Medical Genetics

Medical Genetics Instructor: Prof. Dr. Fadel A. Sharif

Contact Medical Laboratory Sciences University Clinic-Genetics Diagnosis lab fsharif@iugaza.edu

Course Syllabus - Text: Thompson & Thompson Genetics in Medicine, 7th Ed., Nussbaum, McInnes, Willard, 2007. Saunders (Required) - References: Emery’s Elements of Medical Genetics, 13 Ed., Turnpenny & Ellard. 2007. Churchill Livingstone - Jorde, Carey, Bamshad. Medical Genetics, 4th edition. Mosby Elsevier, 2010. Grades Quizzes: 10% Presentation: 10% One Midterm exam worth 30% Final exam: 50%

Topics • Patterns of Single-Gene Inheritance • Genetics of Common Disorders with Complex Inheritance • Principles of (Clinical) Cytogenetics • Clinical Cytogenetics: Disorders of the Autosomes and the Sex Chromosomes • Genetic Variation in Individuals and Populations: Mutation and Polymorphism • Human Gene Mapping and Disease Gene Identification • Treatment of Genetic Disease • Cancer Genetics

Patterns of Single-Gene Inheritance Lecture 1

Occur on average in fixed proportions among the offspring of specific types of matings • The 2015 online version of Mendelian Inheritance in Man (OMIM) lists 3,341 genes with phenotype-causing mutation.

Primarily disorders of the pediatric age range; less than 10% manifest after puberty, and only 1% occur after the end of the reproductive period • In a study of more than 1 million live births, the incidence of serious single-gene disorders was estimated to be 0.36%; among hospitalized children, ~6% to 8%

A survey of OMIM for mendelian forms of 17 of the most common adult diseases, such as heart disease, stroke, cancer, and diabetes, revealed nearly 200 mendelian disorders whose phenotypes included these common adult illnesses. • These mendelian forms are important in individual patients because of their significance for the health of other family members and because of the availability of genetic testing and detailed management options for many of them.

OVERVIEW AND CONCEPTSVariation in genes: • For many genes, there is a single prevailing allele, the wild-type or common allele. The other versions of the gene are variant or mutant alleles • A given set of alleles at a locus or cluster of loci on a chromosome is referred to as a haplotype. • If there are at least two relatively common alleles at the locus in the population, the locus is said to exhibit polymorphism

Genotype and Phenotype • Genotype: set of alleles that make genetic constitution • Phenotype: observable expression of a genotype as morphological, clinical, cellular, biochemical trait • Pleiotropy: a single abnormal gene or gene pair producing multiple diverse phenotypic effects

Compound heterozygous: two different mutant alleles of the same gene • Hemizygous: male with respect to X-linked genes.

Pedigrees • Single-gene disorders are characterized by their patterns of transmission in families • Pedigree: graphical representation of family tree using standard symbols • The extended family depicted in such a pedigree is a kindred • Proband (propositus, index case): affected member through whom a family with genetic disease is brought to attention • Consultand: who brings family to attention by consulting a geneticist. May be an affected individual or unaffected relative of proband

Figure 7-1 Symbols commonly used in pedigree charts. Although there is no uniform system of pedigree notation, the symbols used here are according to recent recommendations made by professionals in the field of genetic counseling.

The proband, III-5, represents an isolated case of a genetic disorder. She has four siblings. Her partner/spouse is III-6, and they have three children. The proband has nine first-degree relatives, nine second-degree relatives, two third-degree relatives (first cousins), and four fourth-degree relatives (first cousins once removed). IV-3, IV-5, and IV-6 are second cousins of IV-1 and IV-2. IV-7 and IV-8, whose parents are consanguineous, are doubly related to the proband.

Consanguineous: couples who have one or more ancestors in common • Isolated case: only one affected member in a family • Sporadic case: if due to new mutation • Fitness: a measure of impact of condition on reproduction. Defined as: number of offspring (who survive to reproductive age) affected individuals can have, as compared to an appropriate control • Patterns of single-gene inheritance: autosomal recessive/dominant, X-inked recessive/dominant

Dominant and Recessive Inheritance • Recessive: a phenotype expressed only in homozygotes (for X-linked, male hemizygotes) and not in heterozygotes • Most recessive disorders are due to mutations that reduce or eliminate function of a gene (i.e., loss-of-function mutations)

Dominant: a phenotype expressed in both homozygotes and heterozygotes for a mutant allele. • Pure dominant disease: homozygotes and heterozygotes for mutant allele are equally affected. Pure dominant disorders rarely if ever exist in medical genetics • Codominant: phenotypic expression of two different alleles for a locus • Dominant disorders are usually more severe in homozygotes. Thus in heterozygotes, disease is incompletely dominant (or semidominant).

