Gregor Mendel’s Contributions

Monogenic traits are also known as mendelian traits, after Gregor Mendel, the 19th-century Austrian monk who deduced several important genetic principles from his well-designed experiments with garden peas. Mendel studied seven traits in the pea, each of which is determined by a single gene. These traits included attributes such as height (tall versus short plants) and seed shape (smooth versus wrinkled). The variation in each of these traits is caused by the presence of different alleles at individual loci.

Several important principles emerged from Mendel’s work. The first, the principle of dominant and recessive inheritance, was discussed in Chapter 3 . Mendel also discovered the principle of segregation, which states that sexually reproducing organisms possess genes that occur in pairs and that only one member of this pair is transmitted to the offspring (i.e., it segregates). The prevalent thinking during Mendel’s time was that hereditary factors from the two parents are blended in the offspring. In contrast, the principle of segregation states that genes remain intact and distinct. An allele for “smooth” seed shape can be transmitted to an offspring in the next generation, which can in turn transmit the same allele to its own offspring. If genes were somehow blended in offspring instead of remaining distinct, it would be impossible to trace genetic inheritance from one generation to the next. Thus the principle of segregation was a key development in modern genetics.

Mendel’s principle of independent assortment was another significant contribution to genetics. This principle states that genes at different loci are transmitted independently. Consider the two loci mentioned previously. One locus can have either the “smooth” or the “wrinkled” allele, and the other can have either the “tall” or the “short” allele. In a reproductive event a parent transmits one allele from each locus to its offspring. The principle of independent assortment dictates that the transmission of a specific allele at one locus (“smooth” or “wrinkled”) has no effect on which allele is transmitted at the other locus (“tall” or “short”).

The principle of segregation describes the behavior of chromosomes in meiosis. The genes on chromosomes segregate during meiosis, and they are transmitted as distinct entities from one generation to the next. When Mendel performed his critical experiments, he had no direct knowledge of chromosomes, meiosis, or genes (indeed, the last term was not coined until 1909, long after Mendel’s death). Although his work was published in 1865 and cited occasionally, its fundamental significance was unrecognized for several decades. Yet Mendel’s research, which was eventually replicated by other researchers at the turn of the 20th century, forms the foundation of much of modern genetics.

The Concept of Phenotype

The term genotype has been defined as an individual’s genetic constitution at a locus. The phenotype is what is actually observed physically or clinically. Genotypes do not uniquely correspond to phenotypes. Individuals with two different genotypes, a dominant homozygote and a heterozygote, can have the same phenotype. An example is cystic fibrosis ( Clinical Commentary 4.1 ), an autosomal recessive condition in which only the recessive homozygote is affected. Conversely, the same genotype can produce different phenotypes in different environments. An example is the recessive disease phenylketonuria (PKU, see Chapter 7 ), which is seen in approximately 1 of every 10,000 European-ancestry births. Mutations at the locus encoding the metabolic enzyme phenylalanine hydroxylase render the homozygote unable to metabolize the amino acid phenylalanine. Although babies with PKU are unaffected at birth, their metabolic deficiency produces a buildup of phenylalanine and its toxic metabolites. This process is highly destructive to the central nervous system, and it eventually produces severe mental impairment. It has been estimated that babies with untreated PKU lose, on average, 1 to 2 IQ points per week during the first year of life. Thus the PKU genotype can produce a severe disease phenotype. However, it is straightforward to screen for PKU at birth (see Chapter 13 ), and damage to the brain can be avoided by initiating a low-phenylalanine diet within 1 month after birth. The child still has the PKU genotype, but the phenotype has been profoundly altered by environmental modification.

Clinical Commentary 4.1

Cystic Fibrosis

Courtesy Dr. Edward Klatt, Florida State University School of Medicine.

Cystic fibrosis (CF) is one of the most common single-gene disorders in North America, affecting approximately 1 in 2000 to 1 in 4000 European-American newborns. The prevalence among African-Americans is about 1 in 15,000 births, and it is less than 1 in 30,000 among Asian-Americans. Approximately 30,000 Americans and 70,000 people worldwide are estimated to have this disease.

CF was first identified as a distinct disease entity in 1938 and was termed “cystic fibrosis of the pancreas.” This refers to the fibrotic lesions that develop in the pancreas, one of the principal organs affected by this disorder ( Fig. 4.1 ). Approximately 85% of CF patients have pancreatic insufficiency, in which the pancreas is unable to secrete digestive enzymes, contributing to chronic malabsorption of nutrients. The intestinal tract is also affected, and approximately 15% to 20% of newborns with CF have meconium ileus (thickened, obstructive intestinal matter). The sweat glands of CF patients are abnormal, resulting in high levels of chloride in the sweat. This is the basis for the sweat chloride test commonly used in the diagnosis of this disease. More than 95% of males with CF are sterile due to absence or obstruction of the vas deferens.

