Genetic Disorders Lecture_Part II_case studies (1).pdf

Genetics Disorder Studies Part ll of II: Case Studies (SDL) Robin T. Varghese Ph.D. [email protected] Note to students: Please read the following clinical scenarios and background information for each of the 4 genetic disorders. These case studies are intended for student directed learning (SDL)...

Genetics Disorder Studies Part ll of II: Case Studies (SDL) Robin T. Varghese Ph.D. [email protected] Note to students: Please read the following clinical scenarios and background information for each of the 4 genetic disorders. These case studies are intended for student directed learning (SDL) lectures scheduled on 10/25 and 10/26. Do not get bogged down on medical terminology but rather focus on the genetics that you have learned in this course. For each disorder, please pay attention to the patterns of inheritance, genes alterations involved, types of diseasecausing mutations (e.g., microsatellite expansions, duplications etc.), major phenotypic features, frequency of genotypes and corresponding disease in the population, and other significant principals that these disorders may exhibit e.g., variable expressivity, full penetrance, gene modifiers, genetic anticipation etc. For your convenience, you may find notes below most slides and the last slide has a list of references. Have a wonderful rest of your week! Achondroplasia (MIM 100800) ( FGFR3 Pathogenic Variant) P.S., a 30-year-old healthy woman, was 27 weeks pregnant with her first child. A fetal ultrasound examination at 26 weeks gestation identified a female fetus with macrocephaly (>97.5%ile for gestation) and rhizomelia (shortening of proximal segments of extremities; <2.5 %ile for gestation). P.S.’s spouse was 45 years of age and healthy; he had three healthy children from a previous relationship. Neither parent had a family history of skeletal dysplasia, birth defects, or genetic disorders. The obstetrician explained to the parents that their fetus had features of achondroplasia. The infant girl was delivered at 38 weeks gestation by cesarean section due to cephalopelvic disproportion. She had the physical features of achondroplasia including frontal bossing, macrocephaly, midface hypoplasia, lumbar kyphosis, limited elbow extension, rhizomelia, trident hands, brachydactyly, and axial and appendicular hypotonia. Radiographs showed characteristic features of achondroplasia, including shortened long bones of the upper and lower extremities, generalized metaphyseal flaring, square iliac bones, lucency of the proximal femora, and interpedicular narrowing of the lumbar vertebrae. Based on these features, sequencing was undertaken of the fibroblast growth factor receptor 3 gene (FGFR3) . This identified the common c.1138 G>A variant found in achondroplasia, which leads to a glycine to arginine substitution at codon 380 (p.Gly380Arg). Author: Julie Hoover-Fong History and Physical Findings Achondroplasia (MIM 100800) ( FGFR3 Pathogenic Variant) Background Disease Etiology and Incidence Achondroplasia (MIM 100800), the most common type of short stature skeletal dysplasia or dwarfism, is an autosomal dominant disorder caused by specific pathogenic variants in FGFR3 . Two pathogenic variants, c.1138 G>A (≈98%) and c.1138 G>C (1–2%), account for more than 99% of cases of achondroplasia, and both result in the p.Gly380Arg substitution. Guanine at position c.1138 in the FGFR3 gene is one of the most mutable nucleotides identified in any human gene. Approximately 20% of all people with achondroplasia inherited the condition from an affected parent. The remaining 80% have a de novo pathogenic variant that occurs exclusively in the father’s germline, increasing in frequency with advanced paternal age (>35 years). Achondroplasia has an incidence of 1 in 15,000 to 1 in 40,000 live births and affects those of all ancestries. Achondroplasia (MIM 100800) ( FGFR3 Pathogenic Variant) Pathogenesis FGFR3 is a transmembrane tyrosine kinase receptor that binds fibroblast growth factors. Binding of fibroblast growth factors to the extracellular domain of FGFR3 activates the intracellular tyrosine kinase domain of the receptor and initiates a signaling cascade. In endochondral bone, FGFR3 activation inhibits proliferation of chondrocytes within the growth plate and thus helps coordinate the growth and differentiation of chondrocytes with the growth and differentiation of bone progenitor cells. The FGFR3 pathogenic variants associated with achondroplasia are gain-of-function changes that cause ligand-independent activation of FGFR3. Such constitutive activation of FGFR3 inappropriately inhibits chondrocyte proliferation within the growth plate and consequently leads to shortening of the long bones as well as to abnormal differentiation of other bones. Phenotype and Natural History Patients with achondroplasia present at birth with rhizomelic shortening of the arms and legs, relatively long trunk as compared to the limbs, trident configuration of the hands, and macrocephaly with midface hypoplasia and prominent forehead. Birth growth parameters (i.e., length, weight, head circumference) typically overlap those of average stature infants. However, in the first few months of life, length rapidly falls below the average stature curve while head circumference accelerates to the 95%ile and above. In general, individuals with achondroplasia have normal intelligence, although most have delayed motor development, which arises from a combination