CHAPTER SUMMARY
If asked for one phrase to define the theme of this text on medical genetics, it might be “the cascade of consequences.” This is a major departure from the simple view that a gene causes a trait. Traits can be appearance, behavior, or body chemistry. For much of recent history, and certainly in common discussion, one imagines that a gene has a simple and direct effect on a character. For example, one might say that albinism is caused by the “a” gene (Figure 1-1). While this view is not quite wrong, the reality is both more complex and more interesting. There is in fact an intricate interaction among genes, hormones, enzymes, membrane receptors, neuron networks, and so on that creates a maze of connections that prescribes our individual functional and developmental path. Many of these pathways and interactions are shared by even distantly related animals. There is both unity and diversity in the genetics of life.
Figure 1-1. Albinism can be traced to homozygosity for a recessive mutation in the pathway for biosynthesis of melanin pigment. (Reprinted with permission from Kelly AP and Taylor ST. Dermatology for Skin of Color. New York: McGraw-Hill, 2009, Fig. 47-1.)
Part 1: Background and Systems Integration
Conception. Development. Birth. Growth. Maturity. Old age. A familiar pattern. A physician’s role may have begun months before birth in prenatal care of the mother or may focus decades later when the patient is elderly. But the genetic encyclopedia the patient is drawing from was written at fertilization and will be expressed progressively from the embryo to old age. Deoxyribonucleic acid (DNA) codes for proteins and for various kinds of ribonucleic acid (RNA) made in the many cell types of the body. It can dictate much about an individual’s physical abilities and limitations. But it is not a static information resource. Throughout life it changes by mutation and by processes that reduce or block the use of various gene sequences. In addition, environmental factors can influence epigenetic processes, the subsequent chemical interactions that cascade from an initial gene action to have major effects both early and late in life.
With the possible exception of identical twins, each of us begins with a unique genotype that defines our individual biochemistry and form. We recognize that uniqueness in ourselves. We take individuality for granted. Now, as a physician, reflect that perspective on a patient. Clearly, understanding the physiological consequences of a treatment is critical to the medical outcome. But patients come from a diverse human population. Not everyone responds in the same way to any given drug. Normally effective dosages of a prescription medicine might have little effect on some and potentially life-threatening side effects on others. A study cited by National Institute of Health (NIH) (1998) found that 2.2 million serious cases of adverse drug reactions had occurred in 1 year and resulted in over 100,000 deaths. That makes adverse reactions to properly prescribed medications one of the leading causes of death in the United States. For that reason, research in biomedical technology is exploring ways to profile a person’s unique genotype to aid in defining biochemical variables that affect individual treatment outcomes. Medicine does not need to take a “one size fits all” approach. Because of our biological diversity, future medical practice will increasingly rely on new insights from genetics and molecular biology.
Yet, human genetic diversity is not uniformly distributed. The same is true in populations of essentially all animals and plants. Due to historical sharing of ancestral lineages, the genetic makeup of human population groups can differ in medically important ways. For example, lactose intolerance is common in people of many African, Asian, Native American, Middle Eastern, and other heritages. But lactose tolerance is typical in those of European and some African ancestries. One hypothesis points to the fact that those with lactose tolerance share a tradition of pastoralism and dependence on milk products. (Throughout this book we will discuss other examples of medically-relevant population genetic diversity.)
Some genetic variation is normal, but not all genetic changes are benign. Major gene mutations or chromosome structural changes can cause severe alterations in development and even death. The challenge for physicians is to understand the range of genetic variability among patients. Genetics and molecular biology can be tools for diagnosis and can offer clues to the most appropriate treatment choice. Genetic resources and the technologies of molecular biology are changing medicine in fundamental ways, and the consequences of that change will have both biomedical and bioethical implications for the future practice of every physician.
The Origin of Life
The unity of life is reflected in its origin. We do not know what that origin was, and alternative explanations do not need to be mutually exclusive. In reality, it is not possible to test directly any hypothesis of events that happened in the distant past. It is possible, however, to test the current environment for principles of evolutionary science, i.e. the change in living systems over time. While these investigations will never establish the origin of life with unambiguous certainty, they do have direct implications for existing biologic organisms.
Genetics is a scientific discipline, which delimits the structure of its hypotheses in an easily recognized fashion. Its data are limited to observations that can be made about the current physical universe and to hypotheses that can be falsified by observation and experimentation. Since the purpose of the present discussion is to explore how possible scientific models of an origin of life might shed light on the unifying concepts of inheritance and gene expression, our focus will be on scientific tests of competing hypotheses regarding the unity among present-day living organisms.
Strong evidence for the unity of life comes from molecular conservation that is from organic molecules that have not changed or that have changed only a small amount from one organism to others that are distantly related. For example, all living organisms share an essentially identical genetic code, like a shared alphabet among languages. Other forms of a genetic code could theoretically be just as efficient. But the same one is used by all. This supports the conclusion that current living forms, from bacteria and viruses to higher plants and humans, share an information storage ancestry. Still, the evidence goes far beyond a common genetic code. Many protein compositions are highly conserved among diverse taxonomic groups. Not surprisingly, the strongest similarities are in proteins that contribute to fundamental structures, such as the histones that compose the globular protein complexes, the nucleosomes, that bind DNA into chromosomes (Figure 1-2). A shared biological ancestry has broad implications for biology in general and for medicine in particular. What we can learn from one organism can help us understand the others.
