project.

NIH and NSF also are the foundations of US science culture, FASEB argues. They support the training of new generations of researchers, fund the awards that graduate students and postdocs use to start their careers, and enable investigators to pursue high-risk, high-reward projects.

May 22, 2013