of hypotonia, hyperextensible joints (although the elbows have limited extension and rotation), and mechanical difficulty balancing their large heads. Motor delays that exceed expected achondroplasia-specific milestones may be related to foramen magnum stenosis and brainstem compression. Abnormal growth of the skull and facial bones results in midface hypoplasia, a small cranial base, and small cranial foramina. The midface hypoplasia causes dental crowding, obstructive apnea, and otitis media. Narrowing of the foramen magnum causes compression of the brainstem at the craniocervical junction in approximately 10 to 20% of individuals. If unrecognized and untreated, critical craniocervical compression may cause central apnea, weakness, hypotonia, quadriparesis, failure to thrive, and even sudden death in up to 5% in the first year of life. Other medical complications include obesity, hypertension, lumbar spinal stenosis that worsens with age, and genu varum. Achondroplasia (MIM 100800) ( FGFR3 Pathogenic Variant) 6 Achondroplasia (MIM 100800) ( FGFR3 Pathogenic Variant) Management Suspected on the basis of clinical features, the diagnosis of achondroplasia is usually confirmed by clinical and radiographic findings. DNA testing for FGFR3 pathogenic variants can be helpful in ambiguous cases but is usually not necessary for the diagnosis to be made. Throughout life, management should focus on the anticipation and treatment of the complications of achondroplasia. During infancy, early assessment for central and obstructive sleep apnea with polysomnography and critical cervicomedullary compression by MRI in conjunction with careful, serial neurologic examinations and developmental assessments are essential. Treatment of patients with brainstem compression by decompression of the craniocervical junction usually results in marked improvement of neurological function. In early childhood, patients also must be monitored for chronic otitis media, hearing deficits, obstructive apnea, and thoracolumbar kyphosis. During later childhood and through early adulthood, patients must be monitored for symptomatic spinal stenosis, symptomatic genu varum, obesity, hypertension, dental crowding, and chronic otitis media and treated as necessary. Treatment of the spinal stenosis usually requires surgical decompression and sometimes stabilization of the spine. Obesity is difficult to prevent and control and often complicates the management of obstructive apnea and joint and spine problems. Management (continued) It is essential to be physically active and exercise dietary discretion to avoid obesity. These individuals should avoid activities in which there is risk for injury to the craniocervical junction, such as collision sports, use of a trampoline, diving from diving boards, and vaulting in gymnastics. Both growth hormone therapy and surgical lengthening of the legs and arms have been promoted for treatment of short stature in patients with achondroplasia. Both therapies remain controversial. Recently, there have been clinical trials of injectable and oral medications to increase growth in individuals with achondroplasia. ClinicalTrials.gov is a publicly available database that outlines such clinical trials and provides relevant links to those medications that are approved by the U.S. Food and Drug Administration. In addition to the management of their medical issues, people with achondroplasia may need help with social adjustment because of the psychological impact of their appearance and physical differences. It is also important to share information about adaptive equipment (i.e., to drive, toilet independently) and how to advocate in school and work settings to make their environment accessible. Support groups often assist by providing interaction with similarly affected peers and social awareness programs. Achondroplasia (MIM 100800) ( FGFR3 Pathogenic Variant) Achondroplasia (MIM 100800) ( FGFR3 Pathogenic Variant) Inheritance For average stature parents with a child with achondroplasia, the risk for recurrence is low but probably higher than that for the general population because of possible germline mosaicism. Gonadal mosaicism for achondroplasia has been documented, but rarely. For relationships in which one partner has achondroplasia and the other is of average stature, each pregnancy has a 50% chance of inheriting achondroplasia because it is an autosomal dominant disorder with full penetrance. For relationships in which both partners have achondroplasia, each pregnancy has a 50% chance of inheriting achondroplasia, a 25% chance of inheriting achondroplasia from both parents (i.e., double dominant or homozygous achondroplasia, which is lethal), and a 25% chance of being of average stature. Cesarean section is required for all pregnant individuals with achondroplasia, regardless of the stature of the fetus. Achondroplasia (MIM 100800) ( FGFR3 Pathogenic Variant) Prenatal testing for achondroplasia is possible through testing of fetal DNA obtained via chorionic villus sampling or amniocentesis or by cell-free DNA in maternal blood. Preimplantation testing may be carried out after in vitro fertilization if both partners have achondroplasia and are seeking to implant an embryo without both parental FGFR3 variants. Recognition of achondroplasia by ultrasound is unlikely at the time of the usual anatomy scan (i.e., around 18–20 weeks gestation) but features may be detectable in a third trimester ultrasound. Conversely, if long bone