Figure 1-2. A nucleosome is an octomer of histone proteins H2A, H2B, H3, and H4. Its overall positive charge covalently binds to the negatively charged DNA molecule. Together with histone H1 and some non-histone proteins that act as linkers, the nucleo-somes help compact DNA into the organized higher-order folds of the chromosome. Nucleosomes can also have general gene regulation effects. In the sea urchin and other advanced animals, the genes for these histones are even arranged in a repeated linear order: spacer–H2A–spacer–H3–spacer–H2B–spacer–H4–spacer–H1–spacer. (Reprinted with permission from Brooker RJ: Genetics: Analysis and Principles, 3rd ed. New York: McGraw-Hill, 2008, Fig. 10-14A).
RNA and the “RNA World”
Deoxyribonucleic acid is the hereditary macromolecule in most life forms, but it was likely not the first. There is strong theoretical and experimental evidence in support of the hypothesis that ribonucleic acid (RNA) formed first. Both DNA and RNA are composed of chains of monomers called nucleotides. As we will see in more detail later, RNA plays a central role in the synthesis of proteins. But it can also have a catalytic function, like that of enzymes (protein catalysts). Catalytic RNA molecules, called ribozymes, can make complementary copies of other short RNAs in addition to producing proteins.
The synthesis of RNA and proteins by self-replicating or catalytic RNA is likely to have been error-prone. The diverse products of such “mutation” events could differ in their successful competition for monomers like amino acids and RNA nucleotides. The performance quality of their products would also vary. This is raw material for natural selection on the molecular scale. RNA can also serve as the template for the creation of DNA strands in a process now used by some RNA viruses to make DNA copies during cell infection. In its complementary double-stranded structure, DNA has the advantage of high molecular stability and an efficient mechanism of accurate duplication. Once in operation, natural selection would favor the improvement of replication and error-correction capabilities, and these are now among the most highly conserved proteins across the taxonomic spectrum. Such a sequence of events leaves RNA, more specifically messenger RNA (mRNA), as the intermediate in the flow of genetic information from the DNA of the nucleus, through the mRNA transcripts created from spliced RNA, to the protein products (Figure 1-3). On that stable foundation, increasingly complex cell structures and activities are possible.
Figure 1-3. The flow of genetic information. The sequence of DNA nucleotides is transcribed into a complementary sequence of RNA nucleotides (transcription). The RNA is processed and transported out of the nucleus where it is translated into a sequence of amino acids, the protein product, on ribosomes in the cytoplasm (translation). The “RNA World” hypothesis is that this information flow began with catalytic RNA coding for protein synthesis. DNA and transcription came later. (Reprinted with permission from Brooker RJ: Genetics: Analysis and Principles, 3rd ed. New York: McGraw-Hill, 2008, Fig. 1-6.)
Ribozymes still play critical roles in the cell. Among other things, they assist in splicing nucleotides out of the initial RNA transcript. Variations in splicing contribute to the wide array of protein products that can come from a single active gene. In later sections we will explore the consequences of both normal splicing variation and the disease states that can arise from ribozyme activity. Practical applications are also on the horizon. Artificially engineered ribozymes can identify and break a specific type of mRNA and prevent expression of its coded protein. Targeting RNAs of a pathogen like HIV thus offers a potential molecular therapy.
Biogenesis and the Cell Theory
Life forms are united by a small set of principles that describe the flow of information required to create each type of organism. Even prokaryotes, simple cells like bacteria that lack a defined nucleus and other membranous organelles, are governed by many of the same processes as found in more complex organisms, including humans. Biogenesis is the principle that all life forms come from reproduction by earlier life forms. Although abiogenesis, the spontaneous creation of a living system under appropriate conditions, must have occurred at the end of the prebiotic world, spontaneous generation of life no longer occurs. Even if a complex molecule happens to form spontaneously today, the oxidizing atmosphere will soon break its chemical bonds or an organism will eat it as food. There is no longer enough time for complex molecules to accumulate in necessary combinations to create a novel living structure.
A related principle is that cells are the fundamental building blocks of life. Technical advances have pushed forward the boundaries of knowledge by increasing the quality of observations that can be made about the natural world. Anton van Leeuwenhoek and others in the seventeenth century began the development of microscopes, and Robert Hooke was the first to report using a magnifying device to see cell structure in a section of cork. This is one of many examples where an invention opens a previously unknown domain to study. Building from Hooke’s discovery and the confirming observations by others, Matthias Schleiden (1838) and Theodor Schwann (1839) independently presented the first clear statement of the Cell Theory, the principle that all organisms are composed of cells.
Although the study of genetics often tends to focus on the organization and use of encoded information in the nucleus, an understanding of the “cascade of consequences” to come from the nucleus requires knowledge about other cell organelles, about membrane structure, and about the molecular components of the cytoplasmic domain. Genetics is only important in its functional context—what does genetically-encoded information do? The unity of life is reflected in the great similarity in cell structures among organisms. For that reason, studies of model organisms, especially animal models, will be called upon frequently to clarify mechanisms at work in human development and disease.
The Molecular Basis of Inheritance
For much of their history, two threads—transmission genetics and molecular genetics—were separate pursuits. Transmission genetics is concerned with the way traits are combined and passed among generations of offspring. Molecular genetics explores the biochemical basis of a trait’s expression.
