Public Health

The number of gene-expression data sets available in public databases has climbed rapidly over the past decade, allowing researchers to spot disease trends without doing time-intensive experiments in the laboratory. The “big data” deluge promises to accelerate the process of understanding disease while driving down the costs of developing new therapies.

To underscore the wealth of opportunities for scientists who can mine these continuously growing databases in innovative ways, Stanford Medicine and Oxford University are sponsoring a three-day conference next month on big data’s role in biomedicine. The event will be held May 22-24 at the School of Medicine’s Li Ka Shing Center for Learning & Knowledge and will feature keynote speeches from Anne Wojcicki, CEO and co-founder of the consumer-genomics company 23andMe, and David Ewing Duncan, author of Experimental Man. In addition, attendees will hear from more than two dozen speakers representing large information-technology corporations, startups, venture-capital firms and academia.

In a release, Stanford systems-medicine chief Atul Butte, MD, PhD, who is the conference’s scientific program committee chair, commented on the motivation for hosting the conference and what participants will learn at the event:

We’re bringing together people from academia, industry, government and foundations who want to learn more about how big data can drive innovation for a healthier world… We expect that attendees will walk away from this with a strong understanding of the latest tools and technologies available for studying and using big data in biomedicine, of where the unmet medical needs are and how they can be addressed with these approaches, and of what the tractable next steps are that they can take to become innovators.

Additional program information and registration details are available on the conference website.

Previously: Mining data from patients’ charts to identify harmful drug reactions, Strength in numbers: Harnessing public gene data to answer a diverse range of research questions, Mining medical discoveries from a mountain of ones and zeroes, The data deluge: A report from Stanford Medicine magazine, Stanford’s Atul Butte discusses outsourcing research online at TEDMED and Health-care experts discuss opportunities and challenges of mining ‘big data’ in health care
Photo by Dwight Eschliman

Recognizing the value of mobile devices in conducting public health research, the Centers for Disease Control and Prevention has launched a project to examine the feasibility of collecting data using smartphone-based surveys and text messages. A recent post on Mobihealthnews offers more details:

The groups aim to first send the surveys to US residents aged 18 to 65 nationwide with questions related to smoking habits and alcohol consumption. Following the survey, the smartphone users will be asked to participate via text message in the feasibility study, which includes a survey immediately following the first and then another one a week later. The texts will include links to the survey on a mobile-friendly site.

Some of those who participate in the initial outreach that are non-smartphone users will be asked to participate in another study, the text message pilot, which will conduct the surveys one question at a time via text.

The study aims to evaluate, among other things, the response bias of data collected from the smartphone users on the mobile site to those responses collected via text.

Previously: Survey shows more than a quarter of American adults are mobile health users and CDC binge-drinking study demonstrates cell phones’ value in research
Photo by Jhaymesisviphotography

Frustrated by inconclusive tests, strange symptoms and a lack of answers from their health-care providers, some patients have turned to the online community for answers about perplexing illnesses. And a new web-based tool, called CrowdMed, aims to make it even easier to diagnose medical mysteries. The New Scientist reports: 

Anyone can join CrowdMed and analyze cases, regardless of their background or training. Participants are given points that they can then use to bet on the correct diagnosis from lists of suggestions. This creates a prediction market, with diagnoses falling and rising in value based on their popularity, like stocks in a stock market. Algorithms then calculate the probability that each diagnosis will be correct.

In 20 initial test cases, around 700 participants identified each of the mystery diseases as one of their top three suggestions.

…

The goal is to help people who come down with any of around 7000 “rare diseases” as defined by health agencies in Europe and the US. In Europe alone, 30 million people have a rare disease, 40 per cent of whom either go undiagnosed or are misdiagnosed at some point.

As the popularity of using the Internet to answer health questions grows, it will be interesting to see how services such as CrowdMed, and search engines like FindZebra, even further redefine the doctor-patient relationship.

