Anonymity not guaranteed: Identity of personal genomic DNA revealed by Web search

A few decades ago, people might have looked at you funny if you asked them to publicly share the intimate details of their personal lives—where they live, their age, what they had for dinner a few nights ago, photos of their children and more. However, between Facebook, Google, LinkedIn and the rest, it’s almost a trivial matter to find out people’s private details today. And soon, a new study suggests, your entire genome could get added to that list of personal information so easily found online—whether you want it or not.

“The issue is the current status of privacy,” says Yaniv Erlich, a geneticist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, who led the research. “We need [sponsors of genomic studies] to be respectful to participants, to tell them the truth: that someone can identify you.”

To lift the mask off of genomic data that had been seemingly stripped of identifying information, Erlich and his team focused on the Y-chromosome, typically passed along with surnames from fathers to sons. Genetic ancestry services such as FamilyTreeDNA and Ancestry.com allow customers to trace their paternal genealogy through an analysis of a series of genetic markers known as short tandem repeats on the Y-chromosome (Y-STRs). As a free service, many of these companies also share their large databases of Y-STRs, with accompanying surnames and built-in search engines, to the public. Since demographic information, including year of birth and state of residency, are often included in published scientific reports, and can also be linked to surname records on sites such as such as PeopleFinders.com or USApeople-search.com, it proved relatively straightforward for Erlich and his colleagues to narrow the identity of DNA contributors down to small lists of likely suspects.

As an example, they tested their procedure on 10 ‘anonymous’ personal genomes, taken from the 1000Genomes project and the European Nucleotide Archive. They recovered surnames for half of these men with a high probability of accuracy. After an internet search, they identified not only the individuals to whom the genomes belonged, but their entire family trees. The findings were published today in Science.

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An ingestible pill-sized device offers a 3D view of the esophagus

Almost everyone gets occasional heartburn, that painful sensation in the chest or throat caused by the reflux of stomach acid back into the esophagus. When it happens too frequently, however, such as in patients with gastroesophageal reflux disease, it can result in a condition known as Barrett’s esophagus. An estimated 3 million Americans suffer from this disorder, where the tissue that lines the esophagus accumulates abnormal changes over time, increasing the risk for esophageal cancer.

Barrett’s esophagus often goes undiagnosed because it causes minor or nonexistent symptoms, and because of the procedure required to identify it. Currently, doctors must sedate a patient, insert a long, flexible camera known as an endoscope down the esophagus to look for abnormal tissue, and then cut off a small piece for analysis in a laboratory. The procedure is invasive, expensive and uncomfortable.

Now, researchers at the Massachusetts General Hospital (MGH) in Boston have invented a tethered, pill-sized endoscope that that allows doctors to construct an image of a person’s esophagus in microscopic detail within a few minutes—and all without anesthesia, intense training or causing pain. Their work was published today in Nature Medicine.

“A lot of people have reflux but don’t feel the pain of heartburn,” says MGH pathologist Gary Tearney, who led the study. These patients are at high risk for developing cancer, because they usually have no reason to get their esophagus inspected. “[Our device] really opens up screening to many more people,” Tearney says.

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Better labeling aimed to spur development of abuse-resistant painkillers

Prescription opioid pain relievers such as codeine and oxycodone are among the most widely abused drugs in the US. The country’s Centers for Disease Control and Prevention (CDC) estimated that in 2010 around 12 million Americans aged 12 or older used this class of drugs for nonmedical purposes, at a cost of up to $72.5 billion in direct healthcare expenses. Worse, the CDC estimates that around 15,000 fatalities occur each year due to overdoses from these meds, a number comparable to the total number of annual murders nationwide.

In response to this growing public health crisis, the US Food and Drug Administration (FDA) yesterday released a draft guidance detailing how the agency plans to evaluate new opioid pain relievers with special formulations designed to reduce abuse. Importantly, it gave pharmaceutical companies labeling guidelines.

