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Genetics, In the News, Pediatrics, Research

New Yorker story highlights NGLY1 research

New Yorker story highlights NGLY1 research

PackardGirl260x190The new issue of the New Yorker, out today, includes a fascinating medical story with a notable Stanford connection. As we’ve described before, a team of scientists from institutions around the world reported earlier this year on their discovery of a new genetic disease, NGLY1 deficiency. Stanford’s Gregory Enns, MB, ChB, was co-lead author of the paper describing the new finding, and one of his patients, Grace Wilsey, was among the small group of children in whom the disease first was identified. Grace’s inability to make tears when she cries was a key clue in unlocking the mystery of the disease.

But, as the New Yorker piece (subscription required) explains in detail, there’s much more to the story than that. In particular, it tells how the families of patients – especially Grace’s parents, Matt and Kristen Wilsey, and Matt and Cristina Might, who are the parents of index patient Bertrand Might – successfully encouraged researchers at different institutions to collaborate with each other in a way that advanced the discovery with exceptional speed. This was counter to the usual practice in science, the story explains. Typically, scientists avoid sharing data with competitors, even if doing so would advance the research:

If a team hunting for a new disease were to find a second case with the help of researchers from a competing lab, it could claim to have “solved” a new disease. But it would also have to share credit with competitors who may have done nothing more than grant access to existing data. When I asked [Duke University geneticist and NGLY1 deficiency co-discoverer Vandana] Shashi if she could imagine a scenario that would result in one research team’s publishing a paper with data from a different research group working on a similar project, she said, “Not that I can think of.”

David Goldstein [another Duke geneticist who collaborated with Shashi] added, “It’s not an overstatement to say that there are inherent conflicts of interest at work.” Daniel MacArthur, a genetics researcher at Massachusetts General Hospital, is even more blunt. “It’s an enormous deal,” he told me. “And it’s a big criticism of all of us, but it’s a criticism we all need to hear. The current academic publication system does patients an enormous disservice.”

Fortunately for patients like Grace and Bertrand, and for the doctors who want to help them, the culture is shifting. One marker of the shift is the NIH’s announcement earlier this month that it will be expanding its Undiagnosed Diseases Program to a network of seven sites across the country (including Stanford) and building in a requirement that all seven centers share data with each other.

Another is that researchers are realizing that families like the Wilseys and Mights will continue to make an impact. In fact, the Wilsey family has recently launched the Grace Wilsey Foundation to raise awareness about NGLY1 deficiency and promote investigation of possible treatments for the disease.

As Shashi puts it at the conclusion of the New Yorker story:

“Gone are the days when we could just say, ‘We’re a cloistered community of researchers, and we alone know how to do this.’”

Previously: NIH network designed to diagnose, develop possible treatments for rare, unidentified diseases and Crying without tears unlocks the mystery of a new genetic disease
Photo of Grace Wilsey courtesy of Lucile Packard Children’s Hospital Stanford

In the News, Science, Stanford News

Internships expose local high-schoolers to STEM careers and academic life

Internships expose local high-schoolers to STEM careers and academic life

beakersIt’s summertime: Do you know where your teenagers are? A piece in the Palo Alto Weekly discusses some of the choice science internships available to local high-school students at Stanford and other universities in the region. Shadowing scientists in the lab and even contributing to research, the young interns learn real-world applications for subjects they learn in school. They also gain work experience and exposure to academic careers in STEM fields. And a high-profile internship couldn’t hurt to include on college applications.

From the piece:

Coordinators often have to sift through hundreds of applications from students applying from all over the country and internationally. One of the most sought after is the Stanford Institutes of Medicine Summer Research Program, which alone received about 1,400 applications this year to fill about 70 to 75 openings. Decisions are based on academic grounds to help narrow down the number of prospective candidates — a tough task in a pool of extremely well-educated candidates.

But coordinators also recognize the need to provide opportunities for students who don’t have the chance to join accelerated science programs and express that oftentimes the most important quality of an applicant is a passion for science.

The article notes that internships gained through family and friend connections can be unevenly distributed, and  how programs like Stanford’s Raising Interest in Science and Engineering (RISE) Summer Internship Program have made the experiences more accessible. More from the piece:

“Typically those are kids with very educated parents who speak fluent English and who are comfortable poking around Stanford a little bit … or have a network and know somebody who works in a lab here. The RISE students typically just don’t have family members that can help them in that way,” [Kate Storm] says. “I think it’s important to serve all students, not just the privileged gifted students who are going to thrive and do well no matter what because they’ve got the backing of their school and parents and siblings.”