Factors affecting pedigree patterns Penetrance and expressivity • Some disorders are not expressed at all in an individual despite having same genotype that causes disorder in others in his family. • In others, same disorder may have extremely variable expression in terms of clinical severity/range of symptoms/onset age • Phenotypic expression can be modified by effects of aging/other genetic loci (modifier loci)/effectsof environment/ allelic heterogeneity

Penetrance: probability that a gene will have any phenotypic expression at all. It is the percentage of people with a predisposing genotype who are actually affected. • When some completely fail to produce phenotype, the gene is said to show reduced penetrance.

Expressivity: severity of expression of phenotype among individuals with same disease causing genotype. • When severity differs, phenotype is said to have variable expressivity

Neurofibromatosis-I (NF1) • A common AD disorder of the NS, eye, and skin (1/3500 births) • Characterized by: • Growth of multiple benign fleshy tumors (neurofibromas) in skin • Multiple flat, irregular pigmented skin lesions (café au lait spots) • Small benign tumors (hamartomas) called Lisch nodules on iris of the eye • Less frequently: MR, CNS tumors, diffuse plexiform neurofibromas, and development of cancer of the NS and muscle. • Thus, the condition has a pleiotropic phenotype.

NF1 • Adult heterozygotes almost always show some sign (i.e., penetrance is 100% in adults) • Some may have café au lait spots, freckles on axillary skin, and Lisch nodules, others may have life-threatening benign tumors in spinal cord or malignant sarcomas of an extremity (i.e., variable expressivity)

Neurofibromatosis-1: café au lait spots, hyperpigmented spots on the skin, are a useful diagnostic sign in family members who otherwise may appear unaffected. Most patients have six or more spots at least 15 mm in diameter, usually on the trunk.

Diagnosis of NF1 is further complicated in children because the signs develop gradually during childhood. • e.g., in the newborn period, less than half of all affected newborns show even the most subtle sign of the disease, an increased incidence of café au lait spots. • Penetrance, therefore, is age dependent. • Many different mutations have been found in the NF1 gene, all of which appear to cause loss of function of its gene product, neurofibromin. Approximately half the cases of NF1 result from a new rather than an inherited mutation

The chief genetic problem in counseling families of patients with NF1 is to decide between two possibilities: Is the disease in the proband sporadic, that is, due to new mutation, or has the patient inherited a clinically significant form of the disorder from a parent in whom the gene is present but only mildly expressed? • If the proband has inherited the defect, the risk that any of his or her sibs will also inherit it is 50%; • but if the proband has a new mutant gene, there is very little risk that any sib will be affected.

The disorder can be detected presymptomatically and even prenatally by molecular genetic analysis. • Unfortunately, molecular testing can generally only answer whether the condition will occur and not how severe it will be. • Except for the association of complete gene deletions with dysmorphic features, mental retardation, and increased number of neurofibromas at an early age, there is no correlation between severity of the phenotype and particular mutant NF1 alleles.

Figure 7-4 Pedigree of family with NF-1, apparently originating as a new mutation in the proband of generation III (arrow). This individual appears to have a new mutant allele of NF1 because his parents and their parents are all unaffected.

Split-hand deformity • Another example of an autosomal dominant malformation with reduced penetrance is the split-hand deformity, a type of ectrodactyly. • The malformation originates in the sixth or seventh week of development, when the hands and feet are forming. • The disorder demonstrates locus heterogeneity, with atleast five loci recognized, although the actual gene responsible has been identified in only a few. • Failure of penetrance in pedigrees of split-hand malformation can lead to apparent skipping of generations, and this complicates genetic counseling because an at-risk person with normal hands may nevertheless carry the gene for the condition and thus be capable of having children who are affected.

Figure 7-5 Split-hand deformity, an AD trait involving the hands and feet, in a 3-month-old boy. A, Upper part of body. B, Lower part of body.

In the pedigree, the consultand’s mother is a nonpenetrant carrier of the split-hand mutation. • Review of the literature on split-hand deformity suggests that there is reduced penetrance of about 70%. Figure 7-6 Pedigree of split-hand deformity demonstrating failure of penetrance in the mother of the consultand. Reduced penetrance must be taken into account in genetic counseling.