The difference between organic and inorganic molecules was recognized by the early 1800s, and by about 1830 three major classes of organic molecules had been distinguished chemically: carbohydrates, lipids, and proteins. But one key class of organic molecules, nucleic acid, was not discovered until 1868 when Friedrich Miescher isolated a phosphorus-rich organic molecule from white blood cell (WBC) nuclei. Initially named “nuclein,” it was later found to have organic acid characteristics and renamed “nucleic acid.” Thus the discovery of what would turn out to be the molecule of inheritance did not occur until after Gregor Mendel published his Experiments on Plant Hybridization (1866) and Charles Darwin published On the Origin of Species by Natural Selection (1859). The discovery of nucleic acid was more than a decade after Florence Nightingale began critical reforms in hygiene and patient care in the Crimean War that led to the modern nursing profession (1854). Modern genetics has matured within a very brief historical time frame. Its practical applications to medicine are even younger.
Like protein, nucleic acids are polymeric chains of sub-units. The nucleic acid subunits are nucleotides, each composed of a 5-carbon sugar, a phosphoric acid group, and a nitrogenous base (Figure 1-4). There are two classes of nucleic acids. DNA nucleotides contain the 5-carbon sugar deoxyribose (thus, DNA); RNA contains ribose (ribonucleic acid). Both classes of nucleic acid have four different nitrogenous bases, two purines and two pyrimidines. The sequence of nitrogenous bases gives these molecules their coding capability.
Figure 1-4. Components of DNA and RNA nucleotides. Deoxyribose sugar differs from ribose in the absence of oxygen (“deoxy”) on the 2′carbon. Adenine, guanine, and cytosine are found in both DNA and RNA, but uracil replaces thymine in RNA. (Reprinted with permission from Brooker RJ: Genetics: Analysis and Principles, 3rd ed. New York: McGraw-Hill, 2008.)
Carbons of the sugar are numbered clockwise in the nucleotide (Figure 1-5). The nitrogenous base is attached to the 1′ carbon and the phosphate group to the 5′ carbon. During synthesis of a new strand, nucleotides are linked together by attaching a new nucleotide to the 3′ carbon of the existing strand (Figure 1-6). RNA remains single-stranded, although regions will fold to produce complex three-dimensional patterns that are important to its function. DNA, on the other hand, is a double-stranded molecule that is produced when one strand, the template, binds sequentially with a complementary nucleotide during synthesis of a new strand (Figure 1-7). When there is the purine adenine (A) on the template, a thymine (T) pyrimidine is linked into the growing strand, and vice versa. When there is the purine guanine (G), the pyrimidine cytosine (C) is attached. This creates a double-stranded DNA molecule (Figure 1-8) connected by large numbers of hydrogen bonds. In Chapter 2 we will discuss the replication of DNA in more detail and explore how the sequence of nucleotides is used to encode the information for creating defined protein sequences. But clearly the sequence of nucleotides is the key. Learning about that sequence and its biomedical importance is a primary goal of genome studies like the Human Genome Project.
Figure 1-5. Nucleotides of DNA and RNA. The atoms shown in red are removed when nucleotides are linked together by phosphodiester bonds to form a single strand. (Reprinted with permission from Brooker RJ: Genetics: Analysis and Principles, 3rd ed. New York: McGraw-Hill, 2008.)
Figure 1-6. A single strand of deoxyribose nucleotides. A phosphodiester bond joins the 3′ carbon of one nucleotide to the phosphate group of the next nucleotide. During synthesis, nucleotides are added at the 3′ end, as shown by the direction of the arrow. At the top end is the most distal 5′ carbon, and the 3′ carbon is the open attachment site at the other end. This 5′ to 3′ directionality plays a critical role in DNA replication and in translation during protein synthesis. (Reprinted with permission from Brooker RJ: Genetics: Analysis and Principles, 3rd ed. New York: McGraw-Hill, 2008.)
Figure 1-7. The DNA molecule is a double helix, produced when a single strand of nucleotides serves as the template for synthesis of a new complementary strand. Stable pairings occur between adenine and thymine with two hydrogen bonds (shown by the pair of dots) and between guanine and cytosine with three hydrogen bonds. This double-stranded DNA molecule then binds with nucleosomes and other proteins into the three-dimensional coils of a chromosome. (Reprinted with permission from Brooker RJ: Genetics: Analysis and Principles, 3rd ed. New York: McGraw-Hill, 2008.)
Figure 1-8. (a) Watson and Crick with a model of DNA. (b) Representation of exact spacing in a DNA double helix (a: Reprinted with permission from Hartwell LH, et al. Genetics: From Genes to Genomes. 4th ed. New York: McGraw-Hill, 2010.)
The Genome
The term “genome” refers to the genetic information needed to code for the biochemical processes and development of an individual. Most of this genetic information is in the “nuclear genome,” but some resides in copies of the “mitochondrial genome” in the cytoplasm. In green plants there is also the “chloroplast genome.” Unless otherwise noted, however, we will use “nuclear genome” and “genome” interchangeably.
Genome can also be defined in terms of the nucleotide content of an individual’s DNA. That is different from the first definition, because not all nucleotide regions are translated into biochemical products. When looking at the complete nucleotide sequence, therefore, comparisons of genome size and information content may not match very closely. True, bacterial genomes are smaller than those of eukaryotes. But among eukaryotes, there is no direct correlation between the genetic complexity of an organism and the amount of DNA or the number of chromosomes it carries. Many cellular and biochemical processes are held in common. Comparisons include these many genetic similarities and thereby tend to overshadow the smaller number of genes that may account for even large phenotypic differences. The same is true of the amount of DNA. Only about 2% or 3% of the DNA in a human nucleus codes for proteins. With that insight, one can appreciate why the DNA amounts in different species can vary a lot without marked effects on the array of protein products.