shortening or other skeletal anomalies are apparent by the time of the anatomy scan, the fetus likely has a more severe and potentially lethal skeletal dysplasia, such as thanatophoric dysplasia. Inheritance Charcot-Marie-Tooth Disease Type 1 A (MIM 118220) ( PMP22 Sequence Variant or Duplication) During the past few years, J.T., an 18-year-old woman, had noticed a progressive decline in her strength, endurance, and ability to run and walk. She also complained of frequent leg cramps exacerbated by cold, and recent difficulty stepping over objects and climbing stairs. She did not recollect a precedent illness, or give a history suggestive of an inflammatory process, such as myalgia, fever, or night sweats. No other family members had similar problems or a neuromuscular disorder. On examination, J.T. was thin and had atrophy of her lower legs, mild weakness of ankle extension and flexion, absent ankle reflexes, reduced patellar reflexes, footdrop as she walked, and enlarged peroneal nerves. She had difficulty walking on her toes and could not walk on her heels. The findings from her examination were otherwise normal. She had graduated high school and had no neurocognitive issues during childhood. As part of her evaluation, the neurologist requested several studies, including nerve conduction velocities (NCVs). J.T.’s NCVs were abnormal on both sides of her body; her median NCV was 25 m/sec (normal, >43 m/sec). Results of a subsequent nerve biopsy showed segmental demyelination, myelin sheath hypertrophy (redundant wrappings of Schwann cells around nerve fibers), and no evidence of inflammation. The neurologist explained that these results were strongly suggestive of a demyelinating neuropathy such as type 1 Charcot-Marie-Tooth (CMT) disease, also known as hereditary motor and sensory neuropathy type 1. Explaining that the most common cause of type 1 CMT disease (CMT1) is a duplication of the peripheral myelin protein 22 gene (PMP22) – the CMT1A duplication – the neurologist requested targeted DNA testing for this duplication. This test confirmed that J.T. had a duplicated PMP22 allele and type 1A Charcot-Marie-Tooth disease. She was informed of the diagnosis and counseled that any pregnancy of hers would have a 50% recurrence risk and that, given different reproductive options, she would benefit from a session with prenatal genetic counselor prior to planning a pregnancy Author: James R. Lupski Background Disease Etiology and Incidence The CMT disorders are a genetically heterogeneous group of hereditary neuropathies involving chronic motor and sensory polyneuropathy, characterized as a distal symmetric polyneuropathy (DSP). CMT has been subdivided according to patterns of inheritance, neuropathological changes, and clinical features. By definition, type 1 CMT (CMT1) is an autosomal dominant demyelinating neuropathy; it has a prevalence of approximately 15 in 100,000 and is genetically heterogeneous. CMT1A, which represents 70 to 80% of CMT1, is caused by increased dosage of PMP22 secondary to duplication of the PMP22 locus in chromosome 17p12. De novo duplications account for 20 to 33% of CMT1A cases; of these, more than 90% arise during male meiosis. Pathogenesis PMP22 is an integral membrane tetraspan glycoprotein. Within the peripheral nervous system, PMP22 is found in compact but not in noncompact myelin. The function of PMP22 has not been fully elucidated, but evidence suggests that it plays a key role in myelin compaction. Either dominant negative sequence variants within PMP22 or increased dosage of PMP22 can cause this peripheral polyneuropathy. Increased dosage of PMP22 arises by tandem duplication of a 1.5-Mb region in 17p11.2 flanked by repeated DNA sequences that are approximately 98% identical. Misalignment of these flanking repeat elements during meiosis can lead to unequal crossing over and formation of one chromatid with a duplication of the 1.5-Mb region and another with the reciprocal deletion. (The reciprocal deletion causes the disease hereditary neuropathy with pressure palsies [HNPP].) An individual inheriting a chromosome with the duplication will have three copies of a normal PMP22 gene and thus overexpress PMP22. Charcot-Marie-Tooth Disease Type 1 A (MIM 118220) ( PMP22 Sequence Variant or Duplication) 12 Charcot-Marie-Tooth Disease Type 1 A (MIM 118220) ( PMP22 Sequence Variant or Duplication) Pathogenesis- continued Overexpression of PMP22 or expression of dominant negative forms of PMP22 results in an inability to form and to maintain compact myelin. Nerve biopsy specimens from severely affected infants show a diffuse paucity of myelin, and nerve biopsy specimens from more mildly affected patients show segmental demyelination and myelin sheath hypertrophy. The mechanism by which PMP22 overexpression causes this pathological process remains unclear, but evidence suggests that potential protein aggregation and the stimulation of the unfolded protein response may play some role. The muscle weakness and atrophy observed in CMT1 result from muscle denervation secondary to axonal degeneration. Longitudinal studies of patients have shown an age-dependent reduction in the nerve fiber density that correlates with the development of disease symptoms. In addition, evidence in murine models suggests that myelin is necessary for maintenance of the axonal cytoskeleton. The mechanism by which demyelination alters the axonal cytoskeleton and affects axonal degeneration has not been completely elucidated. Phenotype