Age of Onset • Genetic disorders can appear at any time in the lifetime of an individual, ranging from early in intrauterine development all the way to the postreproductive years, and all ages in between. • Some may be lethal prenatally, whereas others may interfere with normal fetal development and can be recognized prenatally (e.g., by ultrasonography) but are consistent with a full-live-born infant;

Still others may be recognized only at birth (congenital). Thus, in a pedigree of a family with a lethal disorder affecting a fetus early in pregnancy, the pattern of disease occurrence may be obscure because all that one observes are multiple miscarriages and fetal losses or apparently reduced fertility, rather than recurrence of the prenatal disease itself. • Conversely, in a family with a late-onset dominant disorder, an affected individual may have parents and children reportedly free of disease because the carrier parent died of unrelated causes before the disease could develop, and the children at risk have not reached the age at which the mutant gene reveals itself in a disease phenotype.

Other Factors Affecting Pedigree Patterns • The inheritance pattern of an individual pedigree may be obscured by a number of other factors that may make the mode of inheritance difficult to interpret. • Diagnostic difficulties may be due to reduced penetrance or variable expressivity of the disease; • other genes and environmental factors may affect gene expression; • persons of some genotypes may fail to survive to the time of birth;

accurate information about the presence of the disorder in relatives or about family relationships may be lacking; • the occurrence of new mutations can contribute to the occurrence of dominant and X-linked disease; and finally, • with the small family size typical of most developed countries today, the patient may by chance alone be the only affected family member, making determination of any inheritance pattern very difficult.

CORRELATING GENOTYPE AND PHENOTYPE • An important component of medical genetics is identifying and characterizing the genotypes responsible for particular disease phenotypes. • When a genetic disorder that appears to be inherited as a single-gene disorder is thoroughly analyzed, it is frequently found to be genetically heterogeneous; i.e., it includes a number of phenotypes that are similar but are actually determined by different genotypes at different loci. • Genetic heterogeneity may be the result of different mutations at the same locus (allelic heterogeneity), mutations at different loci (locus heterogeneity), or both.

Recognition of genetic heterogeneity is an important aspect of clinical diagnosis and genetic counseling. • Moreover, distinct phenotypes inherited in different families can result from different mutant alleles in the same gene. This phenomenon, known as clinical or phenotypic heterogeneity, is well known and must be taken into account in correlating genotype and phenotype.

Allelic Heterogeneity • Allelic heterogeneity is an important cause of clinical variation. Many loci possess more than one mutant allele; in fact, at a given locus, there may be several or many mutations. • E.g., nearly 1400 different mutations have been found worldwide in the cystic fibrosis transmembrane conductance regulator (CFTR) among patients with CF. • Sometimes, these different mutations result in clinically indistinguishable disorders. In other cases, different mutant alleles at the same locus produce a similar phenotype but along a continuum of severity; for example, some CFTR mutations cause patients to have classic CF with pancreatic insufficiency, severe progressive lung disease, and congenital absence of the vas deferens in males, whereas patients carrying other mutant alleles have lung disease but normal pancreatic function, and still others have only the abnormality of the male reproductive tract.

Since any particular mutant allele is generally uncommon in the population, most people with rare autosomal recessive disorders are compound heterozygotes rather than true homozygotes. • Because different allelic combinations may have somewhat different clinical consequences, clinicians must be aware of allelic heterogeneity as one possible explanation for variability among patients considered to have the same disease.

There are, however, some well-recognized exceptions to the observation that compound heterozygotes are more common than true homozygotes: • The first is when the affected individuals inherited the same mutant allele from consanguineous parents, who both carry the same mutant allele they inherited from a common ancestor. • Second, one mutant allele may be responsible for a large proportion of the cases of an autosomal recessive condition in a particular ethnic group, and so many patients from that group will be homozygous for this allele. • The third is when the disorder normally has little if any allelic heterogeneity because the disease phenotype caused by a particular mutation is specific to that mutation (e.g., sickle cell disease).

Locus Heterogeneity • For many phenotypes, pedigree analysis alone has been sufficient to demonstrate locus heterogeneity. For example, retinitis pigmentosa, a common cause of visual impairment due to photoreceptor degeneration, has long been known to occur in autosomal dominant, autosomal recessive, and X-linked forms. • In recent years, the heterogeneity has been shown to be even more extensive; pedigree analysis combined with gene mapping has demonstrated that there are at least 43 loci responsible for 5 X-linked forms, 14 autosomal dominant forms, and 24 autosomal recessive forms of retinitis pigmentosa that are not associated with other phenotypic abnormalities. • If one includes disorders in which retinitis pigmentosa is found in conjunction with other defects such as MR or deafness, there are nearly 70 different genetic diseases manifesting retinitis pigmentosa.