About 20,000 to 22,000 genes are required by a human during a lifespan. That is about the same as the 25,300 in Arabidopsis thaliana, the mustard grass, which serves as an important genetic model for plant species. Even the fruit fly, Drosophila melanogaster, is estimated to have only about 13,600 genes. An explanation of how complicated cell activity and developmental processes can be controlled by so few genes had to wait on the results of genome mapping. But it is perhaps less difficult to appreciate why the numbers of genes are so similar. Consider the similarities among organisms at the cellular level where so many life functions are shared.
Chromosome numbers among species are even less diagnostic. Apparently simple animals often have many more chromosomes than the 23 pairs found in humans (Figure 1-9).
Figure 1-9. A karyotype, or chromosome picture, showing the 22 pairs of chromosomes plus two X chromosomes. This karyotype was, therefore, produced from a normal female. The 46 chromosomes make up the diploid (2n) composition of a human somatic cell. (Reproduced with permission of Warren G. Sanger, PhD, University of Nebraska Medical Center, Omaha, Nebraska.)
Chromosomes are simply the structures that carry subsets of the genome of a species during cell division. But within a single individual, a change in chromosome structure or number can alter their genome information content significantly and have severe, even fatal, consequences.
Each chromosome is made up of only one very long double-stranded DNA molecule. Each gene in the nuclear genome is arranged linearly along the DNA molecule of one of its chromosomes. We can therefore describe the information content of each kind of chromosome as a “linkage group.” Ignoring the relatively neutral Y chromosome found only in males, there are 23 linkage groups in humans. If we assume 22,000 genes in the human genome, there must be about 1000 genes per average linkage group. In reality, however, both genes and chromosomes differ a lot in size. Some chromosomes are long and carry more genes. Others are quite small.
One copy of each linkage group, the “haploid” chromosome number (n), will be contributed by the egg nucleus (n = 23), and the other haploid set of each linkage group (n = 23) will be contributed by the sperm. Fertilization establishes the diploid (2n) genetic makeup of the individual’s unique genotype. After fertilization, each of the 46 chromosomes will be duplicated and distributed to the resulting daughter cells in each cycle of cell division. Thus each adult cell retains two copies of each linkage group, with the exception of the single X chromosome found in a male (its partner is the single Y chromosome).
There is some overlap among the terms employed to describe genetic makeup. This can be confusing. One way to clarify the relationships is to recognize that some terms refer to a concrete structure and others are more abstract. Haploid (n) or diploid (2n) chromosome number is concrete. We can fix and stain dividing cell nuclei and then count chromosomes to produce a picture, the karyotype. “Linkage group,” on the other hand, is an abstract reference to the individual DNA content of each different kind of chromosome. One can list the genes that are located on a given chromosome, such as chromosome 4 (Figure 1-10). Whether one is talking about the haploid or diploid set of chromosome 4s, the genetic content remains the same.
Figure 1-10. This figure shows the relationship between the genetic content of a cell and of one of its chromosomes, the linkage group of human chromosome 4. (Reprinted with permission from Brooker RJ: Genetics: Analysis and Principles, 3rd ed. New York: McGraw-Hill, 2008.)
“Haploid” refers to a cell with one copy of that genetic content, or linkage group. “Diploid” is a cell with two. Similarly, since the term “genome” refers to content, it indicates the genetic makeup of one representative of each type of chromosome, the haploid genetic complement. But when considering the specific genetic composition of an individual, we are again thinking concretely. An individual’s genotype can be homozygous (AA or aa) or heterozygous (Aa) for different forms, the A and a alleles, of the “A” gene.
What Is a Gene?
Not long ago, this would have been a fairly easy question to answer. We would have said that a gene is a sequence of nucleotides in a molecule of DNA which, by way of mRNA, codes for the synthesis of a specific protein. But insights from fully sequenced genomes, such as those produced by the Human Genome Project, now show many more subtle and complex informational functions associated with DNA.
One of the first hints at the complexity of the gene concept was the discovery that genes may be split into pieces on the chromosome. The sections that code for protein, the exons, are interspersed with stretches of nucleotides that can be non-coding, the introns. Introns are spliced out of the initial RNA transcript to produce the functional mRNA used in protein synthesis. But the later discovery of alternative splicing complicated even that story. Alternative splicing allows exon and intron modules to be combined in a variety of ways, leading to several different transcripts being translated from the same gene. In fact, the number of different transcripts can be amazingly large. In Drosophila, for example, the Dscam gene (coding for the Drosophila Down syndrome cell adhesion molecule) expresses 38,016 different mRNAs due to alternative splicing.
Other discoveries include overlapping genes, in which one section of nucleotides is transcribed as part of two different genes; genes within genes; and run-ons where transcription continues through one gene into an adjacent gene coding for a totally different protein. These fused transcripts are another way that diversity in proteins can be generated from a comparatively small number of genes.
But perhaps the greatest expansion in complexity of the gene definition comes from discoveries that many more types of RNA play a regulatory role than previously imagined. MicroRNAs are now known to have critical roles in regulating many cellular processes without acting as intermediaries for protein synthesis. Just how important they are, compared to the traditionally recognized RNAs from protein coding genes, is still being debated. Whether the DNA that codes for a microRNA deserves to be called a “gene” is also an unsettled question. But there can be little doubt that detailed information about the genomes of humans and other species will uncover even more complexity.
The Human Genome Project
The genetic makeup of each individual is unique. From that perspective, there is not just one human genome; there are billions. Yet despite genetic variation, there is a surprising degree of similarity in the final structure of our bodies and our physiologies. The great similarity of biochemical events that control normal development is accompanied by extensive genetic diversity within the human gene pool. It yields the common, complex, and often subtle genetic differences that result in the personal individuality upon which a human society is anchored. We recognize and respect each other as equal members of Homo sapiens, but modern medicine must be sensitive to the underlying differences among us. Sequencing a representative human genome is a first step. But it means little until the function, or lack of function, is understood for each portion.