and Natural History CMT1A has nearly full penetrance, although the severity, onset, and progression of CMT1 vary markedly within and among families; variation can even be observed in identical twins. Many affected individuals do not seek medical attention, either because their symptoms are not noticeable or because their symptoms are accommodated easily. On the other hand, others have severe disease that is manifested in infancy or in childhood. Symptoms of CMT1A usually develop in the first two decades of life; onset after 30 years of age is rare. Typically, symptoms begin with an insidious onset of slowly progressive weakness and atrophy of the distal leg muscles and mild sensory impairment. The weakness of the feet and legs leads to abnormalities of gait, a dropped foot, and eventually foot deformities (pes cavus and hammer toes, but pes planus can occur in 10–15% of patients) and loss of balance; it rarely causes individuals to lose their ability to walk. Weakness of the intrinsic hand muscles usually occurs late in the disease course and, in severe cases, causes claw hand deformities because of imbalance between flexor and extensor muscle strength. Hand weakness can manifest as difficulties with buttons or zippers and reduced grip strength. Other associated findings include decreased or absent reflexes, upper extremity ataxia and tremor, scoliosis, and palpably enlarged superficial nerves. On occasion, the phrenic and autonomic nerves are also involved. In electrophysiological studies, the hallmark of CMT1A is the uniform slowing of NCVs in all nerves and nerve segments, on both sides of the body, and as a result of demyelination. The full reduction in NCVs is usually present by 2 to 5 years of age, although clinically apparent symptoms may not be manifested https://www.semanticscholar.org/paper/Charcot-Marie-Tooth-Disease-Casasnovas-Cano/0f7b406e94cc827068b43f1e19345ee78f80bcf9 for many years. Charcot-Marie-Tooth Disease Type 1 A (MIM 118220) ( PMP22 Sequence Variant or Duplication) 14 Management Although the diagnosis of CMT1 is suspected because of clinical, electrophysiological, and pathological features, a definitive diagnosis often depends on the detection of a pathogenic genomic variant. Inflammatory peripheral neuropathies are frequently difficult to distinguish from CMT1 and HNPP. Before the advent of molecular testing, many patients with inherited neuropathies were treated with immunosuppressants and experienced the associated morbidity without improvement of their neuropathy. All forms of CMT appear to cause an increased susceptibility to neurotoxicity of vincristine; treatment of childhood acute lymphocytic leukemia that yields subsequent acute paralysis may elicit a family history of CMT or a parent with CMT signs or symptoms. Molecular therapies for several forms of CMT are now becoming available. Paralleling disease progression, therapy generally follows three stages: strengthening and stretching exercises to maintain gait and function, use of orthotics and special adaptive splints, and orthopedic surgery. Further deterioration may require use of ambulatory supports such as canes and walkers or, in rare, severely affected cases, a wheelchair. All should be counseled to avoid exposure to neurotoxic medications and chemicals. Inheritance Because the PMP22 duplication and most PMP22 single nucleotide variants are autosomal dominant with fully penetrant phenotype, each child of an affected parent has a 50% chance for development of CMT1A. The variable expressivity of the PMP22 duplication and PMP22 variants, however, makes prediction of disease severity challenging Charcot-Marie-Tooth Disease Type 1 A (MIM 118220) ( PMP22 Sequence Variant or Duplication) 15 Cystic Fibrosis (MIM 219700) ( CFTR Pathogenic Variants) L.G., a 13-day-old male infant, was referred to the CF pediatric specialty clinic for evaluation and consultation following a positive newborn screen for cystic fibrosis (CF). L.G. was born after an uncomplicated pregnancy and underwent routine newborn screening in his home state. His immunoreactive trypsinogen (IRT) level was elevated at 102 ng/mL and his newborn screening sample was therefore reflexed to a CFTR genotyping panel, which identified one CFTR variant: c.613 C>T (aka P205S). The combination of an elevated IRT and one identified CFTR variant is considered a positive newborn screen for CF, and L.G. was referred for diagnostic sweat testing at 10 days of age. His results were 71 mmol/L and 75 mmol/L (normal, <30 mmol/L; indeterminate, 30–59 mmol/L), a level consistent with CF. L.G.’s parents reported no concerns about his health prior to learning the newborn screening result. He regained his birth weight, was feeding well, and had normal stooling. During the clinic visit, L.G.’s weight, height, and head circumference all plotted within the normal range and his physical examination was unremarkable. Discussion focused on the typical disease progression of CF, treatment and management, and details regarding L.G.’s CFTR variant. The P205S variant is associated with pancreatic sufficiency and confers a degree of residual CFTR function, making it amenable to treatment with CFTR modulator therapy. Following the visit, additional genetic testing was ordered to identify L.G.’s second causal CFTR variant. Full CFTR sequencing and deletion/duplication analysis confirmed the finding of P205S and identified a common exon deletion: CFTRdele2,3. Parental testing later confirmed that the