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Big data, BigDataMed15, Precision health, Public Health, Research, Videos

How the FDA is promoting data sharing and transparency to support innovations in public health

How the FDA is promoting data sharing and transparency to support innovations in public health

Keynote talks and presentations from the 2015 Big Data in Biomedicine conference at Stanford are now available on the Stanford YouTube channel. To continue the discussion of how big data can be harnessed to improve the practice of medicine and enhance human health, we’re featuring a selection of the videos on Scope.

At the 2014 Big Data in Biomedicine conference, Taha Kass-Hout, MD, chief health informatics officer for the U.S. Food and Drug Administration, announced that the federal agency was launching OpenFDA, a scalable search and big-data analytics platform. In May, he returned to the Big Data in Biomedicine stage to offer an update on the initiative and discuss how the FDA is continuing to foster access and transparency of big data in government.

During his talk, Kass-Hout shared some eye-popping statistics about the information available through OpenFDA. The platform houses close to 70,000 product labels for pharmaceuticals; nearly four million reports on adverse events or malfunctions of medical devices; 41,000 records on recalls of foods, pharmaceuticals or devices and over four and a half million reports of adverse events or side-effects of drugs.

He outlined future plans to build a similar public, cloud-based platform to compliment the Obama Administration’s Precision Medicine Initiative. Watch the full talk to learn more about these exciting efforts to unlock the rapidly growing reservoir of biomedical data and spur innovation in public health.

Previously: A look at the MyHeart Counts app and the potential of mobile technologies to improve human health, Discussing patient participation in medical research: “We had to take this into our own hands,” A look at aging and longevity in this “unprecedented” time in history, Mining Twitter to identify cases of foodborne illness and Discussing access and transparency of big data in government

Big data, BigDataMed15, Cardiovascular Medicine, Medical Apps, Stanford News, Videos

A look at the MyHeart Counts app and the potential of mobile technologies to improve human health

A look at the MyHeart Counts app and the potential of mobile technologies to improve human health

Keynote talks and presentations from the 2015 Big Data in Biomedicine conference at Stanford are now available on the Stanford YouTube channel. To continue the discussion of how big data can be harnessed to improve the practice of medicine and enhance human health, we’re featuring a selection of the videos on Scope.

At last count, the number of iPhone owners who have downloaded the MyHeart Counts app and consented to participate in a large-scale, human heart study had reached 40,000. The first-of-its-kind mobile app was designed by Stanford Medicine cardiologists as a way for users to learn about their heart health while simultaneously helping advance the field of cardiovascular medicine.

Built on Apple’s ResearchKit framework, the app leverages the iPhone’s built-in motion sensors to collect data on physical activity and other cardiac risk factors for a research study. The MyHeart Counts study also draws on the strength of Stanford Medicine’s Biomedical Data Science Initiative.

At the 2015 Big Data in Biomedicine conference, Euan Ashley, MD, a cardiologist at Stanford and co-investigator for the MyHeart Counts study, shared some preliminary findings with the audience. Check out the full talk to learn more about how the app is helping researchers better understand Americans’ health habits and what states have the happiest, most physically active and well-rested residents.

Previously: On the move: Big Data in Biomedicine goes mobile with discussion on mHealth, MyHeart Counts shows that smartphones are catching on as new research tool, Lights, camera, action: Stanford cardiologist discusses MyHeart Counts on ABC’s Nightline, MyHeart Counts app debuts with a splash and Stanford launches iPhone app to study heart health.

Big data, Cancer, Genetics, Immunology, Research, Science, Stanford News

Linking cancer gene expression with survival rates, Stanford researchers bring “big data” into the clinic

Linking cancer gene expression with survival rates, Stanford researchers bring "big data" into the clinic

Magic 8 ball“What’s my prognosis?” is a question that’s likely on the mind, and lips, of nearly every person newly diagnosed with any form of cancer. But, with a few exceptions, there’s still not a good way for clinicians to answer. Every tumor is highly individual, and it’s difficult to identify anything more than general trends with regard to the type and stage of the tumor.

