Week 1: Genetics and Public Health Genomics

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Week 1: Learning goals and objectives

  • You will learn about the difference between “genomics” and “genetics;”
  • How “public health genomics differs from “genomics;”
  • The molecular “language of genomics” and how it works to encode, transcribe, and translate “information;”
  • Some of the ethical and policy issues raised by genomic science and their implications for how the “genomic revolution” will affect health care and your personal life.

Your objectives are to:

  • Define and interpret the fundamental underpinnings of genetics and genomics;
  • Get a sense of the risks and benefits of the application of genomic science to healthcare;
  • Critically analyze the various videos and websites that present genomic science and its applications.

Genomics is the future of medicine whether you like it or not. No matter what we think politically, medically, or morally about “advances” in genomics in healthcare, they will keep happening. Therefore, it’s our individual responsibility to become informed about the health and well-being of ourselves, our families, and the larger world in which we live. It is not enough to be informed about the inevitable future; one must be accurately informed for the present.

Masters of Public Health student, Oregon Health and Sciences University

What is Genomics?

Unlike “genetics” (the study of the functions and effects of single genes), “genomics” is the study of “genomes,” the heredity information of virtually all living organisms: bacteria, fungi, plants, animals, and humans, and the interactions of multiple genes with each other, both endogenously with, for example, the 4014  (40 trillion) cells in our bodies and ~1014 microscopic bugs (microorganisms) living on and within our body of ~100 different cell types – and exogenously, with our constantly-evolving environment.

As a result, “The Genome Era” has great potential for improving not only your personal health but ultimately the health of worldwide populations, in general. A vast array of approaches and methods—and a new generation of investigators with expertise in biology, informatics, computer science, mathematics, statistics and/or bio-engineering—will be needed to meet this challenge.

New genomic technology can tell us more than ever before about who we are, where we came from and what diseases might come our way. But its scientific and social complexity can also give rise to family friction and difficult medical choices. It can provoke concerns about genetic discrimination and privacy, and frustration with information that can be known but not acted on in any meaningful way.

At a time when the use of genetic testing is in many cases outstripping the social debate about its consequences, this website explores some of the key scientific, personal and ethical questions that are arising in the Age of Genomics.

The 9-week course will raise many more questions than deliver answers but by thinking them through, you will be better prepared to find the right answers for yourself, your professional colleagues, patients and family members, among others.

The Language of Genomics

Dr. James Watson

Dr. James Watson

In 1953, James Watson and Francis Crick pieced together the structure of DNA — the now famous double helix.

If you are reading this and you are a human being, you have, like the rest of us, about 100 trillion (1014) cells in your body. In the center of each of those cells is a copy of your DNA, short for deoxyribonucleic acid, which takes the form of a double helix and is spread across 23 pairs of chromosomes. It is comprised of many permutations of just four nucleotides: Adenine, Cytosine, Guanine and Thymine, which are often referred to by their initials, ACGT. They are the alphabet of DNA.

Your DNA is made up of three billion pairs of chemical building blocks, one set from each parent, for a total of six billion. Each set (or nucleotides) makes up about 20,000 genes. This is referred to as your “genome.” (See: 3 billion base pairs per cell)

Your DNA is the blueprint for a significant chunk of who you are. It tells each cell what to do; it controls your development from embryo to death; it orchestrates the workings of your body and your mind. It is crucial to remember that DNA is not definitive, however. Where you live, what you eat and drink, how you are raised, all of the factors that we call the “environment” have a major influence on your health, and how you act.

How the environment interacts with your genome—and to the maintenance of its health (and the diseases which can arise) when it is compromised—reflects a biological system which operates with extraordinary complexity and, in the process, generates a deeply varied and intricate interplay of social, scientific and legal issues.  How we view them, the meaning we attach to them, and how they are understood to matter, shift and change constantly.

The vast majority of our DNA is the same from one person to another. But the tiny portion that is different is what makes each of us unique. Sometimes a change in a single one of the six billion nucleotides can lead to problems. In other cases, chunks of DNA are duplicated, deleted or transposed.

Doctors and scientists are increasingly able to trace these differences to traits like hair and eye color, height, propensity for risk-taking, obesity and predisposition to diseases. The hope is that pinpointing all the variations in DNA that cause diseases will lead to cures for disease. An international effort in the 1990s enabled the first human genome to be decoded. (See: Are genes the software of life?)

