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April 19, 2017 by Elana Fertig, The Conversation A tumor under the microscope. Credit: cnicholsonpath/flickr, CC BY

Two years ago, former President Barack Obama announced the Precision Medicine initiative in his State of the Union Address. The initiative aspired to a "new era of medicine" where disease treatments could be specifically tailored to each patient's genetic code.

This resonated soundly in cancer medicine. Patients can already manage their cancer with therapies that target the specific genes that are altered in their particular tumor. For example, women with a type of breast cancer caused by the amplification of gene HER2 are often treated with a therapeutic called herceptin. Because these targeted therapeutics are specific to cancer cells, they tend to have fewer side effects than traditional cancer treatments with chemotherapy or radiation.

However, such treatments are not available for most cancer patients. In many cancers, the specific genetic alterations that are responsible for a cancer remain unknown. To create individualized cancer treatments, we must know more about the functional genetic alterations.

With data on cancer genetics growing rapidly, mathematics and statistics can now help unlock the hidden patterns in this data to find the genes that are responsible for an individual's cancer. With this knowledge, physicians can select appropriate treatments that block the action of these genes to personalize therapies for individual patients. My research aims to improve precision medicine in cancer by building on the same methods that have been used to find patterns in Netflix movie ratings.

Sifting through the data

Today, there is unprecedented public access to cancer genetics data. These data come from generous patients who donate their tumor samples for research. Scientists then apply sequencing technologies to measure the mutations and activity in each of the 20,000 genes in the human genome.

All these data are a direct result of the Human Genome Project in 2003. That project determined the sequence for all the genes that make up healthy human DNA. Since the completion of that project, the cost of sequencing the human genome has more than halved every year, surpassing the growth of computing power described in Moore's Law. This cost reduction enables researches to collect unprecedented genetics data from cancer patients.

Most scientific studies on cancer genetics performed worldwide release their data to a centralized, public database provided by the U.S. National Institutes of Health (NIH) National Library of Medicine. The NIH National Cancer Institute and National Human Genome Research Institute have also freely released genetic data from over 11,000 tumors in 33 cancer types through a project called The Cancer Genome Atlas.

Every biological function from extracting energy from food to healing a wound results from activity in different combinations of genes. Cancers hijack the genes that enable people to grow to adulthood and that protect the body from the immune system. Researchers dub these the "hallmarks of cancer." This so-called gene dysregulation enables a tumor to grow uncontrollably and form metastases in distant organs from the original tumor site.

Researchers are actively using these public data to find the set of gene alterations that are responsible for each tumor type. But this problem is not as simple is identifying a single dysregulated gene in each tumor. Hundreds, if not thousands, of the 20,000 genes in the human genome are dysregulated in cancer. The group of dysregulated genes varies in each patient's tumor, with smaller sets of commonly reused genes enabling each cancer hallmark.

Precision medicine relies on finding the smaller groups of dysregulated genes that are responsible for biological function in each patient's tumor. But, genes may have multiple biological functions in different contexts. Therefore, researchers must uncover a set of "overlapping" genes that have common functions in a set of cancer patients.

Linking gene status to function requires complex mathematicsand immense computing power. This knowledge is essential to predict of outcome to therapies that would block the function of these genes. So, how can we uncover those overlapping features to predict individual outcomes for patients?

What Netflix can teach us

Fortunately for us, this problem has already been solved in computer science. The answer is a class of techniques called "matrix factorization" and you've likely already interacted with these techniques in your everyday life.

In 2009, Netflix held a challenge to personalize movie ratings for each Netflix user. On Netflix, each user has a distinct set of ratings of different movies. While two users may have similar tastes in movies, they may vary wildly in specific genres. Therefore, you cannot rely on comparing ratings from similar users.

Instead, a matrix factorization algorithm finds movies with similar ratings among a smaller group of users. The group of users will vary for each movie. The computer associates each user with a group of movies to a different extent, based upon their individual tastes. The relationships among users are referred to as "patterns." These patterns are learned from the data, and may find common rankings unforeseen by movie genre alone for example, users may share a preference for a particular director or actor.

