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Genomics and Health Impact Blog

A blog devoted to discussing best practices and questions about the role of genomics in disease prevention, health promotion and healthcare.

Human Disease and Bad Luck: Acting on Genetic & Environmental Factors to Reduce Cancer Risk

Categories: cancer, epidemiology, genomics

a pair of die, DNA and a hand holding a globe with a tree inside wiht sequencing in the backgroundLisa C. Richardson (Director, Division of Cancer Prevention and Control), Centers for Disease Control and Prevention

In January 2015, a paper in Science created a “buzz” in the scientific community and the media. Based on statistical modelling, the authors suggested that “only a third of the variation in cancer risk among tissues is attributable to environmental factors or inherited predispositions. The majority is due to ‘bad luck,’ that is, random mutations arising during DNA replication in normal, noncancerous stem cells.” They went on to suggest that the importance of this finding is not only for understanding disease but also for designing strategies to limit the mortality it causes. The release of the paper was accompanied immediately by sensational headlines such as

Who gets cancer? Bad luck plays a big role, AJC, Jan 1, 2015

Bad luck, not genes or the environment, cause for many cancers, researchers find, PBS Newshour, Jan 2, 2015

Cancer’s random assault, by Denise Grady, New York Times, Jan 5, 2015

100,000 Studies: A Milestone for Human Genome Epidemiology (HuGE) and the HuGE Navigator

Categories: epidemiology, genomics, GWAS

a HUGE odometer with 100000 on it

The HuGE published literature database now contains more than 100,000 citations, a milestone reached at the end of 2014. The Office of Public Health Genomics has compiled this database since 2001 via weekly systematic sweeps of PubMed performed by a single curator. For the first five years, a complex PubMed query was used to identify studies of genotype prevalence, gene-disease association, gene-environment interaction, and the performance characteristics of genetic tests. In 2006, a data mining approach using support vector machines replaced the PubMed query, reducing the time needed for hand curation and improving both sensitivity and specificity. The database and a suite of online tools to explore it were re-launched as the HuGE Navigator.

The Success of Precision Medicine Requires a Public Health Perspective

Categories: genomics, precision medicine, public health

 

a magifying glass focusing on a figure in red with surrounding figures in blueThe announcement of a new major US Precision Medicine initiative comes more than a decade after the completion of the Human Genome Project, the ambitious project that culminated in sequencing all 3 billion base pairs of our genome. Continuous improvement in the quality of sequencing, dramatic reduction in price, and ongoing advances in multiple sectors of biotechnology all promise a new era of medicine known variably as personalized medicine, genomic medicine and more recently precision medicine. With conventional medicine, patients are treated individually but typically with the same treatment that everyone else with that condition receives. Thus an opportunity may be missed: certain medical interventions can be more effective or cause fewer side effects for some patients than for others, making it important to identify in advance which patients are more or less likely to benefit from the intervention. This is where precision medicine comes in. Precision medicine takes into account individual differences in the genes, environments, and lifestyles of people allowing the design of targeted disease interventions from the start. While genomics is often suggested as the leading driver of personalization, other factors may be equally as important. For example, health information technology can be used to integrate medical history into patient-centered approaches to improving health and treating disease.

Newborn screening in the genomics era: are we ready for genome sequencing?

Categories: genomics, newborn screening

Alison Stewart, Office of Public Health Genomics, Centers for Disease Control and Prevention
Ridgely Fisk Green, Carter Consulting, Inc., and Office of Public Health Genomics, Centers for Disease Control and Prevention
Stuart K. Shapira, National  Center on Birth Defects and Developmental Disabilities

a newborn babyRecent advances in next generation sequencing (NGS) could potentially revolutionize newborn screening, the largest public health genetics program in the United States and around the world.  Over the last five decades, newborn screening has grown from screening for one condition (phenylketonuria (PKU)) in one state, to nationwide screening for at least 31 severe but treatable conditions, most of which are genetic.  Each year, thousands of babies in the United States are saved from lifelong disability and even death by timely diagnosis and initiation of treatment. An important aspect of newborn screening is speed; many of the diseases that are screened for are inborn errors of metabolism in which the baby’s body cannot properly break down certain substances in food which can build up to toxic amounts.