A , Normal pancreas. B , Pancreas from a cystic fibrosis patient, showing infiltration of fat and fibrotic lesions. C , Normal lung tissue. D , Lung tissue from a cystic fibrosis patient, which shows extensive destruction as a result of obstruction and infection.

Courtesy Dr. Edward Klatt, Florida State University School of Medicine.

The major cause of morbidity and mortality in CF patients is pulmonary disease. Patients with CF have lower airway inflammation and chronic bronchial infection, progressing to end-stage lung disease characterized by extensive airway damage and fibrosis of lung tissue. Airway obstruction and lung injury are thought to be caused by a dehydrated airway surface and reduced clearance, resulting in thick airway mucus. This is associated with infection by bacteria such as Staphylococcus aureus and Pseudomonas aeruginosa. The combination of airway obstruction, inflammation, and infection leads to destruction of the airways and lung tissue, resulting eventually in death from pulmonary disease in more than 90% of CF patients.

As a result of improved nutrition, airway clearance techniques, and antibiotic therapies, the survival rate of CF patients has improved substantially during the past three decades. Median survival time in the United States is now nearly 40 years. CF has highly variable expression, with some patients experiencing only mild respiratory difficulty and nearly normal survival. Others have much more severe respiratory problems and may survive less than two decades.

CF is caused by mutations in a gene, CFTR, ^∗ that encodes the cystic fibrosis transmembrane conductance regulator ( Fig. 4.2 ). CFTR encodes cyclic AMP-regulated chloride ion channels that span the membranes of specialized epithelial cells, such as those that line the bowel and lung. In addition, CFTR is involved in regulating the transport of sodium ions across epithelial cell membranes. The role of CFTR in sodium and chloride transport helps us to understand the multiple effects of mutations at the CF locus. Defective ion transport results in salt imbalances, depleting the airway of water, and producing the thick, obstructive secretions seen in the lungs. The pancreas is also obstructed by thick secretions, leading to fibrosis and pancreatic insufficiency. The chloride ion transport defect explains the abnormally high concentration of chloride in the sweat secretions of CF patients; chloride cannot be reabsorbed from the lumen of the sweat duct.

Classes of mutations in the CFTR gene and their effects in cells. Class I mutations result in no synthesis of the gene product. Class II mutations produce a defective protein product that is destroyed in proteasomes. Class III mutations produce a protein that gets to the cell surface but is abnormally regulated. Class IV mutations result in defective chloride ion conductance. Class V mutations are typically promoter or intron–exon splicing mutations that reduce the number of mRNA transcripts, allowing some normal protein products. Class VI mutations result in increased rates of turnover of the chloride channel at the cell surface.

Courtesy Dr. Edward Klatt, Florida State University School of Medicine.

DNA sequence analysis has revealed nearly 2000 different mutations at the CFTR locus. The most common of these, labeled F508del, is a three-base deletion that results in the loss of a phenylalanine residue (F) at position 508 of the CFTR protein. F508del accounts for nearly 70% of all CF mutations. This mutation, along with several dozen other relatively common ones, is assayed in the genetic diagnosis of CF (see Chapter 13 ).

Identification of the specific mutation or mutations that are responsible for CF in a patient can help to predict the severity of the disease. For example, the most severe classes of mutations (of which F508del is an example) result in a complete lack of chloride ion channel production or in channels that cannot migrate to the cell membrane. Patients homozygous for these mutations nearly always have pancreatic insufficiency. In contrast, other mutations (e.g., R117H, a missense mutation) result in ion channels that do proceed to the cell membrane but respond poorly to cyclic AMP and consequently do not remain open as long as they should. The phenotype is thus milder, and patients who have this mutation are less likely to have pancreatic insufficiency. Some males with mild CFTR mutations have only congenital bilateral absence of the vas deferens (CBAVD) but little, if any, lung or gastrointestinal disease. The correlation between genotype and phenotype is far from perfect, however, indicating that modifier loci and environmental factors must also influence expression of the disease (see text). In general there is a reasonably good correlation between genotype and pancreatic function and a more variable relationship between genotype and pulmonary function.

The ability to identify CFTR mutations has led to surveys of persons who have one (heterozygous) or two (homozygous) CFTR mutations, but who do not have cystic fibrosis. They have increased risks for a number of disease conditions, including CBAVD, bronchiectasis (chronic dilatation of the bronchi and abnormal mucus production), and pancreatitis (pancreatic inflammation).