Once the association is made between a particular gene variation and a trait, all it takes is a simple DNA test to determine whether an individual has it. Throughout this course, a “DNA test” means simply giving a few of your cells to a laboratory qualified to analyze them. Usually that means a blood sample, taken in a doctor’s office, though some tests can be done with a swab of cells from inside your cheek, the root of a hair or a vial full of your saliva.

To review the above information, watch this animation of “unlocking lives code.”

The Human Genome Project

The Human Genome Project Timeline and History

The Human Genome Project Timeline and History

The Human Genome Project (HGP) was officially launched in 1990 by the Department of Energy and the National Institutes of Health employing a “map-first, sequence later” approach involving an international consortium composed of geneticists in the United States, United Kingdom, France, Australia, and Japan, with numerous other scientific relationships worldwide.

The main goals of the HGP were to provide a complete and accurate sequence of the 3 billion DNA base pairs that make up the human genome and to find all of the estimated 20,000 to 25,000 human genes. The Project also aimed to sequence the genomes of several other organisms that are important to medical research, such as the mouse and the fruit fly.

Ten years later (June 26, 2000) President Bill Clinton announced completion of an 85 percent working draft of the human genome, heralding “cracking of the genetic code” as a landmark moment and further predicting that ”genome science will have a real impact on all our lives and even more on the lives of our children. It will revolutionize the diagnosis, prevention, and treatment of most, if not all, human diseases”

The HGP draft sequence appeared in February 2001 in both Nature and Science. Then, on April 14, 2003, the HGP announced the complete sequencing of the reference human genome, officially ending the project two years ahead of projections and a cost of $3 billion. It is expected that reading an individual’s entire six billion building blocks of DNA will soon cost less than $1,000, giving scientists much more information to work with.

Today, 15 years later, companies advertise machines that can sequence an entire human genome in just a couple of days for about $1,000.. Those who decide to have their genome sequenced can store the information in the Google cloud for as little as $25 a year. And for just a few hundred dollars and a swab of your saliva, a whole host of companies will analyze thousands of genes and identify potential health risks.

In addition to sequencing DNA, the Human Genome Project also sought to develop new tools to obtain and analyze genomic data and to make this information widely available. Also, because advances in genetics have consequences for individuals and society, the Human Genome Project designated 3-5% of its funding to exploring the consequences of genomic research through its Ethical, Legal, and Social Implications (ELSI) Program committed to fulfilling the dream that such knowledge would substantially benefit humankind and the faith that science would develop the necessary technology to make this project feasible and that humankind would use the knowledge generated by the project wisely.

Ethical, Legal and Social Implications (ELSI)

Perhaps the most remarkable thing about the Human Genome Project is that it demonstrated explicitly how the needs of biology can lead to transformational new technologies that, in turn, can revolutionize the field and catalyze the emergence of dramatically different aspects of science, in general.

Leroy Hood, a key player in the HGP and molecular biology, cites the “democratization of genes” (characterized as the accessibility of genes to all biologists) as foremost among the accomplishments of the HGP revolutionizing both biology and medicine.

The HGP was also the first federally funded project that dedicated approximately 5 percent of its annual budget as a set-aside to support multiple external efforts to examine the ethical, legal, and social implications of producing and possessing this new scientific information about the human genome. The federal Ethical, Legal, and Social Implications (ELSI) Research Program is primarily a grant-funding initiative administered by the National Institutes of Health and the DoE.

The investigator-centered ELSI research program is chiefly organized into four critical areas: (1) privacy of genetic information; (2) safe and effective introduction of genetic information in the clinical setting; (3) fairness in the use of genetic information by third parties, including insurance providers, researchers, and employers; and (4) professional and public education involved in educating, informing, and counseling individuals about genetic test results.

In terms of human knowledge, the field of genomics is hurtling toward us at warp speed.  As astonishing new strategies, products and services evolve from genomic technologies in the next decade, it will become increasingly important for healthcare practitioners to enhance awareness, build communication competencies, and develop policy options that facilitate the widespread use of genomic knowledge in 21st century public health settings worldwide. (Watch: ELSI History)

What is Public Health Genomics?