These types of opportunities are important to start curbing the racial disparities that exist in STEM occupations. Roughly 70 percent of the people in STEM occupations were Caucasian, 14 percent Asian, 6.5 percent Hispanic and 6.4 percent African American, according to an American Community Survey Report from the U.S. Census Bureau in 2011. Since 2008, Storm says about 80 percent of RISE graduates have gone on to major in math, engineering or science in college.

Researchers are also passionate about increasing the number of girls in labs since women are also largely underrepresented in STEM fields. The same 2011 U.S. Census Bureau report stated that roughly 25.8 percent of those in STEM occupations are women, compared to 45.7 percent of all jobs.

Previously: Residential learning program offers undergrads a new approach to scientific inquiry, The “transformative experience” of working in a Stanford stem-cell lab, Image of the Week: CIRM intern Brian Woo’s summer projectImage of the Week: CIRM intern Christina Bui’s summer project and Stanford’s RISE program gives high-schoolers a scientific boost
Photo by Amy

In the News, Neuroscience, Research, Stanford News

A spotlight on Stanford scientists’ use of deep-brain stimulation to eavesdrop on problem neural circuits

A spotlight on Stanford scientists' use of deep-brain stimulation to eavesdrop on problem neural circuits

Earlier this week, KTVU-TV aired a segment highlighting Stanford scientists’ ongoing research using deep-brain stimulation to control Parkinson’s patients’ tremors and record brain activity. A patient interviewed for the piece said the treatment “made a huge difference in my life” and called it “revolutionary.” More from the piece:

The new stimulator nicknamed “brain radio” is developed by Medtronic and tested by [Stanford neurologist Helen Bronte-Stewart, MD, and colleagues.]

“We can for the first time record the neural activity in the brain directly from the deep brain stimulator in somebody’s chest,” she said.

Despite decades of research, doctors have only a sketchy ideas of how the brain works, but now using Medtronic’s device they are for the first time opening a window into the human brain.

“I would think there will be developments that we don’t really know about right now that will come from some of the things we find out as we do this research,” said Bronte-Stewart.

Previously: Stanford conducts first U.S. implantation of deep-brain-stimulation device that monitors, records brain activity

In the News, Science

Stanford researcher on elephants: “We should value animals that have the same level of sophistication that we do”

Stanford researcher on elephants: “We should value animals that have the same level of sophistication that we do"

elephantsThe July issue of Smithsonian Magazine has a lengthy feature on the crisis facing elephants in Africa, with writer Joshua Hammer explaining, “Of the 50,000 elephants that roamed Chad 50 years ago, barely 2 percent are left. In the neighboring Central African Republic and Cameroon, the population may be even lower. Poverty, bribery and insecurity are all contributing factors in a region where a single large tusk can sell on the black market for $6,000—ten times the annual salary of a typical worker.”

Quoted in the piece is Stanford’s Caitlin O’Connell-Rodwell, PhD, a consulting assistant professor of otolaryngology, who has done extensive field work with the animals. She describes the connection between elephants and humans and expresses deep concern about the animals’ risk of becoming extinct:

“What is special about elephants is just how similar they are to us—socially and developmentally,” says Caitlin O’Connell-Rodwell, a Stanford ecologist who has written four books based on her Namibian field research on elephants. “If you watch a family group reuniting, their behavior is exactly like ours—the little cousins darting off together, the elaborate greetings of adults. Elephants offer a way of looking into the mirror, for better or worse,” she adds. “If we value human rights, we should also value animals that have the same level of sophistication that we do. We should keep those beings with us here on earth.”

Previously: Listening to elephants, communicating science, and inspiring the next generation of researchers, Elephants chat a bit before departing water hole, new Stanford research shows and Researcher dishes on African elephant soap opera
Photo by Caitlin O’Connell-Rodwell and Timothy Rodwell

Immunology, In the News, Infectious Disease, Parenting, Pediatrics, Public Health

Side effects of childhood vaccines are extremely rare, new study finds

Side effects of childhood vaccines are extremely rare, new study finds

Pneumococcus-vaccineAs you may have heard about elsewhere, a new paper published today on the safety of childhood vaccines provides reassurance for parents and pediatricians that side effects from vaccination are rare and mostly transient. The paper, a meta-analysis appearing in Pediatrics, updates a 2011 Institute of Medicine report on childhood vaccine safety. It analyzed the results of 67 safety studies of vaccines used in the United States for children aged 6 and younger.

