Sunday, 21 July 2013

Next Generation: Smoking Out Cancer

Researchers analyze smoke generated during surgical tumor removal to distinguish healthy and diseased tissues in real time.

By Sabrina Richards

The device: Often, the best way to rid patients of cancer is to cut out the tumor itself, but this strategy risks removing healthy tissue along with malignant. Surgeons hoping to extract tumors without slicing away healthy tissue send samples to pathologists for analysis—a process that can take more than half an hour and is often required several times during surgery. But now, according to a report published today (July 17) in Science Translational Medicine, researchers have successfully used mass spectrometry to distinguish between healthy and cancerous tissue in the operating room, giving surgeons on-the-spot information about the tissue they’re considering removing.

“I believe it’s the first time mass spectrometry has been used this way”—to give real-time information on biological samples in humans, said Zheng Ouyang, a biomedical engineer at Purdue University, who was not involved in the research.

The researchers, led by Zoltán Takáts, an analytical chemist at Imperial College London, created a device they dubbed the iKnife (for “intelligent knife”), which transmits the smoke generated by hot surgical tools to a mass spectrometer for near-instant analysis. After testing the device in mice in 2010, Takáts and his team were ready to make the jump to human patients.

What’s new: Although mass-spectrometry analysis of tumor samples is nothing new, and many researchers are working on devising mass-spec-based biomedical applications, the technique has been difficult to bring into operating rooms because biological samples need to be ionized before the mass spectrometer can read them. Surgeons also balked at the notion of extra equipment in the operating room, which they feared would interfere with the surgeries they’d honed, explained, who collaborated on the current study with biological chemist Jeremy Nicholson, also at Imperial College London.

But Takáts and first author Júlia Balog hit upon an intriguing idea: surgeons use knives that generate an electric current that singes the tissue they’re cutting—creating smoke filled with already ionized molecules that could be fed into a mass spectrometer. What if surgeons could use that smoke to analyze the composition of the tissue?

The iKnife, a small device that attaches to the end of a surgeon’s electrosurgical knife, “inhales” some of the smoke, and immediately sends it to be analyzed in a nearby mass spectrometer.  After compiling a database of more than 3,000 lipid profiles of tumor and healthy tissue samples, Balog and the team tested their method in the operating room. By comparing tissue spectra to their database and a pathologist’s expert diagnosis, the researchers found that their technique could consistently identify cancerous tissue among healthy samples: it had an impressively low rate of false positives—about 3.5 percent—and false negatives, at 2.3 percent. The researchers could even distinguish between different tumor types.

“The major achievement is getting the experiment done in a clinical or surgical setting,” said R. Graham Cooks, an analytical chemist at Purdue University who also aims to devise a mass spectrometry-based tool to aid surgeons but was not involved in the project.

The importance: The new device could help streamline the surgical process by giving surgeons immediate information about the tissue they’re dealing with, noted Ouyang. Additionally, because the iKnife-coupled mass spectrometry technique can analyze samples without previous modification of tissue, it avoids risks inherent in other visualization strategies, like the side effects that can come with injected fluorescent dyes, Takáts noted.

The work is also part of “a paradigm change in histology,” he explained. In the future, Takáts predicts that tissues will be defined by their metabolomic fingerprint instead of characteristics measured by the human eye.

Needs improvement: As promising as the technique is, Cooks cautioned that it’s not yet ready to replace a pathologist. In addition to giving more detailed information about a particular tumor, a pathologist can often make a prognosis, which mass-spec-based bioanalysis cannot yet do.  Such techniques “need to go from diagnosis to prognosis,” he explained.

In the future, adding different molecules to their profiles will allow Takáts’s team to make finer distinctions between tissue types, said Gary Siuzdak, a chemist at The Scripps Research Institute who focuses on metabolomics and did not participate in the study. Additionally, Ouyang predicted that mass spectrometers will be miniaturized to look “like any ordinary equipment you see in the surgical room,” rather than a research lab’s behemoth.

In the meantime, the researchers are already planning studies to examine how their technique affects surgical outcomes, like total time in surgery, the tumor recurrence rate, and the amount of healthy tissue that is spared.