Celebrating a Decade of Evidence-Based Evaluation of Genomic Tests

Categories: EGAPP, evidence-based medicine, genomics

Muin J Khoury, Director, Office of Public Health Genomics, Centers for Disease Control and Prevention

Ira Lubin, Doris Zallen, Dave Dotson, Sheri Schully, Marc Williams, Ned Calonge, Roger Klein, Muin Khoury and Cecile Janssens at the EGAPP meeting

Ira Lubin, Doris Zallen, Dave Dotson, Sheri Schully, Marc Williams, Ned Calonge, Roger Klein, Muin Khoury and Cecile Janssens at the EGAPP meeting

CDC’s Office of Public Health Genomics (OPHG) launched the Evaluation of Genomic Applications in Practice and Prevention Initiative (EGAPP) in 2004. The independent EGAPP Working Group (EWG) celebrated a decade of achievements and accomplishments at their meeting in Atlanta on October 27-28, 2014. The EWG is comprised entirely of volunteers, encompassing multiples areas of expertise who are committed to developing and applying evidence-based methods for evaluation of genomic tests for use in practice. The EWG has published four methods papers, as well as nine recommendation statements addressing genomic testing topics in oncology, psychiatry, cardiovascular disease, and diabetes. A few additional statements are in preparation.

During the past decade, the number of laboratories that offer genetic testing remained relatively flat, however, the number of diseases for which testing is available increased consistently and dramatically. As of November, 2014, there are more than 42,000 tests available for just over 4,000 disorders. In terms of raw numbers, the recommendations from a decade of EGAPP fall drastically short of covering the field. Nevertheless, EGAPP, dubbed by CDC as a pilot initiative, has been enormously influential in prioritizing tests for evaluation, determining what questions need to be asked and answered, and identifying where key crosscutting weaknesses in research must be addressed in genomics.

What is a “rare disease”? Polio eradication and primary immunodeficiency

Categories: genomics, polio, primary immunodeficiency, public health

a child getting the polio vaccine

During the last two decades, surveillance and strategic vaccination campaigns deployed by the Global Polio Eradication Initiative (GPEI) have reduced polio incidence worldwide by more than 99 percent. Wild poliovirus (WPV) cases are now uncommon, with only 222 new cases reported worldwide so far in 2014.* Endemic transmission is now limited to areas of just three countries—Afghanistan, Nigeria, and Pakistan. Of the three WPV strains, only one will remain if, as now seems likely, WPV3 follows WPV2 into oblivion.

The Journal of Infectious Diseases supplement published on Nov 1, 2014, provides an overview of recent progress toward polio eradication, as well as current challenges in surveillance, risk assessment and mitigation, and post-eradication strategies to make sure polio never returns.

In The New Polio Eradication End Game, members of the World Health Organization (WHO) polio team lay out the intricate maneuvers that will be required to eliminate all polioviruses from human populations, including both wild viruses and those derived from oral polio vaccine (OPV).

Family health history is a non-modifiable risk factor—or is it?

Categories: family history, genomics

Ridgely Fisk Green,Office of Public Health Genomics, Centers For Disease Control and Prevention

a family biking

“I met three different women who had been tested [genetic testing for mutations in the BReast CAncer susceptibility (BRCA) genes] early on, in 1996, when the BRCA test first came out. They told me their family history story of mothers, aunts, uncles, and a dad who suffered from breast or ovarian or related cancers, and it was heartbreaking. But then the story changed with them. They were diagnosed with cancer, they got testing, and they shared this information with their family members. So they had stories of children and grandchildren—one woman even had great grandchildren—who were old enough to decide whether or not they wanted to be counseled and some decided to get testing. Many did not carry any of the mutations in the family, and others did. And those who found out that they were a mutation carrier, they had actual things to do. And none of them—none of those family members as we cascade down—have died of cancer.” Summer Lee Cox, Oregon Public Health Division

Every Cause Needs a Champion: Jean Chabut as a Public Health Genomics Pioneer

Categories: genomics, public health

Scott Bowen, Office of Public Health Genomics, Centers For Disease Control and Prevention

Cham·pi·on noun \ˈcham-pē-ən\: someone who fights or speaks publicly in support of a person, belief, cause, etc. 

