Category Archives: Genetic Medicine

In 2007, DNA pioneer James Watson became the first person to have his entire genome sequencedmaking all of his 6 billion base pairs publicly available for research. Well, almost all of them. He left one spot blank, on the long arm of chromosome 19, where a gene called APOE lives. Certain variations in APOE increase your chances of developing Alzheimers, and Watson wanted to keep that information private.

Except it wasnt. Researchers quickly pointed out you could predict Watsons APOE variant based on signatures in the surrounding DNA. They didnt actually do it, but database managers wasted no time in redacting another two million base pairs surrounding the APOE gene.

This is the dilemma at the heart of precision medicine: It requires people to give up some of their privacy in service of the greater scientific good. To completely eliminate the risk of outing an individual based on their DNA records, youd have to strip it of the same identifying details that make it scientifically useful. But now, computer scientists and mathematicians are working toward an alternative solution. Instead of stripping genomic data, theyre encrypting it.

Gill Bejerano leads a developmental biology lab at Stanford that investigates the genetic roots of human disease. In 2013, when he realized he needed more genomic data, his lab joined Stanford Hospitals Pediatrics Departmentan arduous process that required extensive vetting and training of all his staff and equipment. This is how most institutions solve the privacy perils of data sharing. They limit who can access all the genomes in their possession to a trusted few, and only share obfuscated summary statistics more widely.

So when Bejerano found himself sitting in on a faculty talk given by Dan Boneh, head of the applied cryptography group at Stanford, he was struck with an idea. He scribbled down a mathematical formula for one of the genetic computations he uses often in his work. Afterward, he approached Boneh and showed it to him. Could you compute these outputs without knowing the inputs? he asked. Sure, said Boneh.

Last week, Bejerano and Boneh published a paper in Science that did just that. Using a cryptographic genome cloaking method, the scientists were able to do things like identify responsible mutations in groups of patients with rare diseases and compare groups of patients at two medical centers to find shared mutations associated with shared symptoms, all while keeping 97 percent of each participants unique genetic information completely hidden. They accomplished this by converting variations in each genome into a linear series of values. That allowed them to conduct any analyses they needed while only revealing genes relevant to that particular investigation.

Just like programs have bugs, people have bugs, says Bejerano. Finding disease-causing genetic traits is a lot like spotting flaws in computer code. You have to compare code that works to code that doesnt. But genetic data is much more sensitive, and people (rightly) worry that it might be used against them by insurers, or even stolen by hackers. If a patient held the cryptographic key to their data, they could get a valuable medical diagnosis while not exposing the rest of their genome to outside threats. You can make rules about not discriminating on the basis of genetics, or you can provide technology where you cant discriminate against people even if you wanted to, says Bejerano. Thats a much stronger statement.

The National Institutes of Health have been working toward such a technology since reidentification researchers first began connecting the dots in anonymous genomics data. In 2010, the agency founded a national center for Integrating Data for Analysis, Anonymization and Sharing housed on the campus of UC San Diego. And since 2015, iDash has been funding annual competitions to develop privacy-preserving genomics protocols. Another promising approach iDash has supported is something called fully homomorphic encryption, which allows users to run any computation they want on totally encrypted data without losing years of computing time.

Kristen Lauter, head of cryptography research at Microsoft, focuses on this form of encryption, and her team has taken home the iDash prize two years running. Critically, the method encodes the data in such a way that scientists dont lose the flexibility to perform medically useful genetic tests. Unlike previous encryption schemes, Lauters tool preserves the underlying mathematical structure of the data. That allows computers to do the math that delivers genetic diagnoses, for example, on totally encrypted data. Scientists get a key to decode the final results, but they never see the source.

This is extra important as more and more genetic data moves off local servers and into the cloud. The NIH lets users download human genomic data from its repositories, and in 2014, the agency started letting people store and analyze that data in private or commercial cloud environments. But under NIHs policy, its the scientists using the datanot the cloud service providerresponsible with ensuring its security. Cloud providers can get hacked, or subpoenaed by law enforcement, something researchers have no control over. That is, unless theres a viable encryption for data stored in the cloud.

If we dont think about it now, in five to 10 years a lot peoples genomic information will be used in ways they did not intend, says Lauter. But encryption is a funny technology to work with, she says. One that requires building trust between researchers and consumers. You can propose any crazy encryption you want and say its secure. Why should anyone believe you?