The same process can work in cancer. In this case, the measurements of gene dysregulation are analogous to movie ratings, movie genres to biological function and users to patients' tumors. The computer searches across patient tumors to find patterns in gene dysregulation that cause the malignant biological function in each tumor.

From movies to tumors

The analogy between movie ratings and cancer genetics breaks down in the details. Unless they are minors, Netflix users are not constrained in the movies they watch. But, our bodies instead prefer to minimize the number of genes used for any single function. There are also substantial redundancies between genes. To protect a cell, one gene may easily substitute for another to serve a common function. Gene functions in cancer are even more complex. Tumors are also highly complex and rapidly evolving, depending upon random interactions between the cancer cells and the adjacent healthy organ.

To account for these complexities, we have developed a matrix factorization approach called Coordinated Gene Activity in Pattern Sets or CoGAPS for short. Our algorithm accounts for biology's minimalism by incorporating as few genes as possible into the patterns for each tumor.

Different genes can also substitute for one another, each serving a similar function in a different context. To account for this, CoGAPS simultaneously estimates a statistic for the so-called "patterns" of gene function. This allows us to compute the probability of each gene being used in each biological function in a tumor.

For example, many patients take a targeted therapeutic called cetuximab to prolong survival in colorectal, pancreatic, lung and oral cancers. Our recent work found that these patterns can distinguish gene function in cancer cells that respond to the targeted therapeutic agent cetuximab from those that do not.

The future

Unfortunately, cancer therapies that target genes usually cannot cure a patient's disease. They can only delay progression for a few years. Most patients then relapse, with tumors that are no longer responsive to the treatment.

Our own recent work found that the patterns that distinguish gene function in cells that are responsive to cetuximab include the very genes that give rise to resistance. Emerging immunotherapies are promising and appear to cure some cancers. Yet, far too often, patients with these treatments also relapse. New data that track the cancer genetics after treatment is essential to determine why patients no longer respond.

Along with these data, cancer biology also requires a new generation of scientists who can bridge mathematics and statistics to determine the genetic changes occurring over time in drug resistance. In other fields of mathematics, computer programs are able to forecast long-term outcomes. These models are used commonly in weather prediction and investment strategies.

In these fields and my own previous research, we have found that updates to the models from large datasets such as satellite data in the case of weather improve long-term forecasts. We have all seen the effect of these updates, with weather predictions improving the closer that we are to a storm.

Just as tools from computer science used can be adapted to both movie recommendations and cancer, the future generation of computational scientists will adopt prediction tools from an array of fields for precision medicine. Ultimately, with these computational tools, we hope to predict tumors' response to therapy as commonly as we predict the weather, and perhaps more reliably.

Explore further: Study finds recurrent changes in DNA activate genes, promote tumor growth

This article was originally published on The Conversation. Read the original article.

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What Netflix can teach us about treating cancer - Medical Xpress

ALISO VIEJO, Calif.--(BUSINESS WIRE)--

Ambry Genetics Corporation (Ambry) is calling on psychiatrists, psychologists and behavioral specialists to encourage their patients with autism, along with their family members, to sign up for a new study conducted through Ambrys data sharing program, AmbryShare. With this program, Ambry is taking a step towards discovering possible associations between genes and autism, so clinicians can provide their patients with targeted treatments and therapies much earlier in life.

Whats unique about AmbryShares approach is that we collect genetic information from clinics and families from all over the world to answer questions that cant be answered with just a handful of patients, said Brigette Tippin Davis, PhD, Ambrys Director of Emerging Genetic Medicine. The great thing about Ambry partnerships is that we are building connections between research institutions and empowering them to develop new approaches to treating patients with autism based on genetic profiles.

So far, dozens of behavioral clinics and other medical offices have contributed to AmbryShare studies by encouraging participation from their patients. Ambry strives to enroll more than 10,000 patients from clinics nationally and internationally.

Genetic testing would allow us to personalize treatment from a genetic profile and optimize it together with our rich behavioral data, said Dennis Dixon, PhD, Chief Strategy Officer at Center for Autism and Related Disorders (CARD). I really value working with Ambry, knowing this data will have an impact on treatment for our patients and then will still be available for other researchers to access to answer additional research questions. As we each put more samples in, it increases the overall likelihood that were going to find something that really makes a difference.