“There are no surprises here; vaccines are being shown over and over again to be quite safe,” said Cornelia Dekker, MD, medical director of the vaccine program at Lucile Packard Children’s Hospital Stanford, who chatted with me about the study earlier today. “The safety record for our U.S.-licensed vaccines is excellent. There are a few vaccines for which they document that there are indeed adverse events, but the frequency is quite rare, and in almost all cases they are very easy to manage and self-limited.”

A Pediatrics commentary (.pdf) accompanying the new study puts the value of immunization in context:

Modeling of vaccine impact demonstrates that routine childhood immunizations in the 2009 US birth cohort would prevent ~42,000 deaths and 20 million cases of disease and save $13.5 billion in direct health care costs and $68.8 billion in societal costs.

The commentary goes on to contrast the risks of vaccines with the potential complications of vaccine-preventable diseases:

The adverse events identified by the authors were rare and in most cases would be expected to resolve completely after the adverse event. This contrasts starkly with the natural infections that vaccines are designed to prevent, which may reduce the quality of life through permanent morbidities, such as blindness, deafness, developmental delay, epilepsy, or paralysis and may also result in death.

The study found evidence against suspected links between vaccines and several acute and chronic diseases. For instance, the researchers found high-quality evidence that several different vaccines are not linked to childhood leukemia and that the measles, mumps and rubella (MMR) vaccine is not linked to autism. The DTaP vaccine is not linked to diabetes mellitus, and the Hepatitis B vaccine is not connected to multiple sclerosis, according to moderate-quality evidence.

The evidence does connect a few vaccines to side effects. For instance, the MMR, pneumococcal conjugate 13 and influenza vaccines are linked to small risks of febrile seizures, with the risk of such seizures increasing slightly if the PCV-13 and flu vaccines are given together.

“A febrile seizure can be quite alarming, but fortunately it does not have long-lasting consequences for child,” Dekker said, noting that the risk of such seizures from vaccines is around a dozen per 100,000 doses of vaccine administered.

The rotavirus vaccine is linked to risk of intussusception, an intestinal problem that can also occur with rotavirus infection itself. But the benefits of rotavirus vaccination “clearly outweigh the small additional risk,” Dekker said.

The study confirmed earlier research showing that some vaccines, including MMR and varicella, cause problems for immunocompromised children, such as kids who have HIV or who have received organ transplants. Since they can’t safely receive vaccines, this group of children relies on the herd immunity of their community to protect them.

“It’s not as if the parents of immunocompromised kids have a choice about whether to vaccinate,” Dekker told me. “They have to depend on others to keep immunization levels high, and that starts breaking down when more people hold back from having their healthy kids fully immunized.”

Dekker hopes the new findings will encourage more parents to have their healthy kids fully vaccinated.

Previously: Measles is disappearing from the Western hemisphere, Measles are on the rise; now’s the time to vaccinate, says infectious-disease expert and Tips for parents on back-to-school vaccinations
Photo by Gates Foundation

Global Health, In the News, Pediatrics, Public Safety, Sexual Health, Women's Health

Stanford research shows rape prevention program helps Kenyan girls “find the power to say no”

Stanford research shows rape prevention program helps Kenyan girls "find the power to say no"

The San Francisco Chronicle has a great story today about a collaborative project that is reducing rape and sexual assault of impoverished girls in Kenya.

The story highlights the combined efforts of activists Jake Sinclair, MD, and his wife, Lee Paiva Sinclair, who founded nonprofit No Means No Worldwide to provide empowerment training to Kenayn girls, and the Stanford team that has been analyzing the results of their efforts. As we’ve described before, this work is a great example of the academic chops of Stanford experts’ being combined with on-the-ground activism to make a difference for an urgent real-world problem.

As the article explains:

The girls and hundreds of others like them have participated in a rape-prevention workshop created by Jake Sinclair and Lee Paiva, a San Francisco doctor and his artist wife who have been working in Kenya for 14 years.

Their program is working, and that’s not just according to the dozen or so testimonials online, the couple said. Two studies out of Stanford – one published in April this year, one the year before – have found that girls who have gone through the couples’ classes experience fewer sexual assaults after the workshops.

More telling, perhaps: More than half of the girls report using some tool they learned from the classes to protect themselves, from kicking a man in the groin to yelling at someone to stop.

“It’s great to see the girls just find their voice, to find the power to say ‘no,’ ” Sinclair said. “It’s so enlightening. You can see it in their eyes, that something’s changed.”