Thats where federal review comes in. In July, Lauters group, along with researchers from IBM and academic institutions around the world launched a process to standardize homomorphic encryption protocols. The National Institute for Standards and Technology will now begin reviewing draft standards and collecting public comments. If all goes well, genomics researchers and privacy advocates might finally have something they can agree on.

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To Protect Genetic Privacy, Encrypt Your DNA - WIRED

In this photo provided by Oregon Health & Science University, taken through a microscope, human embryos grow in a laboratory for a few days after researchers used gene editing technology to successfully repair a heart disease-causing genetic mutation. The work, a scientific first led by researchers at Oregon Health & Science University, marks a step toward one day preventing babies from inheriting diseases that run in the family.(Oregon Health & Science University via AP)

By Johnny Kung

Mon., Aug. 21, 2017

Recently, an international team of scientists successfully corrected a disease-causing gene in human embryos, using a gene editing technique called CRISPR. This has led to much excitement about the prospects of curing debilitating diseases in entire family lineages.

At the same time, the possibility of changing embryos genes has renewed fear about designer babies. The hype in both directions should be tempered by the fact that both these scenarios are some ways off a lot more work will need to be done to improve the techniques safety and efficacy before it can be applied in the clinic.

And because a lot of diseases, as well as other physical and behavioural characteristics, are controlled by the complex interaction of many genes with each other and with the environment, in many cases simple genetic fixes may never be possible.

But while the technology is still in early stages, now is the time to have frank, open and societywide conversations about how gene editing should be moving forward and genetic medicine more broadly, including the use of advanced genetic testing and sequencing to diagnose disease, personalize medical treatments, screening babies, etc.

We must raise broad awareness of the health benefits as well as the personal, social and ethical implications of genetics. This is important for individuals both to understand their options when making decisions about their own health care, and to participate as informed citizens in democratic deliberations about whether and how genetic technologies should be developed and applied.

In the U.S., affordability and insurance coverage strongly influence access to genetic medicine. In Canada, the reality of strapped budgets means access is far from equal either. But our public health-care system means it is at least conceivable that these technologies will eventually be available to a higher proportion of people who need them.

For example, OHIP currently pays for genetic testing and counselling for a number of diseases, such as http://www.mountsinai.on.ca/care/mkbc/medical-services/genetic-testingBRCA testingEND for breast and ovarian cancer, for patients who satisfy certain eligibility criteria. It also covers a kind of genetic screening tests called non-invasive prenatal testing (NIPT) for eligible pregnant women. Precisely because of this potential for widespread adoption, there is all the greater need for broad-based conversations about genetics.

Crucially, to ensure that the largest possible cross section of society will benefit from, and not be harmed by, advances in genetic technologies, these conversations must include the voices of all communities.

This is especially true for those who, for well-justified historical reasons, may harbour deep distrust of the biomedical establishment. In the U.S., for much of the 20th century, the eugenics movement had resulted in a range of sterilization programs, discriminatory policies and scientific abuses (such as the infamous Tuskegee syphilis trials) that disproportionately targeted the poor and, especially, racial minorities such as African Americans.

While the eugenics movement might have been less established in Canada, where it did occur (e.g., the sterilization program in Alberta or the Indian hospitals in B.C.) it had most heavily affected Indigenous communities. In both countries, this shameful history has led to lower trust and usage of the health-care system by the affected communities.

As genetic medicine advances, many scientists and health researchers are pointing out the importance of having the diversity of human populations represented in genetic studies in order to gain medical insights that can benefit everyone. If we fail to fully engage these under-represented communities and ensure that genetics is not just another way to exploit and discriminate against them, then we risk worsening this historical and ongoing injustice.

New genetic technologies, such as gene editing, also bring issues of disability rights into sharper focus. While designer babies may not be an immediate concern, even the possibility of selecting and changing our offsprings characteristics raises thorny questions.

For example, what conditions count as medically necessarily to treat how about deafness, dwarfism, autism, or intersex conditions? Ultimately, it is about what kinds of people get to live, and who gets to make those decisions. Many disability rights advocates (e.g., the Down syndrome community) are already voicing concerns about what these emerging technologies mean for how their communities are seen and valued today.

