Expansion of data in the GDC - National Cancer Institute

Expansion of data in the GDC - National Cancer Institute

Significant expansion of data available in the Genomic Data Commons

06/29/2016

The recently launched Genomic Data Commons will get a dramatic increase in the power and utility of its resources with the signing today of a data sharing agreement between the NCI and Foundation Medicine, Inc. (FMI), a molecular information company.

Significant expansion of data available in the Genomic Data Commons

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• Posted: June 29, 2016

Contact: 

NCI Press Office

301-496-6641

The recently launched Genomic Data Commons (GDC) will get a dramatic increase in the power and utility of its resources with the announcement today of the signing of a data sharing agreement between the National Cancer Institute (NCI) and Foundation Medicine, Inc. (FMI), a molecular information company that has generated genomic profiles of people with cancer. NCI’s GDC is a unified data system that promotes the sharing of genomic and clinical data among researchers and is a core component of the Cancer Moonshot and the President’s Precision Medicine Initiative. NCI is part of the National Institutes of Health.

The expanded number of cancer cases in the GDC will allow researchers to identify genomic changes that are responsible for the cancerous growth of tumors in individual patients, and identify which drugs may block the effects of these mutations.  Such targeted drugs can produce remissions in certain patients.

When the GDC was launched earlier this month, it was able to immediately capitalize on the genomic data that existed in several large-scale NCI programs, such as The Cancer Genome Atlas (TCGA) and its pediatric equivalent, Therapeutically Applicable Research to Generate Effective Treatments (TARGET). Together, TCGA and TARGET represent some of the largest and most comprehensive cancer genomic datasets in the world, with information generated from about 14,500 patients. 

The addition of data from 18,000 adult patients with a diverse array of cancers that underwent genomic profiling using FMI’s proprietary comprehensive genomic profiling assay, called FoundationOne (trademark registered), will provide a major boost to the GDC.  FMI developed FoundationOne as a commercially available test that uses advanced sequencing technology to routinely analyze cancer specimens.

“This major infusion of data in the GDC will greatly enhance our ability to use this tool to explore genetic abnormalities in cancer,” said Douglas Lowy, M.D., NCI Acting Director. “Through TCGA and TARGET, we had already established a strong cancer genomic foundation for the GDC at its launch, but with the addition of the genomic data from FMI, we believe that the GDC will be an even more useful resource for researchers worldwide to help us unravel the complexities of many forms of cancer.”

Importantly, in both the NCI and the Foundation Medicine databases, all patient information has been de-identified, meaning that personal information, such as addresses, Social Security numbers, and other possible identifiers, are not present — only crucial genetic data and key demographic information are available.

“We’re honored to participate in this important global effort to transform patient care and to be the first commercial entity to contribute data to the NCI’s GDC, which we believe underscores the quality, integrity and richness of the genomics information contained in Foundation Medicine databases,” said Vincent Miller, M.D., chief medical officer, Foundation Medicine. “The amount of genomics information within Foundation Medicine databases has reached unparalleled scale. The insights gleaned from this data release will be instrumental in accelerating research and development efforts for targeted agents and immunotherapies.”

The genomics information contributed by Foundation Medicine can be used by authorized researchers following approval by an NIH Data Access Committee.  Requesters must affirm that their use of the data is solely for biomedical research purposes and for publication or presentation in scientific journals or at research meetings.

The National Cancer Institute leads the National Cancer Program and the NIH’s efforts to dramatically reduce the prevalence of cancer and improve the lives of cancer patients and their families, through research into prevention and cancer biology, the development of new interventions, and the training and mentoring of new researchers. For more information about cancer, please visit the NCI website at http://www.cancer.gov or call NCI's Cancer Information Service at 1-800-4-CANCER.

About the National Institutes of Health (NIH): NIH, the nation's medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.

NETSPOT: New Drug Trials Snapshot Posted

A new DRUG TRIALS SNAPSHOT FOR NETSPOT is now available.

NETSPOT is a drug for detection of a specific type of tumors called somatostatin receptor positive neuro-endocrine tumors (NETs).

NETs are rare tumors that develop in certain hormone-producing cells of the body’s neuro-endocrine system.

Drug Trials Snapshots provide information about who participated in clinical trials that supported the FDA approval of new drugs. The information provided in these Snapshots also highlights whether there were any differences in the benefits and side effects among sex, race and age groups.

See more Drug Trial Snapshots or contact us with questions at Snapshots@fda.hhs.gov.