The Human Genome Project (HGP) is a multinational effort begun in 1990 to obtain the nucleotide sequence of a complete human genome of approximately 3 billion nucleotides and to identify all the protein coding genes it contains. Technological advances in sequencing methodology enabled the project to be completed in 2003, slightly ahead of schedule. Developing the computer databases to manage and search this massive amount of information has led to a new field of genetics called bioinformatics. Sequencing advancements and bioinformatics are at the foundation of many promising medical applications, including the potential to generate personal genome profiles to assist in tailoring diagnosis to the individual.
As envisioned from the beginning, the HGP had several well-defined goals. The major objectives included:
(1) Identify all of the genes coded for in human DNA
(2) Determine the sequences of the 3 billion chemical base pairs that make up human DNA
(3) Store this information in databases
(4) Improve existing tools for data analysis
(5) Transfer related technologies to the private sector
(6) Address the ethical, legal, and social issues (ELSI) that may arise from this knowledge
Particularly important among these goals for the practice of medicine was making the information derived from the project available to the general public. Several excellent databases that are direct spin-offs of HGP are readily accessible and have great utility in the practice of medicine. Among these are GeneTests, Online Mendelian Inheritance in Man (OMIM), and the HGP website itself. The HGP also included a serious effort to understand and address the legal, ethical, and other social issues associated with this advancement in knowledge. Our presentation of genetic applications in medicine will include discussions of some of these issues.
But understanding the range of normal diversity is also very important. That is a goal of the 1000 Genomes Project. Launched in 2008, this international collaboration will sequence the genomes of approximately 1200 people to provide a database of biomedically relevant variation in DNA. Advances in human population genetics and in comparative genomics provide useful insights into the genetic diversity of our species. It also generates information about single nucleotide polymorphisms (SNPs), structural variations, and copy number variations that can serve as DNA landmarks for mapping genes of biomedical interest.
The Importance of Model Organisms
In addition to sequencing human DNA, the HGP also tackled the genomes of several important model organisms, including the human intestinal bacterium Escherichia coli, the fruit fly Drosophila melanogaster, the laboratory mouse Mus musculus, a plant Arabidopsis thaliana, and others (Figure 1-11). Earlier in this chapter we explored the shared ancestry reflected in the conservation of DNA makeup and protein sequences over a broad taxonomic spectrum. Information about gene functions in a simple model organism can aid in identifying the functions associated with coding regions of the human genome. Throughout this book, we will draw examples from model organisms to show how insights from a simpler organism can lead us to understand the complex interactions of genes, inducers, environmental variables, and cell structure in defining the roles that genes play in human development and activity.
Figure 1-11. Some of the organisms that are used as highly informative models to study gene action and development. (a) Escherichia coli is a common bacterium; (b) Saccharomyces cerevisiae is a yeast; (c) the fruit fly Drosophila melanogaster and (d) Caenorhabditis elegans, a nematode, allow sophisticated studies of comparatively simple animal body plans; (e) Danio rerio, the zebrafish, and (f) Mus musculus, the laboratory mouse, represent more complex vertebrate model systems; (g) Arabidopsis was one of the first plant model organisms in genome projects. (a: CDC/Peggy S. Hayes; b: Photograph by Mansur. Released to the public domain, via Wikimedia Commons; c: Photograph by André Karwath. Licenced under CC-BY-SA-2.5, http://creativecommons.org/licenses/by-sa/2.5, via Wikimedia Commons; d: Photograph by Tormikotkas. Licensed under CC-BY-SA-3.0, http://creativecommons.org/licenses/by-sa/3.0, via Wikimedia Commons; e: Photograph by Azul. Released to the public domain, via Wikimedia Commons; f: Steven Berger Photography, licensed under Creative Commons BY-SA 2.0; g: Photo by Peggy Greb, Agricultural Research Service, United States Department of Agriculture.)
Part 2: Medical Genetics
The medical application of the principles described earlier is limitless. There is little question that the field of genetics has become the focal point for most of medicine over the past two decades. It is also likely that the focus on genomics (with its translational components of proteomics and metabolomics) will continue to direct medicine for decades to come. The success of the HGP has acted as a force that has propelled genetics out of the laboratory and into the hospitals and clinics. It has put functional tools into the clinician’s hands that directly improve the health and treatment of patients. All persons working in the health care disciplines need a working knowledge of basic genetic principles. In addition, they will need a firm understanding of the application of “medical genetics” in their own specialty. Of primary importance, this will include a functional knowledge of how to identify at-risk patients effectively and efficiently in the context of regular clinic flow. They will also need a firm grasp of possible testing methods, referral sources, patient and professional resources, and potential therapies. The role of the practicing physician also requires a continuing education component, keeping current with an appreciation for the rapid pace at which things are changing in the realm of medical genetics.
An introduction to the field of medical genetics should probably begin with a few definitions. The broad category of Genetics applies to the scientific study of the principles of heredity and the variation of observable features among organisms. Human Genetics, then, would apply to the study of genetics in people. Human genetics today comprises a number of overlapping fields, which go beyond just the practice of medicine. A list of some of the major disciplines in human genetics is provided in Table 1-1. That subset of human genetics that explores the genetic contributions to the etiology, pathogenesis, and natural history of diseases and disorders is referred to as Medical Genetics. This is to be distinguished from Clinical Genetics, which is the application of Medical Genetics to the diagnosis, prognosis and, in some cases, the treatment of genetic diseases.