We must make sure that the conversations around genetics are not only about generalized notions of safety or effectiveness, or concerns of playing God. These conversations must also encompass questions of access and justice, and acknowledge that the benefits and harms of genetic technologies, like any new technologies, are not distributed equally.

And these conversations must involve all communities (be they of different racial or ethnic background, gender or sexuality, and physical or cognitive abilities) in a way that ensures their voices are respected and heard.

This is a task that will involve concerted efforts from scientists, funders and industry, to build trust with these communities and to genuinely listen and respond to their concerns. And it will need to be done in collaboration with many partners, including schools, community and faith groups, and the art/entertainment industry.

The ability to understand and, perhaps one day, change our genetics has huge potential to improve human well-being. Lets make sure that everyone will enjoy these benefits, and that no communities are left behind, or worse yet, harmed in the process.

Johnny Kung is the director of new initiatives for the Personal Genetics Education Project (www.pged.org ) at Harvard Medical Schools Department of Genetics.

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Designer babies the not most urgent concern of genetic medicine ... - Toronto Star

In 2013, University of Virginia researcher Michael McConnell published research that would forever change how scientists study brain cells.

McConnell and a team of nationwide collaborators discovered a genetic mosaic in the brains neurons, proving that brain cells are not exact replicas of each other, and that each individual neuron contains a slightly different genetic makeup.

McConnell, an assistant professor in the School of Medicines Department of Biochemistry and Molecular Genetics, has been using this new information to investigate how variations in individual neurons impact neuropsychiatric disorders like schizophrenia and epilepsy. With a recent $50,000 grant from the Bow Foundation, McConnell will expand his research to explore the cause of a rare genetic disorder known as GNAO1 so named for the faulty protein-coding gene that is its likely source.

GNAO1 causes seizures, movement disorders and developmental delays. Currently, only 50 people worldwide are known to have the disease. The Bow Foundation seeks to increase awareness so that other probable victims of the disorder can be properly diagnosed and to raise funds for further research and treatment.

UVA Today recently sat down with McConnell to find out more about how GNAO1 fits into his broader research and what his continued work means for all neuropsychiatric disorders.

Q. Can you explain the general goals of your lab?

A. My lab has two general directions. One is brain somatic mosaicism, which is a finding that different neurons in the brain have different genomes from one another. We usually think every cell in a single persons body has the same blueprint for how they develop and what they become. It turns out that blueprint changes a little bit in the neurons from neuron to neuron. So you have slightly different versions of the same blueprint and we want to know what that means.

The second area of our work focuses on a new technology called induced pluripotent stem cells, or iPSCs. The technology permits us to make stem cell from skin cells. We can do this with patients, and use the stem cells to make specific cell types with same genetic mutations that are in the patients. That lets us create and study the persons brain cells in a dish. So now, if that person has a neurological disease, we can in a dish study that persons disease and identify drugs that alter the disease. Its a very personalized medicine approach to that disease.

Q. Does cell-level genomic variety exist in other areas of the body outside the central nervous system?

A. Every cell in your body has mutations of one kind or another, but brain cells are there for your whole life, so the differences have a bigger impact there. A skin cell is gone in a month. An intestinal cell is gone in a week. Any changes in those cells will rarely have an opportunity to cause a problem unless they cause a tumor.

Q. How does your research intersect with the goals of the Bow Foundation?

A. Let me back up to a little bit of history on that. When I got to UVA four years ago, I started talking quite a lot with Howard Goodkin and Mark Beenhakker. Mark is an assistant professor in pharmacology. Howard is a pediatric neurologist and works with children with epilepsy. I had this interest in epilepsy and UVA has a historic and current strength in epilepsy research.

We started talking about how to use iPSCs the technology that we use to study mosaicism to help Howards patients. As we talked about it and I learned more about epilepsy, we quickly realized that there are a substantial number of patients with epilepsy or seizure disorders where we cant do a genetic test to figure out what drug to use on those patients.

Clinical guidance, like Howards expertise, allows him to make a pretty good diagnosis and know what drugs to try first and second and third. But around 30 percent of children that come in with epilepsy never find the drug that works, and theyre in for a lifetime of trial-and-error. We realized that we could use iPSC-derived neurons to test drugs in the dish instead of going through all of the trial-and-error with patients. Thats the bigger project that weve been moving toward.