One in 64 children in the United States is diagnosed with an autism spectrum disorder (ASD), which can impact social interaction, communication and behavior. Genetic testing can help identify an underlying cause in up to 40% of autism spectrum disorders. Some genetic causes include chromosome microdeletions/microduplications, fragile X syndrome, Angelman syndrome, and tuberous sclerosis. New gene discovery can allow clinicians to determine their patients course of treatment and the gene-disease relationship associated with their individual case of autism. Through the recruitment of a massive cohort, more data will be collected to discover more genes, develop medical management plans and enact preventive strategies.

The scientists need the data to be out there, said Charles Dunlop, Ambrys President and Chairman. We need to know what these diseases are actually doing, what causes them, what gene mutations are associated with them so we can move forward as an industry and move onto the next phase where there is no disease of any kind. A phase where pharmaceutical researchers know exactly what to do, or exactly what problems theyre trying to solve at a minutiae levelthats when the cures come.

In 2016, Mayo Clinic and University of Utah collaborated with Ambry on a new research study of more than 60,000 patients to help refine breast cancer risk estimates from predisposition genes that are either previously lacking data or have limited data. The study, Breast cancer risks associated with mutations in cancer predisposition genes identified by clinical genetic testing of 60,000 breast cancer patients represented the largest genetic study of women with hereditary breast cancer. The large amount of data was able to provide researchers with new information about genes that contributed to breast cancer risk. Ambry wants to provide researchers with the same capabilities for autism.

Since 2001, Ambry has been dedicated to scientific research to help empower the scientific community and refine clinician management guidelines so patients may receive tailored medical management. AmbryShares initial launch in 2016 provided scientific researchers and clinicians with the largest open, de-identified database of hereditary breast and ovarian cancer cohorts with the goal of achieving a greater understanding of human disease.

For more information and to enroll in the AmbryShare autism study, visit the AmbryShare portal here.

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ABOUT AMBRY GENETICS

Ambry Genetics is both College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified. Ambry leads in clinical genetic diagnostics and genetics software solutions, combining both to offer the most comprehensive testing menu in the industry. Ambry has established a reputation for sharing data while safeguarding patient privacy, unparalleled service, and responsibly applying new technologies to the clinical molecular diagnostics market. For more information about Ambry Genetics, visit http://www.ambrygen.com.

About the Center for Autism and Related Disorders (CARD)

CARD treats individuals of all ages who are diagnosed with autism spectrum disorder (ASD) at treatment centers around the globe. CARD was founded in 1990 by leading autism expert and clinical psychologist Doreen Granpeesheh, PhD, BCBA-D. CARD treats individuals with ASD using the principles of applied behavior analysis (ABA), which is empirically proven to be the most effective method for treating individuals with ASD and recommended by the American Academy of Pediatrics and the US Surgeon General. CARD employs a dedicated team of over 3,000 individuals across the nation and internationally.

For more information, visit http://www.centerforautism.com or call (855) 345-2273.

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Ambry Genetics Recruits Patient Cohorts to Discover New Links between Genes and Autism - Yahoo Finance

LOS ANGELES--(BUSINESS WIRE)--

EpicGenetics, a privately held biomedical company dedicated to improving the diagnosis and treatment of fibromyalgia, today announced that it has engaged the University of California, Los Angeles (UCLA)* and the University of Illinois College of Medicine Chicago (UIC). Both university research centers will be sequencing the exomes of patients to improve the diagnosis of fibromyalgia through the application of the FM/a Test and to allow EpicGenetics to detect fibromyalgia disease-specific gene markers. Additionally, Bruce Gillis, M.D., CEO of EpicGenetics, has made a research gift to the Immunobiology Laboratory at the Massachusetts General Hospital directed by Denise Faustman, M.D., Ph.D., to continue its robust clinical research regarding a direct treatment for fibromyalgia.