By enhancing our understanding of the pathophysiology of CF, identification of CFTR has opened the possibility of new treatments for this disease. Examples include administration of drugs that cause ribosomes to read through the premature stop codons that account for approximately 7% of CFTR mutations. Other drugs can increase the activity of chloride channels in patients with class III or IV mutations. The first FDA-approved drug for CF treatment, ivacaftor, increases CFTR channel activity in response to ATP. A second FDA-approved drug, lumacaftor, can be used in combination with ivacaftor and has been shown to significantly improve lung function in CF patients homozygous for the common F508del mutation. Gene therapy, in which the normal CFTR gene is placed in viral or other vectors that are then introduced to the patient’s airway (see Chapter 13 ), is also being actively investigated. This strategy, however, has encountered difficulties because viral vectors can induce an inflammatory immune response.

∗ Conventionally the symbol for a gene, such as CFTR , is shown in italics, and the symbol for the protein product is not.

This example shows that the phenotype is the result of the interaction of genotype and environmental factors. It should be emphasized that “environment” can include the genetic environment (i.e., genes at other loci whose products can interact with a specific gene or its product).

Basic Pedigree Structure

The pedigree is one of the most commonly used tools in medical genetics. It illustrates the relationships among family members, and it shows which family members are affected or unaffected by a genetic disease. Typically an arrow denotes the proband, the first person in whom the disease is diagnosed in the pedigree. The proband is sometimes also referred to as the index case or propositus (proposita for a female). Fig. 4.3 describes the features of pedigree notation.

Basic pedigree notation.

For further details, see Bennett RL, French KS, Resta RG, Doyle DL. Standardized human pedigree nomenclature: update and assessment of the recommendations of the National Society of Genetic Counselors. J Genet Couns. 2008;17:424-433.

When discussing relatives in families, one often refers to degrees of relationship. First-degree relatives are those who are related at the parent–offspring or sibling (brother and sister) level. Second-degree relatives are those who are removed by one additional generational step (e.g., grandparents and their grandchildren, uncles or aunts and their nieces or nephews). Continuing this logic, third-degree relatives would include, for example, one’s first cousins and great-grandchildren.

Characteristics of Autosomal Dominant Inheritance

Autosomal dominant diseases are seen in roughly 1 of every 200 individuals (see Table 1.3 in Chapter 1 ). Individually each autosomal dominant disease is rather rare in populations, with the most common ones having gene frequencies of about 0.001. For this reason matings between two individuals who are both affected by the same autosomal dominant disease are uncommon. Most often affected offspring are produced by the union of an unaffected parent with an affected heterozygote. The Punnett square in Fig. 4.4 illustrates such a mating. The affected parent can pass either a disease allele or a normal allele to his or her children. Each event has a probability of 0.5. Thus on the average, half of the children will be heterozygotes and will express the disease, and half will be unaffected homozygotes.

Punnett square illustrating the mating of an unaffected individual (aa) with an individual who is heterozygous for an autosomal dominant disease gene (Aa). The genotypes of affected offspring are shaded.

Postaxial polydactyly, the presence of an extra digit next to the fifth digit ( Fig. 4.5 ), can be inherited as an autosomal dominant trait. An idealized pedigree for this disease, shown in Fig. 4.6 , illustrates several important characteristics of autosomal dominant inheritance. First, the two sexes exhibit the trait in approximately equal ratios, and males and females are equally likely to transmit the trait to their offspring. This is because postaxial polydactyly is an autosomal disease (as opposed to a disease caused by an X chromosome mutation, in which these ratios typically differ). Second, there is no skipping of generations; if an individual has polydactyly, one parent must also have it. This leads to a vertical transmission pattern in which the disease phenotype is usually seen in one generation after another. If neither parent has the trait, none of the children will have it. Third, father-to-son transmission of the disease gene is observed. Although father-to-son transmission is not required to establish autosomal dominant inheritance, its presence in a pedigree rules out some other modes of inheritance (particularly X-linked inheritance; see Chapter 5 ). Finally, as we have already seen, an affected heterozygote transmits the disease-causing allele to approximately half of their children. However, because gamete transmission, like coin tossing, is subject to chance fluctuations, it is possible that all or none of the children of an affected parent will have the trait. When large numbers of matings of this type are studied, the proportion of affected children closely approximates 1/2.

Postaxial polydactyly. An extra digit is located next to the fifth digit.

Pedigree illustrating the inheritance pattern of postaxial polydactyly, an autosomal dominant disorder. Affected individuals are represented by shading.