Clinical Pharmacology Corner: FDA Determines MCP-Mod is Fit-for-Purpose

FDA Determines Multiple Comparison Procedure-Modeling (MCP-Mod) Statistical Approach is Fit-for-Purpose

On May 26, 2016, FDA determined that the Multiple Comparison Procedure – Modeling (MCP-Mod) statistical approach is fit-for-purpose . Fit-for-purpose designation provides a pathway for FDA to assess and comment on the utility of drug development tools. Such tools are made publicly available in an effort to facilitate appropriate utilization in drug development.

Dose selection for phase 3 trials is a critical component in drug development that should be based on the dose (concentration) response relationship obtained from earlier studies (phase 1 and phase 2). MCP-Mod is a hybrid approach that combines hypothesis testing and modeling to analyze phase 2 dose-ranging studies with the purpose of finding suitable dose(s) for confirmatory phase 3 trials. The first step of the procedure (MCP-step) is used to assess presence of a dose-response signal using a trend test deducted from a set of prespecified candidate models. The second step (Mod-step) relies on parametric modeling or model averaging to find the “optimal” dose for confirmatory trials. The approach facilitates more informative phase 2 trial design by encouraging:

• testing three or more active and well separated doses
• investigating doses on the ascending part of the dose-response curve
• interpolation and extrapolation to select dose(s) for pivotal trial(s)

The MCP-Mod method was jointly evaluated by the Office of Biostatistics and Office of Clinical Pharmacology within CDER’s Office of Translational Sciences. MCP-Mod was assessed based on metrics relevant to the analysis of dose ranging trials. These metrics included type I error rate, power to detect a significant dose-response shape, and the power to find the minimal effective dose. The MCP-Mod method was found adequate and appropriate for dose selection based on dose-response data.

Additional information on MCP-Mod and other drug development tools may be found at http://go.usa.gov/x3jPR. 

We always welcome your thoughts regarding the format, content, and utility of information you receive via this Clinical Pharmacology Corner email initiative. Comments may be sent via email to ocp@fda.hhs.gov.

This burst was prepared by Office of Clinical Pharmacology, Office of Translational Sciences, CDER, FDA.

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FDA/Center for Drug Evaluation and Research (CDER)
Office of Translational Sciences
Office of Clinical Pharmacology
Email: ocp@fda.hhs.gov

NIDCR Science News - June 2016

NIDCR Science News - June 2016

NIDCR Science News for June 2016

• Snapshots of Life: Development in Exquisite Detail
  June 2, 2016 - National Institutes of Health
  
• Bioactive Film Improves How Implants Bond With Bone in Animal Study
  June 15, 2016 - North Carolina State University
  
• HHS Awards $156 million to Health Centers to Expand Oral Health Services
  June 16, 2016 - Department of Health and Human Services
  
• NIH Scientists Decode How Anthrax Toxin Proteins Might Help Treat Cancerous Tumors​June 27, 2016 - National Institutes of Health

Living Well with Osteoarthritis - Harvard Health

Living Well with Osteoarthritis - Harvard Health

Joint pain...is it osteoarthritis?

Image: m-gucci/iStock

Your knee aches from time to time. Or maybe your fingers don't seem as nimble as they used to be. Could it be osteoarthritis?

Osteoarthritis, the most common form of arthritis, develops when cartilage, the flexible tissue lining the joints, deteriorates. As a result, the space between bones gradually narrows and the bone surfaces change shape. Over time, this leads to joint damage and pain.

Get your copy of Living Well with Osteoarthritis


This report focuses primarily on osteoarthritis — the most common type of arthritis — which affects 27 million Americans. Many people believe it’s a crippling and inevitable part of growing old. But things are changing. Treatments are better, and plenty of people age well without much arthritis. If you have osteoarthritis, you can take steps to protect your joints, reduce discomfort, and improve mobility — all of which are detailed in this report. If you don't have osteoarthritis, the report offers strategies for preventing it.

People with osteoarthritis often have it in more than one joint. It is most common in the knee, hip, lower back, and neck, and in certain finger joints. The symptoms of osteoarthritis usually develop over many years, and many of the early symptoms are the same no matter which joint it starts in. The first sign is often pain in a joint after strenuous activity or overusing the joint. The joint may be stiff in the morning, but loosen up after a few minutes of movement. Or the joint may be mildly tender, and movement may cause a crackling or grating sensation. Some people have continual joint pain that interferes with sleep.

But some telltale signs of osteoarthritis are specific to certain joints. If you're experiencing any of the types of joint pain listed below, ask your doctor to check you for osteoarthritis.