Table 1-1. Disciplines Within the Field of Human Genetics
Medical genetics. The study of the etiology, pathogenesis, and natural history of diseases and disorders that are at least partially genetic in origin
Clinical genetics. The diagnosis, counseling, treatment, and case management of genetic conditions
Behavior genetics. The study of genetic factors in behavioral disorders including psychiatric disorders and disorders of cognition, mood, and affect
Biochemical genetics. The study of biochemical reactions and the disorders (inborn errors of metabolism) of these reactions
Cytogenetics. The study of the structure and function of chromosomes in health and disease
Developmental genetics. The genetics of normal and abnormal development including congenital malformations and teratogens
Forensic genetics. The application of genetic knowledge and technology to medical-legal investigations
Genetic counseling. A patient care discipline that utilizes both the science of genetics and the social sciences (psychology, social work, and so forth) to provide counseling and support for patients and families with genetic conditions
Molecular genetics. The study of DNA and RNA variability; the effects of changes on human health
Pharmacogenetics. The study of genetic influences on drug response and metabolism
Population genetics. The study of genes within populations including frequencies, movement, and trends
Reproductive genetics. The study of the genetic aspects of reproduction including preconceptional health, preimplantation science, prenatal diagnosis, and pregnancy management
With the development of medical genetics as a recognized discipline in medicine, there has been a commensurate appearance of new health care professionals (genetic professionals). Medical Geneticists are physicians who provide typical physician services for patients with genetic conditions. The major types of medical geneticists working today include subspecialists in pediatric, metabolic, perinatal, and adult care. Genetic Counselors are allied health professionals that specialize in the science of genetics as it relates to conveying complex information to patients and families as well as providing psychosocial support to persons in crisis. They are an invaluable part of the medical genetics team who help bridge the gap between often overwhelming medical care systems and patients in need of access and information. Clinical Genetic Laboratories are managed by doctoral-level scientists with specialized training in biochemical, molecular, and cytogenetic testing. Close communication between the medical geneticist and the genetic counselor is essential for ensuring that the right test is performed and that accurate information is provided to the patient. All of these specialties require specific training in certified training programs with oversight from the primary certifying agency, the American College of Medical Genetics (ACMG). As genetics has evolved as a medical specialty, there has also been an evolution of the medical administration of the field. The development and admission of the ACMG in 1995 as a recognized specialty by the American Medical Association testify to the legitimacy and overall acceptance of these professions within the medical community.
The vast majority of practicing specialists in Medical Genetics work at academic institutions. The scope of practice typically involves consultation in both the outpatient and inpatient settings. Thus health care providers should be familiar with the closest or most readily accessible Medical Genetic service providers in their region. Medical geneticists may also offer services as a member of an interdisciplinary health team that provides integrated and comprehensive services for persons with conditions that require access to multiple specialists. The list of possible interdisciplinary teams that may utilize medical geneticists is extensive. Table 1-2 lists some of the most common such services. Interdisciplinary clinics are especially helpful for persons with complex conditions and their families. They allow the patient to access multiple specialists that they may need to see in one session and allow for direct communication among the specialists about the same patient.
Table 1-2. Common Interdisciplinary Teams That May Incorporate Medical Genetics
Cancer genetics
Connective tissue disorders
Craniofacial
Cystic fibrosis
Down syndrome
Fetal alcohol syndrome
Gender disorders
Hemoglobinopathies
Metabolic disorders
Neurofibromatosis
Neurogenetics
Neuromuscular (including muscular dystrophies)
Neurosensory (hereditary hearing and vision problems)
Orofacial clefting (cleft lip/cleft palate)
Throughout this book consistent language will be used in reference to specific conditions. In this book—as in a good clinical practice—“person first” language will be used. It is better to refer to “a person with diabetes” than “the diabetic.” We refer to a child as having dysmorphic features, not as a funny looking kid (FLK). As society has changed, so has the application of medical terminology. A better understanding and familiarity of rare and often sensational conditions has led to a change in assigned terms—for the better. For instance circa 1912, the accepted classification of mental retardation included the categories of moron, imbecile, and idiot, which roughly correlate with the current groupings of mild, moderate-severe, and profound, respectively. Another more recent example would be that of Angelman syndrome (Figure 1-12). Angelman syndrome is a recognizable genetic syndrome associated with a characteristic facial appearance, cognitive impairments, seizures, and a spastic gait with jerky arm movements said to resemble the movements of a marionette. Dr. Angelman originally described the condition in 1965 as a report of three “puppet children.” Because these individuals often have episodes of inappropriate laughter, they were also described as being “happy.” Subsequently, as late as the mid 1980s, this condition was referred to as the “Happy Puppet syndrome.” This type of designation, not surprisingly, was concerning to many families. Acknowledging this, the medical genetics community has now made a deliberate change in the nomenclature to the eponym “Angelman syndrome.” The power of language and the specific application of medical terms and their effects on the patients and their families cannot be over-stated.
Figure 1-12. Girl with Angelman syndrome. (a) 3 years old. (b) 7 years old.