The FM/a Test is an FDA-compliant blood test that diagnoses fibromyalgia by identifying the presence of specific white blood cell abnormalities that have been documented to exist in these patients. The FM/a Test accurately and objectively diagnoses this chronic disorder that afflicts millions of men, women and children.

EpicGenetics will offer whole exome genetic surveys to FM/a test-positive patients in a search for fibromyalgia-specific gene markers and mutations, analogous to the BRCA1/BRCA2 model for breast cancer. EpicGenetics associated CAMPAIGN 250 seeks to accomplish these gene surveys in up to 250,000 FM/a test-positive individuals. The fees for these genomic surveys will be paid by EpicGenetics.

There has been very little innovation over the past several decades to help patients better understand and manage their fibromyalgia, said Frederick G. Behm, M.D., the Frances B. Geever Professor and head of pathology at the University of Illinois College of Medicine Chicago. Patients with this disorder frequently experience pain and fatigue that prohibits them from being able to engage in their daily lives. These patients are seeking answers to basic questions about the cause and etiology of the disorder and, as physicians, we are frustrated that our previously limited research in this field prevents us from being able to answer these questions.

Since becoming available in 2012, the FM/a Test has successfully and objectively diagnosed patients with fibromyalgia in the U.S. and multiple other countries, thereby providing these patients with a definitive diagnosis and certainty about a medical condition that has often been misunderstood and erroneously denied as a legitimate medical disorder, said Bruce Gillis, M.D., CEO of EpicGenetics. I believe we are at the forefront of advancing scientific information about fibromyalgia and answering these critical questions for patients: 1) Do I have fibromyalgia? 2) How and why did I develop fibromyalgia? and 3) Is there a direct treatment for fibromyalgia?

Denise Faustman, M.D., Ph.D., director of the Immunobiology Laboratory at the Massachusetts General Hospital and a noted immunologist at the Harvard Medical School, will initiate plans for a clinical trial at the Massachusetts General Hospital to test the potential of the Bacillus Calmette-Gurin(BCG) vaccine to change the biology of fibromyalgia.

FM/a test-positive patients will be offered an opportunity to participate in this vaccine trial once the study protocols have received the required institutional and regulatory approvals.

As Dr. Faustman explains, The Massachusetts General Hospital is announcing a new research effort on the application of the BCG vaccine, which will be directed at changing the biology of fibromyalgia as it concerns the foundational immune system discovery of the roleparticular cytokines have in fibromyalgia.

The FM/a Test will consequently not only serve to objectively confirm the diagnosis of fibromyalgia, but also act as the gateway for fibromyalgia patients through these newly announced research efforts to participate in genetic studies to further define their disease.

The cost of the FM/a Test is covered by most insurance companies and Medicare.

Once diagnosed by the FM/a Test, EpicGenetics will cover patients direct laboratory costs for the genetic surveys and for further research on their disease. Patients who are suspected of having fibromyalgia need a licensed health care practitioner to authorize their FM/a Test.

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To learn more about the FM/a Test and these clinical studies, including details on participation, please visit http://www.FMTest.com or http://www.facebook.com/TheFMTest.

About Fibromyalgia

Fibromyalgia is a chronic disorder marked by a variety of symptoms that can include chronic diffuse pain, fatigue, sleep disturbances, muscle tenderness, headaches and depression, as well as problems with thinking and memory function. This disorder is known to impact an estimated 6 percent of the population,1 and it isnt age, gender or ethnic specific. However, due to a previous lack of diagnostic tools and a common denial of the legitimate existence of fibromyalgia, many believe that this number may in fact be much larger.2

Current treatment options for fibromyalgia are limited, offer only indirect and symptom-limited approaches, and primarily include anticonvulsants, opioids and antidepressants which help only some patients manage the disorders symptoms, though they do not treat the cause. Further, several of these treatments carry Black Box Warnings regarding their potentially dangerous side effects.