Now, hematologist and oncologist Ash Alizadeh, MD, PhD; radiologist Sylvia Plevritis, PhD; postdoctoral scholar Aaron Newman, PhD; and senior research scientist Andrew Gentles, PhD, have created a database that links the gene-expression patterns of individual cancers of 39 types with the survival data of the more than 18,000 patients from whom they were isolated. The researchers hope that the resource, which they’ve termed PRECOG, for “prediction of cancer outcomes from genomic profiles” will provide a better understanding of why some cancer patients do well, and some do poorly. Their research was published today in Nature Medicine.

As I describe in our release:

Researchers have tried for years to identify specific patterns of gene expression in cancerous tumors that differ from those in normal tissue. By doing so, it may be possible to learn what has gone wrong in the cancer cells, and give ideas as to how best to block the cells’ destructive growth. But the extreme variability among individual patients and tumors has made the process difficult, even when focused on particular cancer types.

Instead, the researchers pulled back and sought patterns that might become clear only when many types of cancers, and thousands of patients were lumped together for study:

Gentles and Alizadeh first collected publicly available data on gene expression patterns of many types of cancers. They then painstakingly matched the gene expression profiles with clinical information about the patients, including their age, disease status and how long they survived after diagnosis. Together with Newman, they combined the studies into a final database.

“We wanted to be able to connect gene expression data with patient outcome for thousands of people at once,” said Alizadeh. “Then we could ask what we could learn more broadly.”

The researchers found that they were able to identify key molecular pathways that could stratify survival across many cancer types:

In particular, [they] found that high expression of a gene called FOXM1, which is involved in cell growth, was associated with a poor prognosis across multiple cancers, while the expression of the KLRB1 gene, which modulates the body’s immune response to cancer, seemed to confer a protective effect.

Alizadeh and Plevritis are both members of the Stanford Cancer Institute.

Previously: What is big data?Identifying relapse in lymphoma patients with circulating tumor DNA,  Smoking gun or hit-and-run? How oncogenes make good cells go bad and Big data = big finds: Clinical trial for deadly lung cancer launched by Stanford study
Photo by CRASH:candy

Big data, BigDataMed15, Chronic Disease, Videos

Discussing patient participation in medical research: “We had to take this into our own hands”

Discussing patient participation in medical research: "We had to take this into our own hands"

Keynote talks and presentations from the 2015 Big Data in Biomedicine conference at Stanford are now available on the Stanford YouTube channel. To continue the discussion of how big data can be harnessed to improve the practice of medicine and enhance human health, we’re featuring a selection of the videos on Scope.

Two days before Christmas in 1994, Sharon Terry’s two young children were diagnosed with pseudoxanthoma elasticum (PXE), a rare condition that causes calcium and other minerals to be deposited in the body’s tissue. As Terry told the audience at the 2015 Big Data in Biomedicine conference, “[My husband and I] quickly learned that we, in fact, had to take this into our own hands, like many parents have done before us and many parents have done after us.” Despite not having a science background, Terry co-discovered the gene associated with PXE and created a diagnostic test for the disease; over the years, she has conducted clinical trials and authored 140 peer-reviewed papers, of which 30 are PXE clinical studies.

In the above video, Terry recounts the inspiring journey of how she and her husband worked for two decades with scientists worldwide to advance research on PXE in hopes of developing therapeutic treatments. She also explains her current work as president and CEO of Genetic Alliance to help individuals, families and communities participate in scientific research and promote the sharing of health data to improve health.

Previously: A look at aging and longevity in this “unprecedented” time in history, Parents turn to data after son is diagnosed with ultra-rare disease, Nobel Laureate Michael Levitt explains why “biology is information rich” at Big Data in Biomedicine, At Big Data in Biomedicine, Stanford’s Lloyd Minor focuses on precision health and  Experts at Big Data in Biomedicine: Bigger, better datasets and technology will benefit patients

Big data, Stanford News, Videos

What is big data?

What is big data?