variants were in trans . During L.G.’s evaluation, his parents reported no known family history of CF, nor had they undergone CF carrier screening. They reported that they are of Spanish/Irish (maternal) and Russian (paternal) ancestry and denied consanguinity. They have a 3-year-old daughter (S.G.) who is generally healthy but has a history of lingering cough after respiratory infections and has previously been hospitalized with bronchitis. Given L.G.’s recent diagnosis, sweat testing and genetic analysis were performed on his sister. Her sweat chloride levels were 78 and 80 mmol/L and genetic testing identified the same two CFTR variants found in L.G., confirming a CF diagnosis. Notably, S.G. was born when the family’s home state was using an IRT-IRT algorithm for CF newborn screening, in which the threshold for IRT elevation is higher and no genetic testing is performed. Author: Karen Raraigh 16 Background Disease Etiology and Incidence Cystic fibrosis (CF, MIM 219700) is an autosomal recessive disorder of epithelial ion transport caused by variation in the CF transmembrane conductance regulator gene (CFTR). Although CF has been observed in all ancestral backgrounds, it is most common in individuals of northern European ancestry. The live birth incidence of CF ranges from 1 in 313 among the Hutterites of southern Alberta, Canada, to 1 in 90,000 among the Asian population of Hawaii. Among US individuals identified as white, the incidence is 1 in 3200. Pathogenesis CFTR is an anion channel that conducts chloride and bicarbonate. It is regulated by ATP and by phosphorylation by cAMP-dependent protein kinase. CFTR facilitates the maintenance of hydration of airway secretions through the transport of chloride and inhibition of sodium uptake. Dysfunction of CFTR can affect many different organs, particularly those that secrete mucus, including the upper and lower respiratory tracts, pancreas, biliary system, male genitalia, intestine, and sweat glands The dehydrated and viscous secretions in the lungs of individuals with CF interfere with mucociliary clearance, inhibit the function of naturally occurring antimicrobial peptides, provide a medium for growth of pathogenic organisms, and obstruct airflow. Within the first months of life, these secretions and the bacteria colonizing them initiate an inflammatory reaction. The release of inflammatory cytokines, host antibacterial enzymes, and bacterial enzymes damages the bronchioles. Recurrent cycles of infection, inflammation, and tissue destruction decrease the amount of functional lung tissue and eventually lead to respiratory failure. https://opengenetics.pressbooks.tru.ca/chapter/example-of-human-mutations/ Cystic Fibrosis (MIM 219700) ( CFTR Pathogenic Variants) 17 Pathogenesis- continued Loss of CFTR chloride transport into the pancreatic duct impairs the hydration of secretions and leads to the retention of exocrine enzymes in the pancreas. Damage from these retained enzymes eventually causes fibrosis of the pancreas. CFTR also regulates the uptake of sodium and chloride from sweat as it moves through the sweat duct. In the absence of functional CFTR, the sweat has an increased sodium chloride content, and this is the basis of the historical “salty baby syndrome” and the diagnostic sweat chloride test. Cardinal features of cystic fibrosis ( CF ) and relative contribution of genetic modifiers to variation in select cystic fibrosis traits. A diagnosis of CF is based on the presence of clinical findings shown on the left, along with an elevated sweat chloride concentration (>60 mM). The degree of organ system dysfunction varies considerably among affected individuals. Genetic modifiers and nongenetic factors both contribute to airway obstruction and infection with Pseudomonas aeruginosa – two traits that define lung disease in CF. CF transmembrane conductance regulator ( CFTR ) genotype is the primary determinant of the degree of pancreatic exocrine dysfunction. The presence of CFTR variants associated with severe pancreatic exocrine dysfunction is essentially a prerequisite for the development of diabetes and intestinal obstruction. In the setting of severe endocrine dysfunction, genetic modifiers determine when, and if, diabetes occurs and whether neonatal intestinal obstruction occurs. Genetic variation plays the predominant part in nutritional status as assessed by body mass index. Cystic Fibrosis (MIM 219700) ( CFTR Pathogenic Variants) 18 Phenotype and Natural History CF classically manifests in early childhood, although approximately 4% of patients are diagnosed in adulthood; 15 to 20% of patients present at birth with meconium ileus, and the remainder present with chronic respiratory complaints (rhinitis, sinusitis, obstructive lung disease), poor growth, or both later in life. The poor growth results from a combination of increased caloric expenditure because of chronic lung infections and malnutrition from pancreatic exocrine insufficiency. About 5 to 15% of individuals with CF do not develop pancreatic insufficiency. More than 95% of males with CF are azoospermic due to congenital bilateral absence of the vas deferens. The progression of lung disease is the chief determinant of morbidity and mortality. Most patients die of respiratory failure and right ventricular failure secondary to the destruction of lung parenchyma and high pulmonary vascular resistance (cor pulmonale); the current median age of survival is over 50 years in North America and other regions of