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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

 

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

Stanford researchers suss out cancer mutations in genome’s dark spots

Stanford researchers suss out cancer mutations in genome's dark spots

lighted pathOnly a small proportion of our DNA contains nucleotide sequences used to make proteins. Much of the remainder is devoted to specifying how, when and where those proteins are made. These rules are encoded in our DNA as regulatory elements, and they’re what makes one cell type different from another, and keep them from running wild like children in an unattended classroom. When things go awry, the consequences (like rampant growth and cancers) can be severe.

Geneticist Michael Snyder, PhD, and postdoctoral scholar Collin Melton, PhD, recently combined information from The Cancer Genome Atlas, a national effort to sequence and identify mutations in the genomes of many different types of cancers, with data from the national ENCODE Project, which serves as an encyclopedia of DNA functional regions, or elements. Their aim was to better understand the roles that mutations in regulatory regions may play in cancer development.

Snyder and Melton found that fewer than one of every thousand mutations in each cancer type occurs in the coding region of a gene. In contrast, more than 30 percent of the mutations occur in regulatory regions. The study was published this morning in Nature Genetics.

As Snyder explained to me:

Until recently, many mutations outside the coding regions of genes have been mostly invisible to us. Cancer researchers largely focused on identifying changes within coding regions. Using ENCODE data, we’ve been able to define some important regions of the genome and found that certain regulatory regions are often enriched for mutations. This opens up a whole new window for this type of research.

Snyder, who leads Stanford’s genetics department and directs the Stanford Center for Genomics and Personalized Medicine, likens looking for cancer-causing mutations only in coding regions as “looking under the lamppost” for keys lost at night. Until recently, the coding regions of genes were the most well-studied, and unexpected mutations stood out like a sore thumb. We’ve known there’s a lot more of the genome outside the coding regions, but until the ENCODE project was largely completed in 2012, researchers were often in the dark as to where, or even how, they should look.

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Big data, Events, Medicine and Society, Precision health, Public Health, Stanford News

How Stanford Medicine will “develop, define and lead the field of precision health”

How Stanford Medicine will "develop, define and lead the field of precision health"

15313-a-healthy-young-woman-stretching-outdoors-pvPrecision health was the theme of the day here on Friday, with Dean Lloyd Minor, MD, describing to a standing-room-only crowd at a Town Hall event how Stanford Medicine will continue to lead and excel in this area.

Minor, along with colleagues Amir Dan Rubin, president and CEO of Stanford Health Care, and Christopher Dawes, president and CEO of Stanford Children’s Health, offered faculty, staff and students a glimpse of the future of precision health here.

The vision has seven primary tenets, Minor explained:

  • Stanford Medicine will lead a transition from diagnosis and treatment toward prediction and prevention
  • It will develop new scientific advances and paradigms
  • It will bridge the gap between basic scientific research and clinical care
  • It will transform clinical care to emphasize compassion and quality
  • It will deliver quality health care at excellent value
  • It will train the biomedical leaders of today and tomorrow
  • It will develop and share its advances globally

Stanford Medicine’s focus in this area came about as part of a strategic planning process and taps Stanford’s strengths in data science, fundamental bioscience research and specialized care in areas such as cancer, Minor said. It also capitalizes on the nationwide focus on precision medicine, which took center stage in January when President Barack Obama introduced a Precision Medicine Initiative to establish a national system capable of delivering treatments tailored to individual patients.

Precision health includes precision medicine but boldly expands its focus. Precision medicine provides personalized treatments once illness occurs; in contrast, precision health aims to prevent and predict illness, maintaining health and quality of life for as long as possible. Precision health draws on data science tools to translate volumes of research and clinical data into information patients and doctors can use.

A recent Inside Stanford Medicine article described the benefits of such widespread access to data:

Physicians and researchers can better predict individual risks for specific diseases, develop approaches to early detection and prevention, and arm clinicians with information to help them make real-time decisions about the best way to care for patients.