We’ve written a lot about “big data” and the field of data science here on Scope. But for those readers who are still fuzzy on what exactly big data is, or how it’s being used to improve human health, Lloyd Minor, MD, dean of the medical school, and researchers with Stanford’s Biomedical Data Science Initiative (BDSI) are here to help. In the video above they offer their own definitions of big data, discuss how Stanford is leading the way in advancing the field, and share examples of how this so-called “digitization of life” will come to benefit all patients.

Previously: At Big Data in Biomedicine, Stanford’s Lloyd Minor focuses on precision healthExperts at Big Data in Biomedicine: Bigger, better datasets and technology will benefit patientsExamining the potential of big data to transform health careRising to the challenge of harnessing big data to benefit patients and A call to use the “tsunami of biomedical data” to preserve life and enhance health

Applied Biotechnology, Big data, Cancer, Genetics, Research, Science, Stanford News

Peeking into the genome of a deadly cancer pinpoints possible new treatment

Peeking into the genome of a deadly cancer pinpoints possible new treatment

small cell lung cancerSmall cell lung cancer is one of the most deadly kinds of cancers. Typically this aggressive disease is diagnosed fairly late in its course, and the survival rates are so dismal that doctors are reluctant to even subject the patient to surgery to remove the tumor for study. As a result, little is known about the molecular causes of this type of cancer, and no new treatments have been approved by the Food and Drug Administration since 1995.

Now a massive collaboration among researchers around the world, including the University of Cologne in Germany and Stanford, has resulted in the collection of more than 100 human small cell lung cancer tumors. Researchers sequenced the genomes of the tumors and identified some key steps in their development. They also found a potential new weak link for treatment.

The findings were published today in Nature, and Stanford cancer researcher Julien Sage, PhD, one of three co-senior authors of the paper, provided some details in an email:

With this larger number of specimens analyzed, a more detailed picture of the mutations that contribute to the development of small cell lung cancer now emerges. These studies confirmed what was suspected before, that loss of function of the two tumor suppressor genes, Rb and p53, is required for tumor initiation. Importantly, these analyses also identified new therapeutic targets.

The researchers also saw that, in about 25 percent of cases, the Notch protein receptor was also mutated. This protein sits on the surface of a cell; when Notch binds, it initiates a cascade of signaling events within the cell to control its development and growth. As Sage explained:

The mutations in the Notch recepetor were indicative of loss of function, suggesting that Notch normally suppresses small cell lung cancer development. Indeed, when graduate student Jing Lim in my lab activated Notch in mice genetically engineered to develop small cell lung cancer, we found a potent suppression of tumor development. These data identify the Notch signaling pathway as a novel therapeutic target in a cancer type for which new therapies are critically needed.

This is not Sage’s first foray into fighting small cell lung cancer. In 2013, he collaborated with other researchers at Stanford, including oncologist Joel Neal, MD, PhD, to identify a class of antidepressants as a possible therapy for the disease.

Previously: Gene-sequencing rare tumors – and what it means for cancer research and treatment, Listening in on the Ras pathway identifies new target for cancer therapy and Big data = big finds: Clinical trial for deadly lung cancer launched by Stanford study
Image by Yale Rosen

Big data, BigDataMed15, Chronic Disease, Genetics, Videos

Parents turn to data after son is diagnosed with ultra-rare disease

Parents turn to data after son is diagnosed with ultra-rare disease

Keynote talks and presentations from the 2015 Big Data in Biomedicine conference at Stanford are now available on the Stanford YouTube channel. To continue the discussion of how big data can be harnessed to improve the practice of medicine and enhance human health, we’re featuring a selection of the videos on Scope.

Four years ago, Matthew Might, PhD, and his wife, Christina, learned that their son Bertrand was the first person to be diagnosed with ultra-rare genetic disorder called N-Glycanase Disorder. At the 2015 Big Data in Biomedicine conference at Stanford, Might recounted the story of his son’s medical odyssey and explained how a team of Duke University researchers used whole-exome sequencing, which is a protein-focused variant of whole-genome sequencing, on himself, his wife and Bertrand to arrive at his son’s diagnosis.