Previously: The importance of curation and communities when crowdsourcing clinical questions, New search engine designed to help physicians and the public in diagnosing rare diseases, Report shows 35 percent of U.S. adults turn to the Internet to diagnose a medical condition, Dr. Google: Threat or menace? and Patient self-diagnosis: From the browser to the exam room
Photo by Ryan Brooks

As you likely heard, the Supreme Court heard oral arguments yesterday in a case that’s of interest to many biomedical researchers. That case, widely known as the “gene patenting case,” has a single question presented: “Are human genes patentable?” It may irk some researchers and clinicians that the answer isn’t a straightforward “no.” But the issues are surprisingly complex: How does one define a “gene,” and a “human” vs. a “synthetic” one at that? What about primers, probes, and cDNA? And what does one mean by “patentable”?

First, a brief lay of the legal landscape. Typically, an inventor cannot patent a “product of nature.” But ever since a 1911 appellate decision (.pdf), a natural product can be patented if it’s “isolated and purified” from its surrounding environment. Thus, the chemical compound adrenaline was itself patented because it was isolated and purified from adrenal glands. Shockingly, the Supreme Court has never directly reviewed this isolated and purified doctrine, even after 102 years.

This all raises the question of whether human genes should be allowed to be patented as a matter of policy, if not law.

And so, on this basis, isolated human genes have long been patented. In 1994, researchers at the University of Utah finally located and sequenced (.pdf) the BRCA-1 and BRCA-2 genes, variants of which put women at astonishingly high risk for early onset breast and ovarian cancer. Those researchers obtained patents on both the isolated sequences and cDNA variants of those, and assigned them to Myriad Genetics, a diagnostic testing company.

Arguments at the Supreme Court - and the justices themselves – grappled with the distinctions between isolated genomic DNA and cDNA. Lower court opinions had made a significant case out of the fact that because the covalent bonds of isolated genomic DNA were cleaved from the surrounding chromosome, an isolated gene was, in fact, a new chemical entity. Similarly, several justices suggested that because cDNA was not found in nature, it too, was patentable – even if it was simply the product of reverse transcribing an mRNA sequence. (For a further breakdown on the oral arguments themselves, see Stanford’s Center for Law and the Biosciences’ oral argument recap.)

But it seems that at least five justices – and thus, a majority – believe that patents on isolated DNA are not eligible for patent protection. They don’t seem to buy the argument that simple covalent cleavage renders something a new chemical entity. The Court and lawyers deployed various analogies to make this point: gold from ore, a piece of wood from a tree, a liver from a patient, etc. It seems less clear, however, whether a majority will similarly rule cDNA to be patent ineligible.

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Chronic sleep problems affect an estimated 70 million Americans, according to the latest data from the Centers for Disease Control and Prevention. Among those who have trouble sleeping soundly is KQED reporter Scott Shafer, so he recently spent the night at the Stanford Sleep Medicine Center to better understand what was keeping him from resting easy.

Shafer describes his experience staying overnight at the clinic and analyzing his sleep results with Stanford’s Rafael Pelayo, MD, in a new segment on the California Report. In describing what it’s like to snooze at a sleep clinic, he says:

It was time to get ready for bed, no small thing at the Sleep Medicine Center. I went to my room — called simply Sleep 18. Technician Robert Tognoli hooked me up with 28 wires in all — attached to my legs, my head, my abdomen – all of it designed to sense and measure my breathing, eye motions, blood oxygen, snoring, leg and chest movements.

Tognoli told me the wires would monitor the phases of my sleep, when I dreamed and if there were any “interruptions to my sleep architecture,” as shown by my brain waves. Then he stuck all the wires into a box that he hung around my neck. Next, he turned on a machine that blew air to dry the glue holding the wires attached to my head. Finally, I was ready to hit the sack. How did I sleep, and what story did all those wires tell?

Listen to the full segment to find out what Shafer learned from spending a night at the clinic and why it can be tricky to accurately evaluate one’s quality of sleep without having a lot of data.

Previously: Stanford center launches Huffington Post blog on the “very mysterious process” of sleep, Study: Parents may not be as sleep-deprived as they think, Exploring the effect of sleep loss on health and How lack of sleep affects the brain and may increase appetite, weight gain
Photo in featured entry box by Juan Antonio Flores Segal

Whether it’s at a party or in the grocery store aisle, doctors have always been faced with the challenge of patients asking them medical questions outside of the office setting. But now that more physicians are using social media, the question of how to handle medical inquiries in the digital space is becoming an increasing concern.