Stanford research scholar Clea Sarnquist, DrPH, who has played an important role in the project, adds:

“A lot of these girls are using voice and verbal skills first,” Sarnquist said. “That’s one of the key things, is teaching the girls that they have the right to protect themselves – that they have domain over their own bodies, and they have the right to speak up for their own self interest.”

The whole story is definitely worth a read.

Previously: Empowerment training prevents rape of Kenyan girls and Self-defense training reduces rapes in Kenya

Cardiovascular Medicine, Genetics, In the News, Research, Science, Stanford News

A simple blood test may unearth the earliest signs of heart transplant rejection

A simple blood test may unearth the earliest signs of heart transplant rejection

2123984831_b7d09079a4_oIs there an organ more precious than a donated heart? Heart transplant recipients would likely say no. But, in order to keep their new heart healthy, they have to identify any signs of rejection as early as possible. Unfortunately (and ironically), the gold standard procedure to detect rejection – repeated heart biopsies – involves snipping away and analyzing tiny bits of tissue from the very organ they waited so long to receive. The procedure is also uncomfortable, and can cause complications.

Now, Stanford bioengineer Stephen Quake, PhD, and his colleagues have found that a simple blood test that detects donor DNA in the bloodstream of the recipient can detect signs of rejection far earlier than biopsy. Their results were published today in Science Translational Medicine.

From our release:

The study of 65 patients (21 children and 44 adults) extends and confirms the results of a small pilot study completed in 2011 by the Stanford researchers. Whereas the earlier study used stored blood samples and medical histories from seven people, the new study followed patients in real time before and after transplant. The researchers directly compared the results of simultaneously collected biopsies and blood samples, and tracked how the values changed during the rejection process.

The blood test takes advantage of the fact that dying heart cells release genetic material into the recipient’s blood. Any increase beyond a normal baseline level indicates a possible attack by the immune system on the donated organ. As described in our release:

In the pilot study of 2011, the researchers first used the presence of the Y chromosome to track the donor DNA when a woman received a heart from a male donor. Then they hit upon using differences in SNPs instead; this method doesn’t require a gender mismatch between donor and recipient. They found that, in transplant recipients not experiencing rejection, the donor DNA accounted for less than 1 percent of all cell-free DNA in the recipient’s blood. During rejection episodes, however, the percentage of donor DNA increased to about 3 or 4 percent.

In the new study, the researchers monitored 565 samples from the 65 patients to assess the assay under real-time clinical conditions. They found they were able to accurately detect the two main types of rejection (antibody-mediated rejection and acute cellular rejection) in 24 patients who suffered moderate to severe rejection episodes, one of whom required a second transplant. They were also able to detect signs of rejection up to five months before the biopsies indicated anything troubling.

The test will still need to be optimized for regular clinical use. However, cardiologist Kiran Khush, MD, a co-senior author of the study, explained what the advance could mean to heart transplant recipients:

This test has the potential to revolutionize the care of our patients… It may also allow us to conduct several diagnostic tests simultaneously. For example, we could also look for microbial sequences in the blood sample to rule out infection or other complications sometimes experienced by transplant recipients. It could allow us to determine whether shortness of breath experienced by a patient is due to an infection or the start of a rejection episode. It could be a one-stop shop for multiple potential problems.

Full disclosure: Stanford has applied for a patent relating to the test described in this study. Quake is a consultant for and holds equity in CareDX Inc., a molecular diagnostics company that has licensed a patent from Stanford related to a method used in the study and is developing it for clinical use.

Previously: ‘Genome transplant’ concept helps Stanford scientists predict organ rejection, Stanford study in transplant patients could lead to better treatment and New techniques to diagnose disease in a fetus
Photo by Desi

CDC, In the News, Pediatrics, Public Health

Teens these days: smoking less, but engaging in other risky behaviors

Teens these days: smoking less, but engaging in other risky behaviors

teen musicalMr. Camel, tear up those cigarettes. Statistics from the latest Youth Risk Behavior Surveillance System survey, released today by the U.S. Centers for Disease Control and Prevention, show that 2013 marked the lowest incidence (15.7 percent) of teen smoking reported since 1991.

In other news, texting while driving, drinking soda and having unprotected sex are among the behaviors the report notes are worthy of concern. From the report:

During the 30 days before the survey, 41.4% of high school students nationwide among the 64.7% who drove a car or other vehicle during the 30 days before the survey had texted or e-mailed while driving, 34.9% had drunk alcohol, and 23.4% had used marijuana. During the 12 months before the survey, 14.8% had been electronically bullied, 19.6% had been bullied on school property, and 8.0% had attempted suicide.