Watch the video above to find out how Might and his family, who turned a deaf ear to doctors’ advice that nothing could be done for their son, harnessed the power of the Internet to identify 35 more patients with the same disorder and are now leading the charge in helping scientists better understand the disorder.

Previously: Nobel Laureate Michael Levitt explains why “biology is information rich” at Big Data in Biomedicine, At Big Data in Biomedicine, Stanford’s Lloyd Minor focuses on precision health, Experts at Big Data in Biomedicine: Bigger, better datasets and technology will benefit patients, On the move: Big Data in Biomedicine goes mobile with discussion on mHealth and Big Data in Biomedicine panelists: Genomics’ future is bright

Big data, BigDataMed15, Videos

Nobel Laureate Michael Levitt explains why “biology is information rich” at Big Data in Biomedicine

Nobel Laureate Michael Levitt explains why "biology is information rich" at Big Data in Biomedicine

Keynote talks and presentations from the 2015 Big Data in Biomedicine conference at Stanford are now available on the Stanford YouTube channel. To continue the discussion of how big data can be harnessed to improve the practice of medicine and enhance human health, we’re featuring a selection of the videos on Scope.

In 2013, Michael Levitt, PhD, professor of structural biology at the Stanford, was awarded the Nobel Prize in Chemistry for “for the development of multiscale models for complex chemical systems.” His work focuses on theoretical, computer-aided analysis of the protein, DNA and RNA molecules responsible for life at its most fundamental level.

During his keynote at last month’s Big Data in Biomedicine conference, Levitt spoke about big data in computational structural biomedicine and told the audience that “biology is information rich.” Watch his full presentation above to learn more about big data in biology, computer simulations in biomolecules and medical applications of molecular simulation.

Previously: At Big Data in Biomedicine, Stanford’s Lloyd Minor focuses on precision health, At Big Data in Biomedicine, Nobel laureate Michael Levitt and others talk computing and crowdsourcing, Experts at Big Data in Biomedicine: Bigger, better datasets and technology will benefit patients, On the move: Big Data in Biomedicine goes mobile with discussion on mHealth and Big Data in Biomedicine panelists: Genomics’ future is bright

Big data, Health Disparities, Medicine and Society, Men's Health, Research, Stanford News

To live longer, men need to embrace their femininity, new research suggests

To live longer, men need to embrace their femininity, new research suggests

13938506188_faea591a9b_z (1)Scores of scholars have examined a fundamental truth of our time: Women live longer than men. But why?

After poring over data spanning centuries and continents, a team of Stanford researchers has discovered an overlooked aspect of that disparity. When there’s plenty to go around, the gap between men and women shrinks. But when adversity strikes, men die young.

And in cultures where women excel — racking up academic, professional and extracurricular accomplishments equalling or topping men — men live longer too, said Mark Cullen, MD, the first author of the recently published study that also appears in an abridged, reader-friendly form on Vox.

“The punchline is feminism is good for men too,” Cullen said.

The team posits that women are hard-wired to protect each other, an ingrained trait that goes beyond hormones and isn’t culturally dependent.

The researcher’s primary conclusion — that socio-economic stress hits men harder than women — is solid. Cullen and team looked at societies worldwide, finding that in poorer nations women live about 10 years longer than men, while in the United States the gap is closer to five years. When a social safety net is pulled out suddenly, such as following the fall of the Berlin Wall in Eastern Europe, the lifespan of men dropped nearly 15 years, Cullen said.

“Men were just dropping like flies. But that didn’t happen to women,” he said.

The team posits that women are hard-wired to protect each other, an ingrained trait that goes beyond hormones and isn’t culturally dependent.

“Women live differently,” Cullen said. “They seek each other, invest heavily in family and nurturing, which men do much less of. That’s the secret sauce — women have each other and this incredible support network.”

As women enter the workforce, and men invest in family relationships and social networks, the lifespan gap begins to lessen. “It’s the feminization of the way that men live that helps men,” he said.

As evidence, the team points to Alaska and highly developed Asian nations such as Japan and Korea. There, female lifespans far surpass male’s, probably because despite their economic success, their cultures embrace traditional gender roles. “These are places where men are men, and they die like men,” Cullen said.