It is important for all health care providers to understand the context and rationale for multiple terms. There are multiple ways to designate a person receiving medical services. In some settings, terms such as consumer or customer or client may be used. All of these terms convey specific aspects of the provider-patient relationship that may be appropriate. In this book, the term of choice will be “patient.” It is also very important to be aware of the specific connotations of discussing a medical condition that a patient may have. While there are some differences in how people may apply certain terms, they will be used consistently in this text. Disease refers to a condition that causes discomfort or dysfunction for a person (in contrast to injury, which is typically immediate and acquired). A disorder is a condition in which there is a disturbance of normal functioning. Equally important, the health care provider needs to understand the potential impact that the use of such terms may have on their patients. Clearly the context is crucial in the interpretation. For instance, much debate exists about how to describe deafness appropriately. Does a person with a hearing loss have a disorder, or do they simply have a different means of communication (language)?
Another point that needs to be emphasized is the proper way to denote a condition that is associated with a person’s name. Most commonly, syndromes may bear the name of the person with a strong association with the condition, such as the person who first described the condition or who published the first comprehensive description. Such eponyms are typically associated with some of the most well-known common syndromes. More recently, advances in genetic testing are now identifying conditions that do not have an associated name, but rather are described by the actual genetic abnormality (discussed further in Chapter 5) and the specific genetic nomenclature. For conditions that are associated with a particular name, it is important to note that an apostrophe is not used in the designation. For example, it is Down syndrome, not Down’s syndrome. Dr. Langdon Down neither had the condition nor did he “own” it.
What is truly amazing about the application of genetic technology in clinical medicine is the rapidity with which it has occurred. Almost all of the incorporation of genetics into medicine has occurred within a single generation. Only a few currently active practicing geneticists were already training or practicing before the human chromosome count was firmly established at 46 in 1956. Tables 1-3 and 1-4 provide timelines for selected advances in medical genetics. Table 1-3 lists major technological advances, while Table 1-4 highlights clinical milestones. In looking over these, one can begin to appreciate the relative “newness” of the field. Also, the ever-accelerating pace at which things have progressed should be noted. This, in fact, presents us with a somewhat daunting task in writing this textbook. How much of its information will be outdated by the time of publication? Our intention, therefore, will be to establish a firm foundation in concepts and in the ways to think about the role of genes in human development and disease. The specific facts that build upon that foundation will continue to grow.
Table 1-3. Timeline of Major Technological Events in Genetics
Table 1-4. Timeline of Selected Milestones in Modern Medical Genetics
Finally, it is important to be alert to recurring themes that are woven throughout the book. These themes are the essence of the application of genetic principles and technology in the practice of medicine. References to these principles include:
• Genotype—phenotype correlation(s): the need to correlate clinical observations with information obtained by genetic laboratory techniques
What is a phenotype?
Levels of describing a phenotype
Defining endophenotypes as a critical strategy for therapy
• Pathogenesis: how do changes in genes translate into human medical conditions?
• Variability and expanded phenotypes
• Genetic/etiologic heterogeneity
Part 3: Clinical Correlation
Each chapter in this book will have a clinical correlation section to complement the basic science and medical genetic information. This first chapter stands out as somewhat unique. In later chapters, the clinical correlations will present specific conditions that assimilate the principles described in the preceding two sections. Given the introductory nature of this first chapter, however, a specific condition does not readily come to mind as an example that integrates its information. Still, this does not mean that there is not a clinical corollary to the concept of genetic unity and diversity. The concept of personalized medicine will be the correlation provided.
At first glance, personalized medicine might not seem the most logical topic for a clinical correlation. But, in fact, nothing ties together the concept of “unity and diversity” as well as the practice of personalized medicine does. In traditional medical approaches, unity is found within diagnostic categories. At the core of most related medical conditions is a shared physiological and genetic basis. Still, from the inception of medical interventions, it has been readily appreciated that there is great diversity in clinical responses even within an apparently homogeneous diagnostic group. Simply put, patients with exactly the same condition, with exactly the same cause can have a multitude of responses to the same intervention. People differ in how (if at all) they respond to a given treatment, what is the most effective dose, what side effects are experienced, and possible adverse interactions.
Personalized Medicine: Personalized Health Care, Personalized Health Management
A major current movement in health care is the concept of tailoring therapy to the patient based upon patient-specific information. This type of customized medical practice is referred to as personalized medicine. Personalized medicine may be defined as health care targeted to the inherent biology and physiology of an individual leading to improvements in their medical care. The intended goal is that new molecular diagnostic tools will enhance patient care at several different levels. Currently, it is the common medical practice to follow to some degree a trial-and-error process for finding the right treatment and the right pharmaceutical dosage for each patient. By and large, most established dosage recommendations are adjusted based upon a limited number of variables such as size, age, and occasionally gender. In reality, many more variables are at play in differing responses, not the least of which are genetic factors. In theory, personalized medicine should help in arriving at a correct diagnosis in a shorter period of time. It should enable the provider to prescribe the right medication for an individual with less trial-and-error in the decision making process.
Most importantly, the hope is that these tools will prevent, delay, or reduce morbidity and mortality. Depending upon the particular features of a given medical condition, prevention may occur at many different levels. Primary prevention refers to the actual reduction of disease incidence. Secondary prevention involves the earlier detection (potentially pre-symptomatic) and intervention. Tertiary prevention utilizes personalized treatments based upon individually identified parameters. In this regard, subtyping conditions into “endophenotypes” based upon any number of genetic or other parameters should allow for the development of better, more specific therapies. Finally, some would define yet another level—quaternary prevention—as strategies that do not necessarily affect the actual medical aspects of the condition, but that somehow improve the quality of life for the individual. For instance information is typically viewed as being empowering for patients. Increased information that does not necessarily affect disease may reduce psychosocial stressors.