During the 7 days before the survey, 5.0% of high school students had not eaten fruit or drunk 100% fruit juices and 6.6% had not eaten vegetables. More than one-third (41.3%) had played video or computer games or used a computer for something that was not school work for 3 or more hours per day on an average school day.

Previously: Adolescent Health Van wins community award for aiming to “help kids turn their lives around”A reminder that texting and driving don’t mix, To reduce use, educate teens on the risks of marijuana and prescription drugs and National Cancer Institute introduces free text message cessation service for teens
Via The Checkup
Photo by Daniel Oines

Cancer, In the News, Patient Care

“You have cancer”: On being a doctor and receiving the news

"You have cancer": On being a doctor and receiving the news

Inquiring patients might want to know what their doctors would do for themselves in certain medical situations. (And, as recently discussed here, the answers might be surprising.) An article in this morning’s San Francisco Chronicle surveys oncologists and other cancer specialists who have been diagnosed with a disease they study or treat. It describes how they respond to the news “You have cancer” – and if or how they choose to share their personal experiences with patients.

From the piece:

As a pathologist, [Kimberly Allison, MD, associate professor of pathology] typically sees patients’ cells, rather than the patients themselves.

So it’s not surprising that when she had a biopsy on her breast after noticing tissue changes in 2008, her first reaction was to be excited to see her own sample under the microscope. She assumed the sample would be benign, but when her colleagues came to her with the results, looking grim, she knew it was bad.

“I knew I needed to be worried,” said Allison, who is now at Stanford but was working at the University of Washington in Seattle at the time. “I knew I was going to get aggressive treatment, but I was terrified about what that might be like. That fear was just the same as in any patient.”

The article goes on to describe how Allison found support from fellow patients and even wrote a book about her experience with the disease. Her specialized knowledge of cells proved to be a key weapon against her illness:

She could look at her cancer cells under the microscope before they were wiped out by the treatments.

“Whenever I felt like I wanted to talk smack to it, I would look at it,” she said. “I’d tell it, ‘I never want to see you again.’ “

Previously: A doctor recounts his wife’s battle with cancer: “My knowledge was too clear-eyed”, A Stanford physician’s take on cancer prognoses – including his own, Both a doctor and a patient: Stanford physician talks about his hemophilia and Red Sunshine: One doctor’s journey surviving stage 3 breast cancer

Complementary Medicine, Health and Fitness, In the News, Sports

How do you get through the NBA Finals? Practice, practice, practice (yoga)

How do you get through the NBA Finals? Practice, practice, practice (yoga)

LeBron JamesA student in a yoga class I attended in Berkeley, Calif. last Saturday asked the teacher about the origin of the Sanskrit chant we had just repeated. He explained that the words were the lyrics from the theme song to Battlestar Galactica. Inviting pop-culture references into the sometimes-serious space of the studio is a terrific way to normalize the complementary medicine practice. So is welcoming 6’8″, 250-pound athletes to an activity often stereotyped as being for the petite, female and flexible.

That is to say that LeBron James takes yoga. In case you somehow missed it, the Miami Heat star got sidelined by cramps near the end of Game 1 of the NBA Finals. A piece on Sports Illustrated‘s Point Forward describes how yoga played a role in James’ recovery and preparation for the next game of the series:

[Readying his body for Game 2] included, among a more extensive hydration regimen, James’ decision to attend a Sunday morning yoga class at the Heat’s team hotel in San Antonio.

“Yoga isn’t just about the body, it’s also about the mind and it’s a technique that has really helped me,” James told Brian Windhorst (then of the Cleveland Plain-Dealer) in 2009. “You do have to focus because there’s some positions that can really hurt you at times if you aren’t focused and breathing right.”

Upon his arrival in Miami, James also credited yoga for his supernatural level of endurance. Only Kevin Durant has logged more total minutes since James joined the Heat in 2011.

The piece notes that James’ teammate Dwayne Wade and the Heat’s playoffs opponents, the San Antonio Spurs, are among the other NBA affiliates who stand in Mountain Pose.

Previously: Third down and ommm: How an NFL team uses yoga and other tools to enhance players’ well-beingNIH to host Twitter chat on science of yoga and Expert argues that for athletes, “sleep could mean the difference between winning and losing”
Via Tiffany Russo Yoga
Photo by ASSOCIATED PRESS

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