Next, the team plans to continue their inquiry by investigating the hypothesis that equality helps men and search for policy programs that also boost men’s lifespans.

Cullen directs the Stanford Center for Population Health Sciences. His co-authors include Michael Baiocchi, PhD, assistant professor in the Stanford Center for Population Health Sciences; Karen Eggleston, PhD, director of the Asia Health Policy Program; Victor Fuchs, PhD, Henry J. Kaiser Professor, emeritus, of economics and of health research and policy; and statistician Pooja Loftus, MS.

Previously: “Are we there yet?” Exploring the promise, and the hype, of longevity research, Living loooooooonger: A conversation on longevity and Social factors better indicators of premature mortality than skin color or geography
Photo by DVIDSHUB

Big data, Cardiovascular Medicine, Patient Care, Public Health, Research, Stanford News

Widely prescribed heartburn drugs may heighten heart-attack risk

Widely prescribed heartburn drugs may heighten heart-attack risk

PrilosecHeartburn – that burning sensation in the chest that occurs when stomach acid rises up into your esophagus – has absolutely nothing whatsoever to do with the heart. People with heartburn (that’s a lot of us) are at no increased risk of developing heart disease. At least, not unless they’re taking the most commonly used class of drugs for treating heartburn.

That drug class would be proton-pump inhibitors, or PPIs, and it includes omeprazole (Prilosec), lansoprazole (Prevacid), esomeprazole (Nexium) and a few more. All three are available over the counter. Although the labels direct users not to take these drugs for longer than a couple of weeks without consulting their physicians, people often pop them on a daily basis for months or years on end.

But a new PLOS ONE study, led by Stanford biomedical-informatics expert Nigam Shah, PhD, MBBS, and cardiovascular surgeon Nick Leeper, MD, shows a clear association between prior use of PPIs for heartburn and elevated risk of serious cardiovascular events including heart attacks. In a news release covering that “big data” study, which combed through nearly 3 million electronic health records to ferret out the PPI/cardiovascular-risk connection, I wrote:

… PPIs are among the world’s most widely prescribed drugs, with $14 billion in annual sales… In any given year, more than 20 million Americans – about one in every 14 – use PPIs… More than 100 million prescriptions are filled every year in the United States for PPIs, a class of drugs long considered benign except for people concurrently taking the blood thinner clopidogrel (Plavix). However, the new study upends this view: It indicates that PPI use was associated with a roughly 20 percent increase in the rate of subsequent heart-attack risk among all adult PPI users, even when excluding those also taking clopidogrel.

That increased risk was seen among younger adults (under age 45), too.

The study, in other words, found that everybody’s cardiovascular risk goes up if they use PPIs. Now, a 20 percent increase in risk may not amount to much if your baseline risk is very low to begin with (say, that of a 20-year-old woman in top physical condition with no genetic predisposition to high blood pressure or elevated cholesterol). But for many of us, especially if we’re middle-aged, a little pudgy, or struggling with hypertension or hypercholesterolemia, that 20 percent looms larger.

Importantly, people who take the second-most-widely prescribed class of drugs prescribed for heartburn, so-called H2 blockers, appear to suffer no ill effects from them in the cardiovascular-risk department, according to the study’s findings. H2 blockers, which have been around longer than PPIs, are reasonably effective.

So, why do PPIs, but not H2 blockers, cause trouble? As I noted in my release:

The study’s findings lend support to an explanation for an untoward effect of PPIs on heart-disease risk proposed by Stanford scientists a few years ago. Research done then showed that PPIs impede the production of an important substance, nitric oxide, in the endothelial cells that line all of the nearly 100,000 miles of blood vessels in an averag adult’s body.

Nitric oxide relaxes blood vessels. So it figures that chronic use of a drug that shuts down that chemical’s generation could cause chronic blood-vessel constriction and follow-on cardiovascular problems.

Read those labels, people.

Previously: How efforts to mine electronic health records are beginnning to influence critical care, New research scrutinizes off-label drug use and Damage to dead-cell disposal system may increase heart disease
Photo by John

 

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