About The FM/aTest

The FM/a Test is the first FDA-compliant, objective blood test to diagnose fibromyalgia. It is a multi-biomarker-based test that analyzes immune system white blood cell production of critical chemokine and cytokine/protein patterns. These proteins demonstrate an abnormal pattern in fibromyalgia patients which the FM/a Test can identify so it will correctly and objectively diagnose this medical illness. Results of the FM/a Test are based upon a 1-100 scoring system, with fibromyalgia patients having scores higher than 50. The test has been clinically validated to diagnose fibromyalgia with a 93 percent sensitivity.

The FM/a Test is a result of research and clinical studies that were performed at the University of Illinois College of Medicine Chicago. It has been recognized by the American Association for Clinical Chemistry (AACC) for Outstanding Research in Clinical and Diagnostic Immunology. Peer-reviewed published medical studies have served as the basis of the FM/a Test, based upon the testing of hundreds of patients.

The FM/a Test is a Laboratory-Developed Test (LDT) that was developed and is performed in a CLIA certified and CAP accredited laboratory. The test fulfills the FDA regulation (21CFR 866.5700) for an immunological test system.

About EpicGenetics

EpicGenetics, Inc. is a privately held biomedical company based in Los Angeles, California, that developed and manufactures the FM/a Test. EpicGenetics is dedicated to improving the diagnosis and treatment of fibromyalgia by offering the first conclusive diagnostic test for fibromyalgia, and by investing in and developing further comprehensive clinical studies at leading medical research centers. More information is available at http://www.FMTest.com.

*UCLA has been engaged to sequence the exomes of research subjects.

i About Fibromyalgia: Prevalence. National Fibromyalgia & Chronic Pain Association. http://www.fmcpaware.org/fibromyalgia/prevalence.html. ii Arnold LM, Clauw DJ, McCarberg BH, and FibroCollaborative. Improving the recognition and diagnosis of fibromyalgia. Mayo Clin Proc. 2011;86(5):457-464.

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EpicGenetics, with the Assistance of Leading Medical Centers, Expands Clinical Study of FM/a Test to Diagnose ... - Yahoo Finance

Theres no question that there are a considerable amount of sleep-deprived people out there. According to the Centers for Disease Control and Prevention, more than a third of Americans fall short of achieving the recommended seven-plus hours of sleep per night. Additionally, nearly 20 percent of Americans fall into the night owl category, meaning their internal clocks are out of sync with societys external ones, according to an article in The Wall Street Journal.

Now a newly published study by Rockefeller University researchers says some peoples clocks could be off because of a variant in their CRY1 gene, which slows the internal clock that determines when you feel sleepy. In other words, people with this gene variant have longer circadian cycles, which means that when its time to hit the hay, they may not be ready yet.

Carriers of the mutation have longer days than the planet gives them, so they are essentially playing catch-up for their entire lives, said Alina Patke,lead author of the study and a research associate in the Laboratory of Genetics at The Rockefeller University, in a statement.

The problem with being a night owl, the Wall Street Journal article explains, is that society is hard on evening types. These people go to bed later, yet many still wake early to meet societys expectationssuch as arriving at work on time. This leads to continuous sleep deprivation, which is associated with a higher risk of diabetes, obesity, cardiovascular issues, and other diseases, as well as poor mental health, impaired immunity, and a higher risk of death.

Of the approximately 10 percent of people who experience delayed sleep phase disorder (DSPD), not all have the CRY1 mutation. Other cues such as artificial lightthink smartphone screens in bedare also known to greatly disrupt a persons biological clock.

However, researchers think understanding at least one genetic mutation behind the disorder can lead to the exploration of new treatments.

Understanding how the rhythms are controlled opens the door to eventually manipulating them with drugs, Patke told LiveScience.

The implications of treatment move beyond just helping those with DSPD. Pakte explained to LiveScience that if medicine finds a way to reset night owls sleep patterns, similar treatment options could potentially be used to assist people with jet lag after traveling.

That said, night owls curious if they have the gene mutation will have to wait. No approved medical test for the variation is available yet.

In the meantime, research suggests maintaining a healthy sleep schedule by keeping consistent bed and wake times, avoiding artificial light an hour before going to bed, and exposing yourself to the sun first thing in the morning.

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Is Being a Night Owl Genetic? New Study Says It Might Be - Associations Now