The Bow Foundation was formed by patient advocates after this rare genetic mutation in GNAO1 was identified. GNAO1 is a subunit of a G protein-coupled receptor; some mutations in this receptor can lead to epilepsy while others lead to movement disorders.

Were still trying to learn about these patients, and the biggest thing the Bow Foundation is doing is trying to address that by creating a patient registry. At the same time, the foundation has provided funds for us to start making and testing iPSCs and launch this approach to personalized medicine for epilepsy.

In the GNAO1 patients, we expect to be able to study their neurons in a dish and understand why they behave differently, why the electrical activity in their brain is different or why they develop differently.

Q. What other more widespread disorders, in addition to schizophrenia and epilepsy, are likely to benefit from your research?

A. Im part of a broader project called the Brain Somatic Mosaicism Network that is conducting research on diseases that span the neuropsychiatric field. Our lab covers schizophrenia, but other nodes within that network are researching autism, bipolar disorder, Tourette syndrome and other psychiatric diseases where the genetic cause is difficult to identify. Thats the underlying theme.

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Researcher Seeks to Unravel the Brain's Genetic Tapestry to Tackle Rare Disorder - University of Virginia

Mathematics professor Qiuying Sha studies statistical genetics and is ready to do health by the numbers.

Sha is the new Portage Health Foundation Endowed Professor of Population Health. In her new role, she wants to make sure people arent treated as numbers in a systemrather number crunching should work in favor of peoples individual health.

You can tell the person from the data, Sha says. Im a statistician, so when I apply for funding or pursue research its always with dataand in this new role, Ill be able to help on data analysis-tell what the data says and find any patterns from the data.

Specifically, Sha plans to develop statistical models for personalized medicinea practice where lots of genetic data, family information, and medical history inform recommendations for an individual persons medical treatment. Her work could also be applied to genetic screenings to help catch early signs of diseases and assist with preventative care.

Sha is joining health care specialists, inventors, movers and shakers to push for better health science in the Upper Peninsula through a $2.5 million grant from the Portage Health Foundation. Michigan Tech will match and exceed the grant, bringing the total to more than $6 million; the funds will support two other endowed professors focusing on health tech and community health. The five-year grant also makes scholarships available to undergraduate students, helps support graduate student positions and funds research to improve health infrastructure and economic growth in Keweenaw, Houghton, Baraga and Gogebic counties.

For Sha, she sees this as an opportunity to give back to her community.

I moved here in 2001so Ive been living here for 16 yearsand Im happy to help make the community better, its really exciting, she says. Im eager to work with local people and to see what I can do to help our community, to make the community better.

Specifically, Sha works in a field called genetic epidemiology. That means she applies statistical methods to genetic data to identify the genes responsible for a particular disease. She analyzes DNA sequences from the whole genome. Her work gets nitty-gritty: she looks at the building blocks of DNAnucleotidesand variations that occur at key locations in the genome. These are called single nucleotide polymorphisms (SNPpronounced like snip) and there are close to 10 million SNPs in the human genome.

So, we say, okay, lets find which genes are associated with a disease, Sha explains, adding that she targets the locations of causal SNPs in her analyses because they may indicate an increased risk of a disease. But thats a challenge because our data, all those SNPs, become a very large dataset.

Once all the dataset is wrangled, though, Sha is able to study the risk for individuals and the prevalence of diseases in a given population. She has applied statistical genetic analyses to hypertension, type II diabetes, and neurodegenerative diseases like Alzheimers and ALS.

"We live in the age of 'big data', and Sha's research can help us better understand if certain genetic and/or environmental factors are contributing to chronic diseases in our area," says Jason Carter, who is the lead researcher on the Portage Health Foundation grant and the Chair of the Department of Kinesiology and Integrative Physiology at Michigan Tech. "People ask me all the timedo we have a higher incidence of cancer in our area, and if so, why? These are the types of questions Sha can help us address, which will allow us to provide better and more targeted care and preventative interventions for our community."

Kevin Store, the executive director of the Portage Health Foundation, says Sha's background in statistical genetics research will bring a different perspective to projects.

By digging deeper into the numbers, Sha can help personalize medicine. The first step is decrypting the genetic code of diseases and their triggers.