Recurrence Risks

Parents at risk for producing children with a genetic disease typically want to know the risk, or probability that their future children will be affected. This probability is termed the recurrence risk. If one parent is affected by an autosomal dominant disease and the other is unaffected, the recurrence risk for each child is 1/2 (assuming that the affected parent is a heterozygote, which is nearly always the case). It is important to keep in mind that each birth is an independent event, as in the coin-tossing examples. Thus even if the parents have already had a child with the disease, their recurrence risk remains 1/2. Even if they have had several children, all affected (or all unaffected) by the disease, the law of independence dictates that the probability that their next child will have the disease is still 1/2. Although this concept seems intuitively obvious, it is commonly misunderstood by the lay population. Further aspects of communicating risks to families are discussed in Chapter 15 .

Characteristics of Autosomal Recessive Inheritance

Fig. 4.8 is a pedigree showing the inheritance pattern of an autosomal recessive form of albinism that results from mutations in the gene that encodes tyrosinase, a tyrosine-metabolizing enzyme. ^∗ The resulting tyrosinase deficiency creates a block in the metabolic pathway that normally leads to the synthesis of melanin pigment. Consequently the affected individual has very little pigment in the skin, hair, and eyes ( Fig. 4.9 ). Because melanin is also required for the normal development of the optic fibers, persons with albinism can also display nystagmus (rapid uncontrolled eye movement), strabismus (deviation of the eye from its normal axis), and reduced visual acuity. The pedigree demonstrates most of the important criteria for distinguishing autosomal recessive inheritance ( Table 4.1 ). First, unlike autosomal dominant diseases in which the disease phenotype is seen in one generation after another, autosomal recessive diseases are usually observed in one or more siblings, but not in earlier generations. Second, as in autosomal dominant inheritance, males and females are affected in equal proportions. Third, on average, one-fourth of the offspring of two heterozygous carriers will be affected with the disorder. Finally, consanguinity is present more often in pedigrees involving autosomal recessive diseases than in those involving other types of inheritance (see Fig. 4.8 ). The term consanguinity (Latin, “with blood”) refers to the mating of related persons. It is sometimes a factor in recessive disease because related persons are more likely to share the same disease-causing alleles. Consanguinity is discussed in greater detail later in this chapter.

∗ This form of albinism, termed tyrosinase-negative oculocutaneous albinism (OCA1), is distinguished from a second, milder form termed tyrosinase-positive oculocutaneous albinism (OCA2). OCA2 is typically caused by mutations in a gene on chromosome 15, whose protein product is thought to be involved in the transport and processing of tyrosine and tyrosinase.

Pedigree showing the inheritance pattern of tyrosinase-negative albinism, an autosomal recessive disease. Consanguinity in this pedigree is denoted by a double bar connecting the parents of the affected individuals.

An African woman with oculocutaneous albinism, illustrating a lack of pigmentation in the hair and skin. She is looking away from the camera because her eyes are more sensitive to light than are those of persons with normally pigmented retinas.

Courtesy Dr. Phil Fischer, Mayo Clinic.

Recurrence Risks

As already discussed, the most common mating type seen in recessive disease involves two heterozygous carrier parents. This reflects the relative commonness of heterozygous carriers and the fact that many autosomal recessive diseases are severe enough that affected individuals are less likely to become parents.

The Punnett square in Fig. 4.7 demonstrates that one-fourth of the offspring from this mating will be homozygous for the disease gene and therefore affected. The recurrence risk for the offspring of carrier parents is then 25%. These are average figures. In any given family, chance fluctuations are likely, but a study of a large number of families would yield a figure quite close to this fraction.

Occasionally a carrier of a recessive disease-causing allele mates with a person who is homozygous for this allele. In this case, roughly half of their children will be affected, and half will be heterozygous carriers. The recurrence risk is 50%. Because this pattern of inheritance mimics that of an autosomal dominant trait, it is sometimes referred to as quasidominant inheritance. With studies of extended pedigrees in which matings of heterozygotes are observed, quasidominant inheritance can be distinguished from true dominant inheritance.

When two persons affected by a recessive disease mate, all of their children must also be affected. This observation helps to distinguish recessive from dominant inheritance because two parents who are both affected by a dominant disease are almost always both heterozygotes and one-fourth of their children, on average, will be unaffected.

“Dominant” Versus “Recessive”; Some Cautions

The preceding discussion has treated dominant and recessive disorders as though they belong in rigid categories. However, these distinctions are becoming less strict as our understanding of these diseases increases. Most dominant diseases are actually more severe in affected homozygotes than in heterozygotes. An example is achondroplasia, an autosomal dominant disorder in which heterozygotes have reduced stature ( Fig. 4.10 ). Heterozygotes have a nearly normal life span, estimated to be about 10 years less than average. Affected homozygotes are much more severely affected and usually die in infancy from respiratory failure (see Chapter 10 for further discussion of achondroplasia).