“Our goal here is to encourage the development of abuse deterrent formulations that work to reduce abuse in the real world, in the community. The intent of this guidance is to incentivize that, to encourage the development of that science,” said Douglas Throckmorton, deputy director of the FDA’s Center for Drug Evaluation and Research, in a conference call to reporters.

Drugs with abuse-deterrent properties have already been developed and sold on the market. For example, Endo Pharmaceuticals of Chadds Ford, Pennsylvania, sells a tablet called Opana ER that releases its active painkilling ingredient slowly over time and is harder to abuse by crushing or snorting. But Endo is not allowed to include any permutation of the term “abuse-deterrent” on the drug’s label, a major issue for a company that’s trying to differentiate its product from the pharmacopeia of other painkillers. Last year, Endo went so far as to sue the FDA to prevent a generic version of their drug’s older, non-abuse-deterrent formulation from entering the market. The generic was ultimately approved, but the timing and language of yesterday’s draft guidance should help mitigate some of the concerns raised by Endo going forward.

Despite the added clarity for drugmakers, questions remain for the health care industry as to whether doctors will ultimately prescribe the abuse-resistant painkillers, not to mention whether health insurers and patients will be willing to pay for their higher premiums next to the cheaper generic—and tamperable—alternatives.

Nathaniel Katz, president of Analgesic Solutions, a Massachusetts-based consulting firm, believes there are obvious incentives. “[Doctors] want to always prescribe the safer product,” he says. For health insurers, “from a pure financial perspective, prescription opioid abuse is a huge problem. They will increasingly recognize that, and recognize there’s a financial return on investment.”

That just leaves patients. Many people seeking pain relief, especially those who do not identify as at-risk for abuse issues, will probably not accept higher co-pays when much cheaper but abusable options are still available. Katz sees a simple solution to that problem: “Eventually the idea is perhaps that the option will no longer be available to them,” he says. As yet, however, the FDA hasn’t taken that option off the table.

Image: Ondřej Karlík, Wikimedia Commons

Ancient medicinal tablets had Cold-Eeze-like ingredients

Two thousand years ago, people could not go to the nearest pharmacy for Cold-Eeze, but they appear to have concocted their very own zinc remedy, according to a new analysis of ancient remnants.

Scientists have characterized the mineralogical and chemical ingredients of medicine from a 2,200-year-old shipwreck, revealing new insights into the pharmaceutical practices of the ancient world. Their work was published today in the Proceedings of the National Academies of Sciences.

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New techniques could improve reprogrammed-immune-cell treatment of HIV and cancer

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Recent experiments exploring the use of patients’ own genetically reprogrammed immune cells toward the treatment of chronic diseases such as HIV and cancer have had encouraging and sometimes high-profile results. Yet, these studies have only been conducted in a limited number of individuals, and outcomes have been inconsistent, ranging from complete remission to complete inefficacy.

Now, two teams of researchers have demonstrated a method of using patients’ cells to create long-lived immune cells that target specific HIV and cancer antigens, and appear to resist degradation over time. Their work was published today in two separate papers in Cell Stem Cell.

“Our method has realized the functional rejuvenation and unlimited production of mature cytotoxic T cells with desired antigen-specificity for the first time in vitro,” says Shin Kaneko a stem cell biologist at Kyoto University in Japan and a co-author of the HIV-related study.

Difficulties in previous attempts to extract and reengineer T cells from patients are thought to be due in part to a phenomenon known as ‘cellular senescence’, a type of aging process. Naïve, quiescent T cells can survive for decades in the body. But active T cells, particularly those expanded outside the body in the laboratory, can gradually lose the ability to proliferate and be effective. This can lead to insufficient numbers of active immune cells to combat disease.

“Replicative senescence is likely to be a major issue for adoptive cell therapy,” says Carl June, an immunologist at the University of Pennsylvania’s Perelman School of Medicine in Philadelphia. “[These papers] address this issue and are exciting demonstrations of the progress in cell and developmental biology.”

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