In this TEDxNijmegen 2013 video, Bertalan Mesko, MD, PhD, discusses using online communication tools to create medical social networks and the challenges in harnessing these communities to crowdsource clinical questions. Pointing to the example of comedian Conan O’Brien jokingly asking his Twitter followers for dermatology advice, Mesko notes that social media can yield misleading medical information and warns, “Crowdsourcing in medicine only works if you know your communities.” Watch Mesko’s full talk to learn more about how he effectively uses online networks to share trusted medical information and why curation is imperative when it comes to crowdsourcing health-care questions.

Via @StanfordMedX
Previously: How, exactly, can Twitter benefit physicians?, How can physicians manage their online persona? KevinMD offers guidance, 33Charts’ Bryan Vartabedian talks about physician blogging, A guide to the social web for physicians and Physician 2.0: Do doctors risk becoming irrelevant if they ignore social media?

Health-care providers know there’s a wealth of valuable information trapped in the hand-written notes on patients’ charts. But the challenge of collecting and interpreting the data on a large scale remains to be solved. Now researchers at Stanford have taken a step forward in mining patient-based information by using existing language-analysis methods to identify drug side effects in advance of the Food and Drug Administration issuing official alerts.

My colleague writes in a release:

Although their application is new, their information-gathering methods are based on well-established text processing techniques. It’s also simpler and faster than current strategies used in the same arena, said [engineering research associate Paea LePendu, PhD, the lead author of the paper]. Content is first grouped via “ontologies,” which are information graphs organized by associative relationships instead of a rigid linear structure. For example, melanoma is a kind of skin cancer, and so is Kaposi’s sarcoma; by knowing “skin cancer” encompasses both kinds of cancer, the search process picks up this medical knowledge. The system also de-identifies patient information in the process, so sensitive data, such as names and addresses, doesn’t get revealed. With these methods, LePendu said, the technique allows them to process 11 million clinical notes in about seven hours on hardware no different from a laptop computer — a pace that other programs can’t match.

The information is also current: It’s generated from what is observed and recorded in the hospital or doctor’s office. That’s an advantage over the FDA’s AERS reports, which rely on patients and health providers to make the additional effort to report adverse events.

The researchers developed the computerized method to sift through the contents of clinical notes in electronic medical records and used it to examine how often specific drugs and diseases were mentioned in roughly 10 million notes for about 1.8 million patients over 15 years. The goal was to organize these notes into a data-mining substrate they refer to as a patient-feature matrix. “Everyone is excited about the prospect of ‘big data’ mining on electronic health record data,” Shah said. “We demonstrate it in practice.”

Previously: Researchers mine Internet search data to identify unreported side effects of drugs
Photo by The National Guard

New findings analyzing Internet search data for major mental illnesses shows that seasonal weather changes may have a larger impact on such health conditions than previously believed.

In the study (.pdf), researchers used Google’s public database of queries to identify and monitor users’ searches for mental-health disorders, including anxiety, eating disorders, schizophrenia, ADHD, bipolar and obsessive compulsive disorder (OCD), in the United States and Australia from 2006 through 2010. According to a release:

The research showed eating disorder searches were down 37 percent in summers versus winters in the U.S., and 42 percent in summers in Australia. Schizophrenia searches decreased 37 percent during U.S. summers and by 36 percent in Australia.

Bipolar searches were down 16 percent during U.S. summers and 17 percent during Australian summers; ADHD searches decreased by 28 percent in the U.S. and 31 percent in Australia during summertime. OCD searches were down 18 percent and 15 percent, and bipolar searches decreased by 18 percent and 16 percent, in the U.S. and Australia respectively.

Searches for suicide declined 24 and 29 percent during U.S. and Australian summers and anxiety searches had the smallest seasonal change – down 7 percent during U.S. summers and 15 percent during Australian summers.

While some conditions, such as seasonal affective disorder, are known to be associated with seasonal weather patterns, the connections between seasons and a number of major disorders were surprising. “We didn’t expect to find similar winter peaks and summer troughs for queries involving every specific mental illness or problem we studied, however, the results consistently showed seasonal effects across all conditions – even after adjusting for media trends,” said James Niels Rosenquist, MD, PhD, a psychiatrist at Massachusetts General Hospital.