Achondroplasia. This girl has short limbs relative to trunk length. She also has a prominent forehead, low nasal root, and redundant skinfolds in the arms and legs.

Although heterozygous carriers of recessive disease genes are clinically unaffected, the effects of recessive genes can often be detected in heterozygotes because they result in reduced levels of enzyme activity. This is usually the basis for biochemical carrier detection tests (see Chapter 13 ). A useful and valid way to distinguish dominant and recessive disorders is that heterozygotes are clinically affected in most cases of dominant disorders, whereas they are almost always clinically unaffected in recessive disorders.

Another caution is that a disease may be inherited in autosomal dominant fashion in some cases and in autosomal recessive fashion in others. Familial isolated growth hormone deficiency (IGHD), another disorder that causes reduced stature, is one such disease. DNA sequencing of a pituitary growth hormone gene on chromosome 17 (GH1) has revealed a number of different mutations that can produce IGHD. Recessive IGHD can be caused by nonsense, frameshift, or splice-site mutations that have a loss-of-function effect in which a mature protein product is not synthesized. Because they have one normal copy of GH1, heterozygotes still produce half of the normal amount of growth hormone. This is sufficient for normal stature. Homozygotes for these mutations produce no GH1 product and have reduced stature.

Dominant IGHD can result from dominant negative mutations (see Chapter 3 ) in GH1. In one form of dominantly inherited IGHD, a splice-site mutation deletes the third exon of GH1, producing an abnormal protein that proceeds to the secretory granules. Here the abnormal GH1 product interacts with the normal protein encoded by the normal GH1 allele. The abnormal molecules disable the normal growth hormone molecules, resulting in greatly reduced production of GH1 product and thus reduced stature.

Another example is given by β-thalassemia, a condition discussed in Chapter 3 . Although the great majority of β-thalassemia cases occur as a result of autosomal recessive alleles, a small fraction of cases are inherited in autosomal dominant fashion. Some of these are caused by nonsense or frameshift mutations that terminate translation in exon 3 of the β-globin gene or in downstream exons. The resulting messenger RNA (mRNA) proceeds to the cytoplasm and produces unstable β-globin chains. In heterozygotes, these abnormal chains exert a dominant negative effect on the normal β-globin chains produced by the normal allele. In contrast, frameshift or nonsense mutations that result in termination of translation in exons 1 or 2 of the gene result in very little abnormal mRNA in the cytoplasm, leaving the product of the normal allele intact. In these cases the heterozygote is unaffected.

These examples illustrate some of the complexities involved in applying the terms “dominant” and “recessive.” They also show how molecular analysis of a gene can help to explain important disease features.

A final caution is that the terms dominant and recessive apply to traits, strictly speaking, not genes. To see why, consider the sickle cell mutation discussed in Chapter 3 . Homozygotes for this mutation develop sickle cell disease. Heterozygotes, who are said to have sickle cell trait, are usually clinically normal. However, a heterozygote has an increased risk for splenic infarctions at very high altitude. Is the mutant gene then dominant or recessive? Clearly it makes more sense to refer to sickle cell disease as recessive and sickle cell trait as dominant. Nonetheless, it is common (and often convenient) to apply the terms dominant and recessive to genes.

De Novo Mutation

If a child is born with a genetic disease that has not occurred previously in the family, it is possible that the disease is the product of a de novo (new) mutation. That is, the gene transmitted by one of the parents underwent a change in DNA sequence, resulting in a mutation from a normal to a disease-causing allele. The alleles at this locus in the parent’s other germ cells would still be normal. In this case the recurrence risk for the parents’ subsequent offspring would not be elevated above that of the general population. However, the offspring of the affected child might have a substantially elevated risk (e.g., it would be 50% for an autosomal dominant disease). A large fraction of the observed cases of many autosomal dominant diseases are the result of de novo mutations. For example, approximately 7/8 of all cases of achondroplasia are caused by de novo mutations, and only 1/8 are inherited from an affected parent. This is primarily because the disease tends to limit the potential for reproduction. To provide accurate risk estimates, it is essential to know whether a patient’s disease is due to an inherited mutation or a de novo mutation. This can be done only if an adequate family history has been taken.

De novo mutations are a common cause of the appearance of a genetic disease in a person with no previous family history of the disorder. The recurrence risk for the person’s siblings is very low, but the recurrence risk for the person’s offspring may be substantially increased.

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