In April of 2005, an international expert workshop convened in Bellagio, Italy, settled on the term “public health genomics” to address the challenges of using genome-based research to benefit population health, a new field within public health that combines knowledge from genetic and molecular science tempered with insights from population sciences, humanities and the social sciences, and uses this integrated knowledge to develop programs and policies aimed at protecting and improving the health of the population.

BellagioConferenceFlowSchemeDiagramThe Bellagio workshop developed a visual representation of this effort designed to promote relevant research, support the development of an integrated knowledge base, encourage communication and engagement with the pubic and other stakeholders, inform public policy, and promote education and training.

Since the complete mapping and sequencing of the human genome in 2003, understanding of the role of genes in health and disease has begun to expand beyond rare genetic diseases to common diseases such as cancer, diabetes, heart disease and stroke. The new era of healthcare – genomic medicine – is rapidly advancing, and provides a powerful means for tailoring health care at the individual level.

Important considerations for this era are multi-dimensional. They include healthcare providers’ knowledge, competency, perceptions, and views of genetics and genomics; the challenges presented by individuals who have, at most, a passing interest in genetics/genomics, and how they will react if they or a family member have validated risks or are diagnosed with a disease; and access to genetic and genomic services for underserved communities and how their voices are not only heard, but incorporated and understood.

The public must be engaged in order to ensure that their interests are effectively addressed. Given the potential implications of genomic medicine for healthcare professionals and the general public, the development of new educational, outreach, and community engagement strategies mus be developed.

Realizing the promise of the “Genomic Revolution” in health care will require the education of physicians and other health-service providers concerning the capabilities, limitations, implementation of standards and quality-control, and the social and ethical implications of genomic science and its application to improve population health.

Indeed–

“The biggest bottleneck to the realization of the ‘genomic revolution’ in healthcare is the capacity of health professionals—and their patients—to make meaningful use of these new tools.”

—Eric Green, Director, National Human Genome Research Institute (NHGRI).

Whither genomics and public health?

In case you’re not up on your Old English the use of the word, “Whither” is to suggest a generalizable frame for reaching the respective goals of public health and genomics in the (rapidly evolving) “Genomic Revolution,” a paradigmatic shift with its eye firmly planted on the practice of global health care.

The field of “Public Health” is well understood, but enhancing “genomic literacy” among health care practitioners, students, and the general public is increasingly seen as a critical step toward achieving the ultimate goals of both disciplines in the wake of recent applications of genomic discovery to: Genetically edit HIV T-cells to make them resistant to the virus; Use whole genome sequencing to guide breast cancer treatment; and Identify a rare mutation that “kills off” the gene for Diabetes.

What are the respective goals of genomic science and public health?

The overarching goal of genomic science is to develop genome-based tools designed ultimately to improve the health of individuals. That is, genomics focuses on the internal biological factors that will cause only some individuals to be affected, even by triggers (like drugs), that are asymptomatic in the majority of people and, therefore, don’t make a dent in “population health.”

On other hand, “public health” is all about the common environmental and social factors that drag down the collective health of a population e.g, infectious disease, epidemics, pollution, food quality, occupational hazards, and living conditions, among others. All of these objectives are best served by assessing the health status of the population, diagnosing its problems and searching for–and addressing–the root medical causes for the problems.

In light of the purposes of both fields aimed at improving health, would it make sense to subsume both disciplines (and approaches) into a new field of integrated interdisciplinary knowledge being described as “Public Health Genomics”? (See: Introduction to Genomics)

Or, alternatively, is the science of genomics widening the schism between medicine and public health?

 

Resources and Discussion

Questions for Discussion

  • How do we define genetics as being different from genomics?
  • How does “public health genomics” differ from “genomics”?
  • What is a “gene”?
  • How does DNA encode, transcribe and translate “information”?
  • How does one construct and interpret a family genotypic history?
  • What do the terms “The Age of Genomics,” and “The Genomic Revolution” connote?
  • Are genes the software of life?
  • What role(s) ought public health play in an era of genomic information? That is, would the quest for improved global health be better served by pubic heath and genomic science acting independently or as partnership between the two similar to the new field of “public health genomics”? Give reason(s) for your responses.