Michigan Technological University is a public research university, home to more than 7,000 students from 60 countries around the world. Founded in 1885, the University offers more than 120 undergraduate and graduate degree programs in science, engineering and technology; forestry; business and economics; health professions; humanities; mathematics; and social sciences.

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Portage Health Foundation Endowed Professor Brings Big Data to Rural Medicine - Michigan Tech News (press release)

More than 1 million American women who have had breast or ovarian cancer are not getting a simple genetic test that will determine whether they carry a mutation that puts them at higher risk of a recurrence, according to a UCLA study published Friday.

Up to 10 percent of women who have, or have had, breast cancer, and up to 15 percent of those with a history of ovarian cancer, carry inheritable mutations that put them at higher risk of the cancer returning, says the study, which was published Friday in the Journal of Clinical Oncology.

The test to detect the mutations involves taking blood or saliva, but the study found that 70 percent of eligible breast cancer patients and 80 percent of patients with ovarian cancer have never taken the initial step of discussing testing with their health care provider.

"We want to figure out who are the women in this country that have those genetic changes," says lead author Dr. Christopher Childers, a resident physician at UCLA's David Geffen School of Medicine. That information, he says, can inform decisions about their treatment and surgery. It can also help family members detect cancer early and make lifestyle changes to try to prevent the disease.

National Cancer Center Network guidelines recommend genetic testing for women in these categories:

The study, based on surveys of more than 47,000 women nationwide, asked whether women were discussing the test or had taken it. It did not assess why patients aren't discussing or undergoing testing, but Childers says both providers and patients must play a role in closing the gap. He says all providers should ask women about their cancer history, inquire about prior genetic testing and be aware of the latest testing guidelines.

"Genetic testing is not just something that is under the care of an oncologist, it's something that all health care providers, from surgeons to primary care doctors to cardiologists, should be thinking about when we see patients with a history of cancer," he says.

Patients with a history of breast or ovarian cancer should see their doctors and inquire about genetic testing, even if they were diagnosed many years earlier, says Childers. The mutations detected by the test can affect the BRCA1 and BRCA2 genes. Tests for the mutations have been around since the mid-1990s, but science, testing guidelines and test availability have evolved since then.

"It's not something that you can just assume was taken care of when you had the diagnosis five or 10 years ago," he says. "This is something that is as important 10 years, 20 years, 30 years after your cancer, because it can not only affect your own health, but can also affect the health of your family members."

From her experience as a genetic counselor at Providence Health & Services Southern California, study co-author Kimberly Childers says some patients want to know the potential risks for themselves and their family so they can take steps to prevent future cancers, while others say ignorance is bliss.

Those patients typically say, "I'd rather just see what happens and not worry about it, and if something happens, I'll deal with it when it happens," says Childers, who is married to the study's lead author. She notes that testing might not be right for these people.

On the flip side, Kimberly Childers also sees women who have breast cancer in their history, but learn through testing that they didnt inherit the gene mutation.

"While our focus is on identifying those at risk who can benefit from early prevention and detection, it also can help give people peace of mind who might be living with a cancer cloud," she says.

The genetic test is covered by Medicare, Medi-Cal and most private insurance plans, says Kimberly Childers.

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Many breast, ovarian cancer survivors should take this genetic test - 89.3 KPCC

Ross Pomeroy | August 18, 2017 | Real Clear Science

Chiropractic, homeopathy, acupuncture, juice diets, and other forms of unproven alternative medicine cannot cure cancer, no matter what some quacks might claim.

[A]s a newstudypublished in theJournal of the National Cancer Institutemakes painfully clear, as a treatment for cancer, alternative medicine does not cure; it kills.

A team of scientists from Yale University perused theNational Cancer Database, a collection of 34 million records of cancer patients along with their treatments and outcomes, to identify patients who elected to forgo conventional cancer treatments like chemotherapy, radiotherapy, and surgery in favor of alternative medicine.

After five years, 78.3% of subjects who received conventional treatments were still alive, compared to only 54.7% of subjects who used alternative medicine. Even more startling, breast cancer patients who used alternative medicine were five times more likely to die. Colorectal cancer patients were four times more likely to die. Lung cancer patients were twice as likely to die.

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:Alternative Medicine Kills Cancer Patients, Study Finds

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Alternative medicine can kill you - Genetic Literacy Project