Phenotypic Heterogeneity • Different mutations in the same gene can sometimes give rise to strikingly different phenotypes. For example, certain loss-of-function mutations in the RET gene, which encodes a receptor tyrosine kinase, can cause dominantly inherited failure of development of colonic ganglia, leading to defective colonic motility and severe chronic constipation (Hirschsprung disease). • Other mutations in the same gene result in unregulated hyperfunction of the kinase, leading to dominantly inherited cancer of the thyroid and adrenal glands (multiple endocrine neoplasia type 2A and 2B). • A third group of mutations in RET causes both Hirschsprung disease and multiple endocrine neoplasia in the same individuals.

A comparable situation occurs with the LMNA gene, which encodes lamin A/C, a nuclear membrane protein. • Different LMNA mutations have been associated with half a dozen phenotypically distinct disorders, including Emery-Dreifuss muscular dystrophy, one form of hereditary dilated cardiomyopathy, one form of the Charcot-Marie-Tooth peripheral neuropathy, a disorder of normal adipose tissue called lipodystrophy, and the premature aging syndrome known as Hutchinson-Gilford progeria.

AUTOSOMAL PATTERNS OF MENDELIAN INHERITANCEAutosomal Recessive Inheritance • Autosomal recessive disease occurs only in homozygotes or compound heterozygotes. • Homozygotes (affected) must have inherited a mutant allele from each parent (barring uniparental disomy or new mutation, which is rare in autosomal recessive disorders). • Three types of matings can lead to homozygous affected offspring. The mutant recessive allele is symbolized as r and its normal dominant allele as R. Although any mating in which each parent has at least one recessive allele can produce homozygous affected offspring, the most common mating by far is between two unaffected heterozygotes.

The proband may be the only affected family member, but if any others are affected, they are usually in the same sibship and not elsewhere in the kindred. Figure 7-7 Typical pedigree showing autosomal recessive inheritance

Sex-Influenced Disorders • Autosomal recessive disorders generally show the same frequency and severity in males and females. • Some autosomal recessive phenotypes, however, are sex-influenced, i.e, expressed in both sexes but with different frequencies or severity. • Among autosomal disorders, hemochromatosis is an example of a phenotype more common in males. • This autosomal recessive disorder of iron metabolism occurs most commonly in the approximately 0.5% of individuals of northern European extraction that are homozygous for a missense mutation replacing cysteine at position 282 with a tyrosine (Cys282Tyr) in the HFE gene.

Cys282Tyr homozygotes have enhanced absorption of dietary iron and often demonstrate laboratory abnormalities suggestive of excessive body stores of iron, although the condition only rarely leads to iron overload and serious damage to the heart, liver, and pancreas. • The lower incidence of the clinical disorder in females (one fifth to one tenth that of males) is believed to be related, among other factors, to lower dietary intake of iron, lower alcohol usage, and increased iron loss through menstruation among females.

Gene Frequency and Carrier Frequency • The mutant alleles responsible for a recessive disorder are generally rare, and so most people will not have even one copy of the mutant allele. • Among individuals with at least one copy of the mutant allele, however, the frequency of clinically unaffected heterozygotes with one normal allele and one mutant allele is always much greater than the frequency of affected individuals with two rare mutant alleles. • Because an autosomal recessive disorder must be inherited through both parents, the risk that any carrier will have an affected child depends partly on the chance that his or her mate is also a carrier of a mutant allele for the condition. • Thus, knowledge of the carrier frequency of a disease is clinically important for genetic counseling.

The most common autosomal recessive disorder in white children is cystic fibrosis (CF), caused by mutations in the CFTR gene. • CF is virtually unknown in Asian populations and is relatively rare in African American populations, but in white populations, about 1 child in 2000 has two mutant CFTR alleles and has the disease. • The frequency of carriers for one of the hundreds of possible mutant CFTR alleles can be calculated to be approximately 1/29.

In a population of 3247 white individuals, therefore, you can expect 1 CF patient, 112 unaffected carriers of a CFTR mutation, and 3134 normal homozygotes. • Because a patient has two mutant CFTR alleles and a carrier has only one, (112 ×1)/(112 ×1+1×2)=112/114 (about 98%) of all mutant CFTR alleles in this population of 3247 individuals are hidden in carriers (who usually are unaware that they are carriers), and only 2% are in patients.

Medical Genetics