The work appears in the latest issue of American Journal of Preventive Medicine.

Previously: Sweating the small stuff may harm your mental health and Ask Stanford Med: David Spiegel answers your questions on holiday stress and depression
Via The Atlantic
Photo by Tom Hilton

I admit to a certain sense of mounting dread about the news of the new H7N9 influenza virus arising in China. And the never-ending supply of Tweets (alarmist and otherwise) are not helping one little bit. That’s why I appreciated this article posted today by Wired reporter and author Maryn McKenna (she’s sometimes referred to as Scary Disease Girl, due to her focus on global health and infectious diseases).

McKenna breaks the current news down into a quick primer, based on her past experiences reporting on that ‘other bird flu’ H5 N1 (remember that one?) ten years ago. She follows with a caution to beware– or at least to be aware– of the sources of news of this quickly moving story, and an explanation of some peculiarities in Chinese media that may hamper or distort reporting. She also draws a parallel between what’s happening now with H7N9 and H5N1– pointing out that the latter never erupted in humans as it was first feared. Says McKenna:

And H7N9 might not, as well. It is far too soon to say, despite the rapidly escalating case count and the reports — which came in while I was writing this — of a possible animal reservoir in pigeons and a possible human-to-human case. I have been writing about flu and possible pandemics since 1997 — for what it’s worth, I wrote the first story in the US in 1997 about that first H5N1 case in Hong Kong — and so at this early point, what I most want to say is this: We all love scary diseases. (If you didn’t, you wouldn’t be reading this blog.) But there is a fog of war in disease emergencies, just as there is in military ones, and it is very easy to get lost in it.

It will take a while for this story to become more clear. Anticipating that, I want to suggest some things to think about as you follow the news.

She ends with this great advice:

[...] Don’t assume that everyone who is loading information onto their blogs or pushing it onto Twitter is doing it in a sharing spirit of helpfulness. There are people — you can see this already — who are opportunistically using this to feed their egos, angle for jobs, or generally to stir up trouble. More than ever, it’s important to be skeptical about the sources of the information you consume.

McKenna makes it easier for us to practice what she preaches by listing several reputable news sources–traditional, web-based and, even on, Twitter– that should be reliable sources of information. You can follow McKenna on Twitter at @marynmck.

Previously: “Superbug” author discusses dangers, history and treatment of MRSA and Image of the week: What H5N1 looks like

While debating what to order for lunch last week, my brother explained that he was participating in a Biggest Loser-style contest with a group of co-workers and the winner received a sizable cash prize. As he described the competition, I took note of how he focused on strategies for beating other contestants, his weight-loss progress and odds at winning, rather than feeling deprived of his favorite foods or complaining about having to exercise more. The experience seemed to have given him a positive outlook on dieting and even motivated him to keep the weight off. When I mentioned that he only had to “be good” for a few more months and could go back to indulging afterwards, he said “No, I wouldn’t want to ruin my hard work.”

So I was interested to read about new research showing that weight-loss programs involving group competitions for financial prizes motivate people to shed more pounds than those offering individual rewards. Reuters reports:

Researchers compared two incentive scenarios. Under one, employees got $100 for each month they met the goal of dropping at least one pound per week. Under the second scenario, $500 was set aside each month for a group of five co-workers and the ones who met their goal got to split the prize.

“People may be more motivated to achieve a particular goal when a particular resource that had been allocated for them is given to someone else if they don’t achieve their goal,” said Dr. Jeffrey Kullgren, the study’s lead author from the University of Michigan Medical School and the Ann Arbor VA Healthcare System.

In the randomly controlled trial, participants offered individual incentives lost 3.7 pounds, on average, compared to 10.6 pounds among those with group-based incentives. The findings were published online today in the Annals of Internal Medicine.

Previously: The trouble with the current calorie-counting system, How learning weight-maintenance skills first can help you achieve New Year’s weight-loss goals, Can a food-tracking app help promote healthy eating habits?, Examining how friends and family can influence our weight loss and Research shows remote weight loss interventions equally effective as face-to-face coaching programs
Photo by healthydieting