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Big data, BigDataMed15, Events, Medicine and Society, Research, Stanford News, Technology

A look back at Stanford’s Big Data in Biomedicine

A look back at Stanford's Big Data in Biomedicine

Ashley - 560

We reported many of the happenings at last week’s Big Data in Biomedicine here on Scope. Writer Bruce Goldman was also in attendance for the three-day event, and he captured the conversation in a just-published Inside Stanford Medicine piece.

Previously: At Big Data in Biomedicine, Stanford’s Lloyd Minor focuses on precision healthAt Big Data in Biomedicine, Nobel laureate Michael Levitt and others talk computing and crowdsourcingExperts at Big Data in Biomedicine: Bigger, better datasets and technology will benefit patientsOn the move: Big Data in Biomedicine goes mobile with discussion on mHealth and Big Data in Biomedicine panelists: Genomics’ future is bright
Photo of Euan Ashley, MD, welcoming conference attendees last Wednesday, by Saul Bromberger

Big data, BigDataMed15, Events, Precision health, Research, Stanford News, Technology

At Big Data in Biomedicine, Stanford’s Lloyd Minor focuses on precision health

At Big Data in Biomedicine, Stanford's Lloyd Minor focuses on precision health

Minor talking - 560

In the next decade, Stanford Medicine will lead the biomedical revolution in precision health, Dean Lloyd Minor, MD, told attendees of the final day of the Big Data in Biomedicine conference.

Involving all aspects of Stanford Medicine — including research and patient care — the focus on precision health will draw on Stanford’s existing strengths while propelling the development of new discoveries and transforming health-care delivery, Minor explained.

The choice of “precision health” rather than “precision medicine” is deliberate and a distinction that is reflective of Stanford’s leadership role. While both precision health and precision medicine are targeted and personalized, precision health is proactive, with an emphasis on maintaining health. In contrast, precision medicine is reactive, with a focus on caring for the sick. Precision health includes prediction and prevention; precision medicine involves diagnosis and treatment.

Minor used the model of a tree to describe Stanford’s focus on precision health.

Basic research and biomedical data science form the trunk, the foundation that supports the entire endeavor. Nine “biomedical platforms” form the major branches; these platforms include immunology, cancer biology and the neurosciences, among others. The tree’s leaves are its clinical core, with treatment teams in cardiac care, cancer and maternal and newborn health, for example.

The growth of the tree, its tippy top, is fueled by predictive, preventative and longitudinal care — where innovations in knowledge and care drive further changes in the future of health-care.

Minor made two key points about the tree, and its implications for research and care at Stanford.

First, the tree is big and growing. “There is room for everyone on the tree,” he said. “That is one thing that will make this plan — this tree — so powerful.”

Secondly, the tree is ever-changing. “Care will be analyzed and fed back. That’s really the true heart and meaning of the learning health-care system,” Minor said. “Every encounter is part of a much bigger whole.”

The entire effort will be fueled by big data, Minor said. To recognize its importance, and help train future leaders, Stanford Medicine also plans to create a new biomedical data science Department.

“We’re poised to lead,” Minor said. “We build upon a history of innovation, an entrepreneurial mindset, visionary faculty and students and a culture of collaboration.”

Previously: Big Data in Biomedicine conference kicks off todayStanford Medicine’s Lloyd Minor on re-conceiving medical education and Meet the medical school’s new dean: Lloyd Minor
Photo by Saul Bromberger

Big data, BigDataMed15, Events, Medicine and Society, Microbiology, Research, Technology

At Big Data in Biomedicine, Nobel laureate Michael Levitt and others talk computing and crowdsourcing

At Big Data in Biomedicine, Nobel laureate Michael Levitt and others talk computing and crowdsourcing

Levitt2Nobel laureate Michael Levitt, PhD, has been using big data since before data was big. A professor of structural biology at Stanford, Levitt’s simulations of protein structure and movement have tapped the most computing power he could access in his decades-long career.

Despite massive advances in technology, key challenges remain when using data to answer fundamental biological questions, Levitt told attendees of the second day of the Big Data in Biomedicine conference. It’s hard to translate gigabytes of data capturing a specific biological problem into a form that appeals to non-scientists. And even today’s supercomputers lack the ability to process information on the behavior of all atoms on Earth, Levitt pointed out.