the world. In addition to CF, variation within CFTR has been associated with a spectrum of diseases, including isolated obstructive azoospermia, idiopathic pancreatitis, disseminated bronchiectasis, allergic bronchopulmonary aspergillosis, atypical sinopulmonary disease, and asthma. In certain individuals, such conditions may be diagnosed as CFTR-related disorders, indicating modest loss of CFTR function that does not result in enough symptoms to meet the clinical diagnostic criteria for CF. These conditions may be associated with heterozygous variants within a single CFTR allele or – like CF – may be observed only when variants are present in both CFTR alleles. A direct causative role for pathogenic CFTR alleles has been established for some, but not all of these disorders. Correlation between specific CFTR variant alleles, their resulting level of CFTR dysfunction, and CF disease severity exists for pancreatic insufficiency and sweat chloride. Secondary variation or other variants within a CFTR allele may alter the efficiency of splicing or protein maturation, thereby expanding the spectrum of disease associated with some variants. In addition, some variants in CFTR cause disease manifestations only in certain tissues; for example, some affecting the efficiency of splicing have a greater effect on Wolffian duct derivatives than in other tissues because of a tissue-specific need for full-length transcript and protein. Environmental factors, such as exposure to cigarette smoke or inequities in access to healthcare, markedly worsen the severity of lung disease among individuals with CF Cystic Fibrosis (MIM 219700) ( CFTR Pathogenic Variants) 19 Management Because over 2000 different variants have been described across the CFTR gene, the diagnosis of CF is usually based on clinical criteria and sweat chloride concentration, though a genetic diagnosis following identification of two CF-causing variants in trans is permitted as long as sweat chloride concentration is used as a confirmatory measure. Sweat chloride concentrations are normal in 1 to 2% of patients with CF; in these individuals, an abnormal nasal transepithelial potential difference measurement is usually diagnostic of CF. Currently there are no curative treatments for CF, although improved symptomatic management has increased the average longevity from early childhood to over 50 years of age in some countries. The estimated life expectancy is predicted to increase even more with widespread use of newly developed small molecule therapies (termed CFTR modulators) that target the basic defect causing CF, by correcting or enhancing the function of CFTR protein-bearing specific variants. Modulators primarily increase lung function and decrease sweat chloride, with additional benefits observed in other aspects of health and quality of life. For those ineligible for such modulator intervention, or when used in addition, medical therapy has the following objectives: clearance of pulmonary secretions; control of pulmonary infection; pancreatic enzyme replacement; adequate nutrition; and prevention of intestinal obstruction. Although medical therapy slows the progression of pulmonary disease, the only effective treatment of respiratory failure in CF is lung transplantation. Pancreatic enzyme replacement and supplementation of fat-soluble vitamins treat the malabsorption effectively; because of increased caloric needs and anorexia, however, many patients also require caloric supplements. Therapies that act on the DNA or RNA level, including gene editing or replacement, are also under development. Most patients also require extensive counseling to deal with the psychological effects of having a chronic life-limiting disease. Cystic Fibrosis (MIM 219700) ( CFTR Pathogenic Variants) 20 Management-continued Newborn screening for CF has been implemented in all 50 US states, in all Canadian provinces and territories, in Australia, and throughout parts of Europe. Such detection in the newborn period prevents the malnutrition seen in clinically undiagnosed pancreatic insufficient patients and allows early initiation of other treatments. Long-term effects of newborn screening for CF on survival and on progression of pulmonary disease are emerging, so far indicating a modest but significant decrease in CF-related mortality in children. Most CF newborn screening protocols utilize IRT – a pancreatic enzyme precursor measured from dried blood spot – as the first-tier test and progress to another IRT measurement and/or screening for specific CFTR variants as a second tier. Sweat chloride testing is performed on infants with a positive CF newborn screening result and typically either confirms or refutes a CF diagnosis. When a diagnosis remains equivocal after CFTR genotyping and sweat chloride testing, an infant may be labeled as having CFTR-related metabolic syndrome or CF screen positive, inconclusive diagnosis (CRMS/CFSPID) and followed at regular intervals to monitor for the development of CF symptoms. Cystic Fibrosis (MIM 219700) ( CFTR Pathogenic Variants) 21 Inheritance Carrier frequency for CF varies greatly among ancestral groups. For North Americans who do not have a family history of CF and are of northern European ancestry, the empirical probability for each to be a carrier is approximately 1 in 29; for each child of such a couple, the likelihood of CF is therefore 1 in 3200. For couples who already have an affected child, the probability for future children to have CF is 