• Knees. When osteoarthritis affects the knee, the result is pain, swelling, and stiffness of that joint. What starts out as some discomfort after a period of disuse can progress to difficulty walking, climbing, bathing, and getting in and out of bed.
• Hands. Osteoarthritis of the hand often starts with stiffness and soreness of the fingers and in the base of the thumb, particularly in the morning. You may find that it becomes harder to pinch, and that your joints crackle when moved. People with hand osteoarthritis may have difficulty doing routine movements, like opening a jar, turning a key, or typing.
• Hips and spine. When osteoarthritis affects the hip, pain may be felt in the groin, down the inside thigh, or even as far away as the knee. Osteoarthritis of the cervical spine (in the neck) can cause pain in the shoulders and arms. When it affects the lower spine, pain can spread to the buttocks or legs.

For more on keeping your joints healthy, plus ways to ease the pain caused by osteoarthritis, buy Living Well with Osteoarthritis, a Special Health Report from Harvard Medical School.

4 ways exercise helps arthritis

Image: iStock

Even the healthiest people can find it hard to stick with an exercise regimen — and if you suffer from the joint pain of arthritis, moving your body may be the last thing you want to think about. But regular exercise not only helps maintain joint function, it also relieves stiffness and reduces pain and fatigue.

If you have arthritis, you want to be sure your exercise routine has these goals in mind:

1. A better range of motion (improved joint mobility and flexibility). To increase your range of motion, move a joint as far as it can go and then try to push a little farther. These exercises can be done any time, even when your joints are painful or swollen, as long as you do them gently.
2. Stronger muscles (through resistance training). Fancy equipment isn't needed. You can use your own body weight as resistance to build muscle. For example, this simple exercise can help ease the strain on your knees by strengthening your thigh muscles: Sit in a chair. Now lean forward and stand up by using only your thigh muscles (use your arms for balance only). Stand a moment, then sit back down, using only your thigh muscles.
3. Better endurance Aerobic exercise — such as walking, swimming, and bicycling — strengthens your heart and lungs and thereby increases endurance and overall health. Stick to activities that don't jar your joints, and avoid high-impact activities such as jogging. If you're having a flare-up of symptoms, wait until it subsides before doing endurance exercises.
4. Better balance. There are simple ways to work on balance. For example, stand with your weight on both feet. Then try lifting one foot while you balance on the other foot for 5 seconds. Repeat on the other side. Over time, work your way up to 30 seconds on each foot. Yoga and tai chi are also good for balance.

Arthritis doesn't have to keep you from enjoying life. To learn the latest on new treatments and practical strategies for living well with arthritis, buy Living Well with Osteoarthritis, a Special Health Report from Harvard Medical School.

Living Well with Osteoarthritis

Featured content:

•	When joints cause pain
•	What is osteoarthritis?
•	Diagnosing osteoarthritis
•	Treating osteoarthritis without surgery
•	Surgical treatment of osteoarthritis
•	... and more!

Click here to read more »

Dos & Don'ts for Easy Splinter Removal: MedlinePlus

Dos & Don'ts for Easy Splinter Removal: MedlinePlus

Dos & Don'ts for Easy Splinter Removal

The sooner you take it out, the better, dermatologist says

     

By Randy Dotinga

Monday, June 20, 2016

MONDAY, June 20, 2016 (HealthDay News) -- Along with the hot days of summer will come a perennial hazard of outdoor living: splinters.

Fortunately, dermatologists say splinters are usually easy to remove so you or your child can move on to more pleasant activities.

"Splinters come in all shapes and sizes, and they can really hurt," said Dr. Robert Sidbury, division chief of dermatology at the University of Washington School of Medicine in Seattle.

"To reduce pain and the possibility of an infection, splinters should be removed as quickly as possible," he added in a news release from the American Academy of Dermatology.

Sidbury provided the following tips for safe and easy splinter removal:

• With soap and water, gently wash and dry the area where the splinter has entered the skin.
• Use a magnifying glass if the splinter is very small. Look to see its size and the direction it entered the skin.
• To remove the splinter, use tweezers to grab on to the part sticking out of the skin. But first sterilize the tip of the tweezers with rubbing alcohol.
• Don't risk splitting the splinter into parts by trying to squeeze it out.
• If the entire splinter is under the skin, you may need a small needle to remove it. Sterilize the needle with rubbing alcohol and pierce the skin surface at one end of the splinter. (Use a magnifying glass, and ask for help, if necessary). Then, use the sterilized tweezers to pull the splinter out once it comes up out of the skin.
• Finally, clean the skin area with soap and water and apply petroleum jelly and a bandage.