Personalized genomics is a subset of this practice. It has been defined as specific genetic testing that identifies individual risk profiles for a specific medical condition and/or treatment option. It also involves modifying treatment and surveillance based on genotype. Personalized genomic strategies are already being applied in a variety of clinical settings. There are many possible venues in which genetic information can be used to direct medical interventions (Table 1-5). A few examples include:
Table 1-5. Applications of Genomics in Personalized Medicine
Targeted cancer therapy
• HER2/neu and trastuzumab (Herceptin) therapy
• Chronic myelogenous leukemia and tyrosine kinase inhibitors
• Neurofibromatosis and ras inhibitors
Pharmacotherapy
• Warfarin and CYP2C9/VKORC1
• Proton pump therapy and CYP2D6, CYP2C19, CYP2CP
• Clozapine and serotonin neurotransmitter receptor
• ACE inhibitors and ACE polymorphisms
• HIV mutation detection and drug resistance
• Bucindolol and adrenergic receptors polymorphisms
Genetic susceptibility
• Cancer susceptibility genes (clinical testing available)
BRCA1/BRCA2 (breast/ovarian cancer)
APC (Familial adenomatous polyposis)
p53 (Li-Fraumeni syndrome)
MLH1, MSH2, MSH6, PMS2 (hereditary nonpolyposis colorectal cancer)
PTEN (Cowden disease)
• Altered susceptibility to other conditions
ApoE (Alzheimer, outcome in head trauma)
DRD (complex decision making, smoking cessation, delinquency)
TPH2 (affective disorder spectrum)
CCR5 receptor (HIV infections)
Type 1 diabetes (at least 11 genes including HLA-DR)
Type 2 diabetes (multiple genes including HNF4A)
Diseases for which clinically significant SNP associations have been identified
• Age-related macular degeneration
• Type 2 diabetes
• Prostate cancer
• Asthma
• Cardiovascular disease
• Crohn disease
• Alzheimer disease
• Amyotrophic lateral sclerosis
• Progressive supranuclear palsy
• HIV/AIDS
1. Cancer therapeutics. Personalized genomics is probably best established in the realm of oncology. Genetic information, such as cytogenetic findings, has been used for decades to stratify patients into the best predicted treatment option(s). Recent advances have identified a number of single gene changes that help direct cancer treatments. In addition, targeted therapies are available in which the use of the medication is designed to target known pathophysiological processes in the disease. Individual testing is typically needed to identify if a specific process is at work in that individual (Figure 1-13).
Figure 1-13. Tools are being developed to help clinicians predict the patient’s prognosis, as in this example of breast cancer outcomes based on the primary tumor’s gene expression profile
2. Pharmacogenetics. There are many variables in the use of pharmaceuticals among people. Individual differences exist in uptake, metabolism, clearance, and response. At the present time over 30 gene variations that can affect the way individuals respond to different drugs are known. Understanding these genetic variations can help determine the best drug and optimal dosing for individual patients.
3. Candidate genes for disease susceptibility. Many human medical conditions occur as the result of specific individual genetic differences (polymorphisms) that invoke a specific susceptibility to that condition. Often interactions with the right environmental trigger(s) can elicit the onset of the disorder.
4. Single nucleotide polymorphisms (SNPs). Minor variations in short DNA sequences have been linked to the occurrence of particular diseases. Numerous SNPs have been reported to associate with an increased risk of common diseases. SNPs may be identified rapidly and in large numbers using microchip technology. These tests typically scan 500,000 to 1,000,000 SNPs, although the clinical significance is known for only a small percentage. For those in which the significance is known, physicians can create a disease risk profile for individual patients.
Personalized genomics is ushering in a new role for the patient and blurring the lines of the traditional doctor to patient relationship. For instance, the first commercially available SNP chips for disease susceptibility predictions were introduced in 2007 with direct-to-consumer (DTC) marketing. This system of bypassing the health care provider and providing a direct link from the consumer to the genetics laboratory has raised a number of fascinating ethical and practical questions.
Lastly, the question remains as to how close these technologies are to truly helping prevent or ameliorate disease. While the pace of information development may be occurring at an extremely rapid rate, there are competing forces that are appropriately slowing down the introduction of these services in an effort to guarantee consumer safety. In this light, validation and incorporation of new genetic testing products and new bioinfor-matics in standard clinical practice will take years to decades.
Board-Format Practice Questions
1. In reference to a “genome”
A. the term exclusively refers to DNA that is found in the nucleus.
B. it is the genetic information needed to code for the development of an individual.
C. it can be defined in terms of the protein content of an individual’s cells.
D. the genome size and the amount of information coded typically have a 1:1 correlation.
E. is the small person who lives underground and hoards treasure.
2. The Human Genome Project
A. gave a best estimate of 100,000 as the total number of functioning human genes.
B. has identified a much greater diversity of the genetics among different species than expected.
C. is completed and has identified the sequence of all human genetic conditions.
D. made a concerted effort to address ethical and social issues associated with the information generated.
E. in general has kept the information it generated locked up and away from public access.
3. Personalized medicine
A. is likely to drive up medical costs if implemented.
B. is a theoretical type of practice that may have future applications in clinical practice.
C. should have little impact on the diagnostic process.
D. may be used to direct therapy or identify individual susceptibilities.
E. should have application in the primary prevention of disorders.
4. Medical Genetics
A. is a unique field that has relatively little interaction with other aspects of clinical medicine.
B. is so new that it currently is not an officially recognized specialty.
C. is the subset of human genetics that explores the genetic contributions to disease.
D. as a medical practice is largely limited to defining syndromes.
E. is better understood if catchy terms are applied to specific conditions or syndromes.