1 in 4 (25%). In 1997, a U.S. National Institutes of Health consensus conference recommended offering CF carrier testing to all pregnant women and couples considering a pregnancy in the United States. The American College of Obstetrics and Gynecology adopted and have periodically reaffirmed those recommendations. Carrier screening has traditionally been performed using a panel of verified disease-causing variants but tests based on next-generation sequencing – many of which screen for CF among several hundred other genetic conditions – are increasing in popularity. These more comprehensive tests offer a greater carrier detection rate within some populations, particularly among individuals not of European ancestry. They may also detect variants of uncertain significance, making risk assessment challenging. Prenatal diagnosis of CF is based on identification of disease-causing CFTR variants in DNA from fetal tissue, such as chorionic villi or amniocytes; use of cell-free fetal DNA to detect monogenic diseases such as CF is also an emerging screening tool. Effective identification of affected fetuses usually requires that the variants responsible for CF in a family have already been identified. Cystic Fibrosis (MIM 219700) ( CFTR Pathogenic Variants) 22 Huntington Disease (MIM 143100) ( HTT Pathogenic Variant [CAG Expansion]) M.P., a 45-year-old man, first noted declining memory and concentration, followed by involuntary movements of his fingers and toes, facial grimacing, and pouting. He was aware of his condition, became depressed, and consulted his family doctor. He had been previously healthy and was unaware of any similarly affected relatives; however, he had been raised by his single mother after his biological father abandoned them. M.P. had an older brother (B.P.) and one healthy daughter (D.P.). M.P. was referred to a neurologist who suspected Huntington disease (HD). This was confirmed by laboratory analysis of his DNA, which showed an expanded CAG repeat tract in one HTT gene on chromosome 4p16.3. M.P. asked the neurologist about options for treatment. He was advised that some medications are helpful for specific symptoms in some patients, that research is very active toward therapies targeting the cause of the disease, and that these might be more effective in the future. At present, no cure is possible, but there might be the option to participate in a clinical trial. M.P. was offered multidisciplinary assistance, including physical and occupational therapy, and encouraged to contact a local Huntington patient support group. M.P. was then referred to a Genetics clinic specializing in HD, along with his daughter (D.P.) and brother (B.P.). The genetics specialists helped with the shock of a diagnosis that was new to this family and explained that given a firm diagnosis in M.P., the probability that D.P. had inherited the expanded allele predisposing to HD was about 50% (reduced marginally because she was apparently unaffected at age 25). B.P. was also at somewhat less than 50% risk. They discussed the option of presymptomatic genetic testing, and both D.P. and B.P. went ahead with this after several more counseling sessions. The lab results (gel image on next slide) showed that B.P. had not inherited the pathogenic allele, but D.P. had inherited the CAG-expanded HTT allele from her father. D.P. then asked about options for her future potential children. The geneticist described the possibility of preimplantation genetic testing as a means to avoid passing her expanded allele on to future offspring, with the offer of further discussion when the situation was right. Authors: Christopher Pearson & Janet A. Buchanan 23 Background Disease Etiology and Incidence Huntington disease (HD) is an autosomal dominant, progressive neurodegenerative disorder caused by tandem repeat expansions in the HTT gene The prevalence of HD is at least 10-fold higher in Europe, North America, and Australia (in the range of 1/10,000 population) than in Asia. Estimates depend on the means of ascertainment, and variation in prevalence reflects population distribution of haplotypes associated with predisposition to expansion in the gene. Pathogenesis The HTT gene product – huntingtin – is ubiquitously expressed but its function remains unknown. Huntington Disease (MIM 143100) ( HTT Pathogenic Variant [CAG Expansion]) 24 Pathogenesis-continued Pathogenic variants in HTT usually result from expansion of a polyglutamine-encoding CAG repeat sequence in exon 1; normal HTT alleles have 10 to 26 CAG repeats, whereas pathogenic HD-causing alleles have 36 or more repeats. Approximately 3% of patients develop HD as the result of a new CAG repeat expansion, but most inherit the pathogenic expanded allele from an affected parent. Newly pathogenic expanded alleles arise from further expansion of an intermediate allele (27–35 CAG repeats) (sometimes previously called a premutation). When such an event occurs, the transmitting parent is nearly always the father. Expansion of the huntingtin polyglutamine tract appears to confer a deleterious novel property that is necessary and sufficient for the induction of an HD phenotype. In addition to the diffuse, severe atrophy of the neostriatum – the hallmark of HD – expression of mutant huntingtin causes transcriptomic dysregulation, neuronal dysfunction, generalized brain atrophy, and changes in neurotransmitter levels. Accumulating neuronal nuclear and cytoplasmic aggregates comprise mutant elongated huntingtin