J. Balog et al., “Intraoperative tissue identification using rapid evaporative ionization mass spectrometry,” Science Translational Medicine, 5:194ra93, 2013.

Saturday, 19 January 2013

Anonymity Under Threat

Scientists uncover the identities of anonymous DNA donors using freely available web searches.

By Ruth Williams from The Scientist

A person donating their DNA sequence anonymously for research purposes may in fact be identified by a few simple web searches, according to a paper published today (January 17) in Science. But rather than trying to protect anonymity, some scientists believe efforts should instead be focused on educating DNA donors and on legislating against the misuse of sequence data.

“The paper is a nice example of how simple it is to re-identify de-identified samples and that the reliance on de-identification as the mechanism of ensuring privacy and avoiding misuse is one that is not viable,” said Nita Farahany, a professor of law and research at Duke University in Durham, North Carolina, who was not involved in the study.

Participants in public sequencing projects are told that their anonymity is not 100 percent guaranteed, but the risk of a person’s identity being discovered was perceived to be miniscule, explained Yaniv Erlich, a computational geneticist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, who led the study. However, a 2005 Washington Post article about a teenage boy who tracked-down his biological sperm-donor father via online genealogy searches suggested the risk may be significant. According to the article, the boy had submitted a sample of his own DNA to a genealogy service that used repeat sequences from his Y-chromosome to search their sequence databases for related males. Although the search did not uncover his father directly, it did find weak matches to two men who importantly shared a surname. Along with his father’s place and date of birth—information released to the mother—the likely surname enabled the boy to find and contact his father.

“We heard about this story and we thought, wow, this could be a threat for [the privacy of] personal genomes,” said Erlich.

To see how easy it might be to discover the identity of DNA donors, his team built software for retrieving Y-chromosome repeat information from whole genome sequences. With those repeat sequences, they could perform genealogy searches. “We thought, cool, let’s try it on the genome of Craig Venter,” said Erlich. “And it worked!”

They searched the available genealogical sequence database at and, sure enough, the strongest match by far was to someone named Venter from Lincolnshire in England. The surname, together with Craig Venter’s known age and state of residence—two pieces of information commonly accompanying anonymous genome sequences—were then used to search the online public record, The search came up with just two possible people, and one was Craig Venter.

Taking the experiment further, Erlich and his colleagues used their software to retrieve Y chromosome information from the anonymous DNA sequences of male participants in a public sequencing project and showed that, using the same methods, they could accurately determine the identities of multiple individuals. They could even identify anonymous women donors related to the males, by virtue of family tree data accompanying the genome sequences and the ability to search online public records. The important point, said Erlich, is that “everything was publically available. We didn’t break into any database. We didn’t need any special passwords.”

Although, the authors find the probability of discovering someone’s identity is still low, the study raises the question of whether more should be done to protect donors’ anonymity. But George Church, professor of genetics at Harvard Medical School, who was not involved in the study, thinks there is little point. “You can keep trying to adjust the protocols” - information about participants’ ages might be kept private, for example-“but that’s kind of putting a bandage on it.... It’s only going to get easier to re-identify [anonymous sequences], not harder,” he said. Although the Genetic Information Nondiscrimination Act in the United States prohibits employers and health insurance companies from discriminating on the basis of genetic information, “there is still a fear of the unknown,” said Brad Malin, a professor of biomedical informatics and computer science at Vanderbilt University in Nashville, Tennessee, who is worried that the study will frighten away members of the public from participating in genome sequencing projects. “It is important to highlight these problems, but at the same time, when you highlight them it is very difficult to temper the result,” he said.

Farahany agreed. “What we need to do is better educate people about the facts,” she said. Furthermore, she added, efforts might be better spent on regulating the use of sequence data, rather than ensuring anonymity. “That’s where we should focus our legal and ethical analyses,” she said - “not on trying to prevent the flow of information, but on trying to prevent the misuse of information.”

 M. Gymrek et al., “Identifying Personal Genomes by Surname Inference,” Science, 339: 321-324, 2013.