Jean Ellen Chabut

Jean Ellen Chabut 1942-2014

Most public health programs can point to a key person or group who was instrumental in assuring not only the program’s successful introduction but also its long-term viability. Jean Chabut was that champion for public health genomics in Michigan. First as the state chronic disease director, and later as deputy director for public health at the Michigan Department of Community Health, she took a keen interest in the role of genomics in public health, then a bold new concept. Jean was ahead of her time in many ways. When Michigan was starting its public health genomics odyssey in the late 1990’s, a formal framework to evaluate the evidence of genomic applications did not exist. However, as a nurse and forward-thinking public health administrator, Jean believed that family history and genetics would one day be very important for improving population health. From 2003-2008, she took on the role of project co-director for Michigan’s genomics cooperative agreement and worked with 3 other states to provide early insight into the integration of genomics into public health. She insisted that staff positions funded by the grant be established as permanent civil service jobs rather than as temporary contractual positions, a move that would signal greater integration and sustainability within the health department. She also established an internal Genomics Work Group to provide a forum for regular discussion of family history and other genomics developments, encouraging involvement from all chronic disease programs. Jean also enthusiastically supported a “Six Weeks to Genomics Awareness” lunch and learn series open to all MDCH staff. Always willing to listen and lend her influence to whatever needed to be accomplished, Jean was eager to learn how genetics could be fully integrated into public health programs, providing support to her Genomics Team from the top down.

Public Health Approach to Big Data in the Age of Genomics: How Can we Separate Signal from Noise?

Categories: big data, epidemiology, evidence-based medicine, genomics, public health

Picture1

Figure 1: The Big Data Cloud

The term Big Data is used to describe massive volumes of both structured and unstructured data that is so large and complex it is difficult to process and analyze. Examples of big data include the following: diagnostic medical imaging, DNA sequencing and other molecular technologies, environmental exposures, behavioral factors, financial transactions, geographic information & social media information. It turns out that Big Data is all around us! As Leroy Hood once commented, “We predict that in 5 to 10 years each person will be surrounded by a virtual cloud of billions of data points” (see figure 1). Genome sequencing of humans and other organisms has been a leading contributor to Big Data, but other types of data are increasingly larger, more diverse, and more complex, exceeding the abilities of currently used approaches to store, manage, share, analyze, and interpret it effectively. We have all heard claims that Big Data will revolutionize everything, including health and healthcare.

Outsmarting Antimicrobial-Resistant Pathogens

Categories: antimicrobial resistance, genomics

Marta Gwinn, Consultant, McKing Consulting Corp, Office of Public Health Genomics, Centers for Disease Control and Prevention & Clifford McDonald, Division of Healthcare Quality Promotion, NCEZID, CDC

The evolution of antibiotic resistance in bacteria is occurring at an alarming rate and is outpacing the development of new countermeasures.

White House Office of Science and Technology Policy, September 18, 2014

bacterial culturesIn the contest between humans and pathogens, each faction has an evolutionary advantage: we have the brains to plot antimicrobial strategies but they have the means to defeat them through rapid reproduction, genetic selection, and recombination. Pathogens act faster, so we have to act smarter.

CDC’s recent report on antibiotic resistance threats estimated that 2 million people each year are infected with antibiotic-resistant bacteria and 23,000 die as a result. This month, the White House issued a new National Strategy on Combating Antibiotic Resistant Bacteria [PDF 481.02 KB]. CDC is working with state, national and international public health partners to address this threat through a combination of preventive strategies, stronger surveillance, and use of innovative diagnostic tests.

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