"Most splinters can be safely removed at home, but some may require medical assistance," Sidbury said. "See your doctor or a board-certified dermatologist if your splinter is very large, deep, located in or near your eye or if the area becomes infected."

SOURCE: News release, American Academy of Dermatology

HealthDay

Copyright (c) 2016 HealthDay. All rights reserved.

News stories are provided by HealthDay and do not reflect the views of MedlinePlus, the National Library of Medicine, the National Institutes of Health, the U.S. Department of Health and Human Services, or federal policy.

Zika Can Also Strike Eyes of Adults: Report: MedlinePlus

Zika Can Also Strike Eyes of Adults: Report: MedlinePlus

Zika Can Also Strike Eyes of Adults: Report

Case of man with potentially severe condition suggests virus can damage vision in more than babies

     

Wednesday, June 22, 2016

WEDNESDAY, June 22, 2016 (HealthDay News) -- Doctors in Brazil report that a man infected with Zika developed a potentially severe eye condition, in another sign that the dreaded virus can harm vision in both babies and adults.

"Zika patients should report every single symptom to their doctors, especially if they present with any kind of eye symptoms," said report co-author Dr. Benedito Antonio Lopes da Fonseca, an associate professor at the University of Sao Paulo.

The patient, who was in his early 40s, recovered from the condition called uveitis, a kind of inflammation in the eye. But the condition can lead to cataracts and high blood pressure in the eye, said report lead author Dr. Joao Furtado, an infectious disease specialist and professor at the University of Sao Paulo.

The mosquito-borne Zika virus has struck countries around the world, and travelers have brought it to the U.S. mainland. The American territory of Puerto Rico is facing an especially high risk, potentially placing hundreds of pregnant women in jeopardy of delivering babies with debilitating birth defects.

But no nation has been more affected than Brazil. As a result of the Zika epidemic there, almost 5,000 babies have been born with a devastating birth defect known as microcephaly after their mothers were infected with Zika early in pregnancy.

The virus is typically mild in adults, according to the U.S. Centers for Disease Control and Prevention. The most frequent symptoms are fever, rash, joint pain, and red eyes, possibly caused by conjunctivitis.

In addition to the cases of conjunctivitis, many children born with microcephaly are also blind, Fonseca added. But until now, only conjunctivitis has been seen in adults with Zika virus, Furtado noted.

The new case, reported in the June 22 issue of The New England Journal of Medicine, describes a man who was infected with Zika and developed uveitis. Based on tests and observation of the patient, it's clear that Zika was the cause of the condition, Fonseca said.

"We cured this patient," Fonseca said, and he hasn't had any further eye problems.

Will other Zika patients with this kind of eye problem have a similar good prognosis?

"These are questions to be answered with time. Zika is a new disease, and many aspects of it are still unclear," Fonseca said. However, he said, patients seen by his team have done well so far after treatment.

People with the condition can be treated in a variety of ways, such as drops to the eye, injections of medications in or around the eyes, and medications taken by mouth, via injection or intravenously, said Dr. Debra Goldstein, director of the Uveitis Fellowship Program at Northwestern University Feinberg School of Medicine, in Chicago. Mild cases like this one tend to have a good prognosis, she said.

Both Fonseca and Furtado believe that Zika may cause eye problems -- both conjunctivitis and the more severe uveitis -- because the virus affects the central nervous system. The eye is closely linked to that system, they explained.

Matthew Aliota, a professor who studies viruses at the University of Wisconsin, pointed out that the eye doesn't have a strong immune system, meaning that viruses may more easily replicate there.

"This has been documented among survivors of Ebola virus disease," he said, although it's not clear how widespread the phenomenon is.

What now?

"Ophthalmologists who see patients with uveitis should be aware that Zika is a potential cause of it," Furtado said. "And general doctors should know that a red eye associated with Zika is not necessarily only conjunctivitis. It can be more severe than it looks."

SOURCES: Benedito Antonio Lopes da Fonseca, M.D., Ph.D., associate professor, and Joao Furtado, M.D, Ph.D., professor, University of Sao Paulo, Brazil; Debra Goldstein, M.D., professor and director, Uveitis Fellowship Program, department of ophthalmology, Northwestern University Feinberg School of Medicine, Chicago; Matthew Aliota, Ph.D., department of pathobiological sciences, School of Veterinary Medicine, University of Wisconsin, Madison; June 22, 2016, The New England Journal of Medicine

HealthDay

Copyright (c) 2016 HealthDay. All rights reserved.

News stories are provided by HealthDay and do not reflect the views of MedlinePlus, the National Library of Medicine, the National Institutes of Health, the U.S. Department of Health and Human Services, or federal policy.

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