along with other characteristic biomarkers. Ultimately, expression of this abnormal huntingtin leads to neuronal death; however, it is likely that clinical symptoms and neuronal dysfunction precede both the development of intracellular aggregates and neuronal death. The mechanism by which expression of this expanded polyglutamine tract causes HD remains unclear. Huntington Disease (MIM 143100) ( HTT Pathogenic Variant [CAG Expansion]) 25 Phenotype and Natural History As a group average, the age at disease onset is inversely proportional to the number of HTT CAG repeats. Individuals with adult-onset disease usually have 40 to 55 repeats; those with juvenile-onset disease usually have more than 60 repeats. Those with 36 to 39 HTT CAG repeats represent reduced penetrance and may or may not develop HD in their lifetime. The number of repeats does not correlate with features of HD other than age at onset. Instability and further expansion of the CAG repeats within expanded HTT alleles often results in genetic anticipation: progressively earlier onset with succeeding generations. Once the number of CAG repeats is 36 or more, expansion generally continues during paternal transmission. During maternal transmission, expansions are less frequent and less extensive. Individuals with juvenile onset (before age 20) often have a massive expansion of the CAG repeat (60–350 units), of which about 75% are inherited paternally. Approximately one-third of patients present with psychiatric abnormalities; two-thirds have a combination of cognitive and motor disturbances. The mean age at presentation is 35 to 44 years. Approximately 25% of cases develop HD after age 50, and 10% before age 20. The median survival after diagnosis is 15 to 18 years, and the mean age at death is approximately 55 years. Huntington Disease (MIM 143100) ( HTT Pathogenic Variant [CAG Expansion]) 26 Phenotype and Natural History-continued HD is characterized by progressive motor, cognitive, and psychiatric abnormalities. The motor disturbances involve both voluntary and involuntary movement, initially interfering little with daily activities but generally becoming incapacitating as HD progresses. Chorea, which is present in more than 90% of those with HD, is the most common involuntary movement, characterized by nonrepetitive, nonperiodic jerks that cannot be suppressed. Cognitive abnormalities begin early in the disease course; language is usually affected later than are other cognitive functions. Behavioral disturbances, which usually develop later in the disease course, include social disinhibition, aggression, outbursts, apathy, sexual deviation, and increased appetite. The psychiatric manifestations can develop at any time and include personality changes, affective psychosis, and schizophrenia. Advancement of the disease coincides with ongoing somatic expansion of HTT , especially in vulnerable brain regions, supporting the concept that these dynamic variants drive disease progression. In the end stages of HD, individuals usually develop such severe motor impairments that they are fully dependent on others. They also experience weight loss, sleep disturbances, incontinence, and mutism. Behavioral disturbances tend to decrease as the disease advances. Management Currently no curative treatments are available for HD. Therapy focuses on supportive care as well as pharmacological management of the behavioral and neurological problems. Potential therapeutics are under active investigation, including in clinical trials. Some approaches involve attempts at gene silencing, targeting the expanded HTT allele ( https://huntingtonstudygroup.org ). Huntington Disease (MIM 143100) ( HTT Pathogenic Variant [CAG Expansion]) https://www.verywellhealth.com/huntingtons-disease-symptoms5091956 27 Inheritance Each child of a parent with HD has a 50% risk for having inherited a pathogenic HTT allele. HD has incomplete penetrance with alleles of 36 to 39 CAG repeats, but all children who inherit a full penetrance HTT allele (40 or more CAG repeats) will develop HD, given a sufficient lifespan. From a father with an intermediate allele, the empirical risk of a full penetrance HTT allele in an offspring is approximately 3%. Presymptomatic testing and prenatal testing are forms of predictive testing and are best interpreted after confirmation of a pathogenic HTT allele in an affected family member. Family members at risk can be tested using the same molecular analysis as that for diagnosis. Recommendations regarding presymptomatic genetic testing for untreatable conditions such as HD include the need for neurological and psychological evaluation before testing and for psychological support from family members or friends. Additionally, the individual should be deemed old enough (typically an adult) and competent to make an informed choice regarding such testing. The implications of such results are obviously life altering. Huntington Disease (MIM 143100) ( HTT Pathogenic Variant [CAG Expansion]) 28 References & Notes for Review Case Studies from: Nussbaum, R.L., McInnes, R.R. and Willard, H.F. (2016). Thompson & Thompson Genetics in Medicine, 8th ed. Elsevier. ISBN 1437706967. Available in VCOM library •MedlinePlus Medical Encyclopedia •Medical Dictionary of Health Terms - Harvard Health Publishing •WebMd Online Medical Dictionary •Achondroplasia •Charcot-Marie-Tooth Disease Type 1 A •Cystic Fibrosis •Huntington disease •Huntington Study Group •Online Mendelian Inheritance in Man (OMIM)