Levitt’s address followed a panel discussion on computation and crowdsourcing, featuring computer-science specialists who are developing new ways to use computers to tackle biomedical challenges.

Kunle Olukotun, PhD, a Stanford professor of electrical engineering and computer science, had advice for biomedical scientists: Don’t waste your time on in-depth programming. Instead, harness the power of a domain specific language tailored to allow you to pursue your research goals efficiently.

Panelists Rhiju Das, PhD, assistant professor of biochemistry at Stanford, and Matthew Might, PhD, an associate professor of computer science at the University of Utah, have turned to the power of the crowd to solve problems. Das uses crowdsourcing to answer a universal problem (folding of RNA) and Might has used the crowd for a personal problem (his son’s rare genetic illness).

For Das, an online game called Eterna – and its players – have helped his team develop an algorithm that much more accurately predicts whether a sequence of RNA will fold correctly or not, a key step in developing treatments for diseases that use RNA such as HIV.

And for Might, crowdsourcing helped him discover other children who, like his son Bertrand, have an impaired NGLY1 gene. (His story is told in this New Yorker article.)

Panelist Eric Dishman, general manager of the Health and Life Sciences Group at Intel Corporation, offered conference attendees a reminder: Behind the technology lies a human. Heart rates, blood pressure and other biomarkers aren’t the only trends worth monitoring using technology, he said.

Behavioral traits also offer key insights into health, he explained. For example, his team has used location trackers to see which rooms elderly people spend time in. When there are too many breaks in the bathroom, or the person spends most of the day in the bedroom, health-care workers can see something is off, he said.

Action from the rest of the conference, which concludes today, is available via live-streaming and this app. You can also follow conversation on Twitter by using the hashtag #bigdatamed.

Previously: On the move: Big Data in Biomedicine goes mobile with discussion on mHealthGamers: The new face of scientific research?, Half-century climb in computer’s competence colloquially captured by Nobelist Michael Levitt and Decoding proteins using your very own super computer
Photo of Michael Levitt by Saul Bromberger

Big data, BigDataMed15, Events, Patient Care, Research, Stanford News, Technology

Experts at Big Data in Biomedicine: Bigger, better datasets and technology will benefit patients

Experts at Big Data in Biomedicine: Bigger, better datasets and technology will benefit patients

population health panelThe explosion of big data is transforming the way those in health care are diagnosing, treating and preventing disease, panelists at the Big Data in Biomedicine said on its opening day.

During a five-member panel on population health, experts outlined work that is currently being done but said even bigger datasets and better technology are needed to ramp up the benefits from digital data and to save lives.

“Using the end-of-millions to inform care for the end-of-one – that is exactly where we’re going,” said Tracy Lieu, MD, MPH, director of research at Kaiser Permanente Northern California, a health-care network that includes 21 hospitals, 8,000 physicians and 3.6 million patients. “And we think that in a population like ours, in an integrated system like ours, we are in an ideal setting to do personalized medicine.”

Stanford Medicine professor Douglas Owens, MD, director of the Center for Health Policy and Center for Primary and Outcomes Research, led the panel on Wednesday. He said that big data is also changing how research is being conducted.

“There’s been an explosion of data of all kinds: clinical data, genomics data, data about what we do and how we live,” said Owens. “And the question is how can we best use that data to improve the health of the individual and to improve the health of populations.”

Lieu said two key trends are central to medical researchers: informatics and genomics. She told attendees that Kaiser utilizes a “virtual data warehouse” with the digital data of 14 million patients dating back to 1960. But Lieu cautioned that the data are not always the means to an end, particularly if the findings are not tested and implemented.

“Sometimes we fail. And we fail when we identify a problem of interest, we make a decision to study it, we assemble the data, we analyze and interpret the results – and then we send them off to journals. So we fail to close the loop,” she said, because researchers typically don’t go beyond the publication of data.

Lieu said Kaiser is now focused on trying to close that loop. “To do that, we need the kinds of tools that you in this group and the speakers at this conference are developing,” she explained. “We need better and better technology for rapidly analyzing and aggregating data.”

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