The clinical setting in which patients are evaluated determines the scope of practice, diagnostic, and therapeutic interventions. For the purposes of general discussion, the typical encounters between patients and genetic practitioners may involve: • Referral to an out-patient genetics clinic (pediatric, adult, or combined) or an in-hospital consultation, most often for diagnostic evaluation. • Specialty genetics clinics focusing on management of
inborn errors of metabolism,
skeletal dysplasia, or
lysosomal storage diseases. • Referral for counseling in a prenatal genetics clinic to discuss risks to the pregnancy (
advanced maternal age, teratogen exposure, family history of a genetic disease), test results (abnormal maternal serum screen, abnormal ultrasound), and/or options for prenatal diagnosis (typically non-invasive prenatal screening, diagnostic amniocentesis or chorionic villus sampling). • Multidisciplinary specialty clinics that include a clinical geneticist or genetic counselor (cancer genetics, cardiovascular genetics, craniofacial or cleft lip/palate, hearing loss clinics, muscular dystrophy/neurodegenerative disorder clinics).
Diagnostic evaluation Each patient will undergo a diagnostic evaluation tailored to their own particular presenting signs and symptoms. The geneticist will establish a
differential diagnosis and recommend appropriate testing. These tests might evaluate for
chromosomal disorders,
inborn errors of metabolism, or single gene disorders.
Chromosome studies of a human, with annotated
bands and sub-bands as used in the
International System for Human Cytogenomic Nomenclature for
chromosomal abnormalities. It shows dark and white regions on
G banding. It shows 22
homologous chromosomes, both the male (XY) and female (XX) versions of the
sex chromosome (bottom right), as well as the
mitochondrial genome (at bottom left). Chromosome studies are used in the general genetics clinic to determine a cause for developmental delay or intellectual disability, birth defects, dysmorphic features, or autism. Chromosome analysis is also performed in the prenatal setting to determine whether a fetus is affected with aneuploidy or other chromosome rearrangements. Finally, chromosome abnormalities are often detected in cancer samples. A large number of different methods have been developed for chromosome analysis: • Chromosome analysis using a
karyotype involves special stains that generate light and dark bands, allowing identification of each chromosome under a microscope. •
Fluorescence in situ hybridization (FISH) involves fluorescent labeling of probes that bind to specific DNA sequences, used for identifying aneuploidy, genomic deletions or duplications, characterizing chromosomal translocations and determining the origin of
ring chromosomes. • Chromosome painting is a technique that uses fluorescent probes specific for each chromosome to differentially label each chromosome. This technique is more often used in cancer cytogenetics, where complex chromosome rearrangements can occur. •
Array comparative genomic hybridization is a newer molecular technique that involves hybridization of an individual DNA sample to a glass slide or microarray chip containing molecular probes (ranging from large ~200kb
bacterial artificial chromosomes to small oligonucleotides) that represent unique regions of the genome. This method is particularly sensitive for detection of genomic gains or losses across the genome but does not detect balanced translocations or distinguish the location of duplicated genetic material (for example, a tandem duplication versus an insertional duplication).
Basic metabolic studies Biochemical studies are performed to screen for imbalances of metabolites in the bodily fluid, usually the blood (plasma/serum) or urine, but also in cerebrospinal fluid (CSF). Specific tests of enzyme function (either in leukocytes, skin fibroblasts, liver, or muscle) are also employed under certain circumstances. In the US, the
newborn screen incorporates biochemical tests to screen for treatable conditions such as
galactosemia and
phenylketonuria (PKU). Patients suspected to have a metabolic condition might undergo the following tests: • Quantitative amino acid analysis is typically performed using the ninhydrin reaction, followed by
liquid chromatography to measure the amount of amino acid in the sample (either urine, plasma/serum, or CSF). Measurement of amino acids in plasma or serum is used in the evaluation of
disorders of amino acid metabolism such as
urea cycle disorders,
maple syrup urine disease, and
PKU. Measurement of amino acids in urine can be useful in the diagnosis of
cystinuria or renal
Fanconi syndrome as can be seen in
cystinosis. • Urine organic acid analysis can be either performed using quantitative or qualitative methods, but in either case the test is used to detect the excretion of abnormal
organic acids. These compounds are normally produced during bodily metabolism of amino acids and odd-chain fatty acids, but accumulate in patients with certain
metabolic conditions. • The acylcarnitine combination profile detects compounds such as organic acids and fatty acids conjugated to carnitine. The test is used for detection of disorders involving fatty acid metabolism, including
MCAD. • Pyruvate and lactate are byproducts of normal metabolism, particularly during
anaerobic metabolism. These compounds normally accumulate during exercise or ischemia, but are also elevated in patients with disorders of pyruvate metabolism or mitochondrial disorders. •
Ammonia is an end product of amino acid metabolism and is converted in the liver to
urea through a series of enzymatic reactions termed the
urea cycle. Elevated ammonia can therefore be detected in patients with
urea cycle disorders, as well as other conditions involving
liver failure. • Enzyme testing is performed for a wide range of metabolic disorders to confirm a diagnosis suspected based on screening tests.
Molecular studies •
DNA sequencing is used to directly analyze the genomic DNA sequence of a particular gene. In general, only the parts of the gene that code for the expressed protein (
exons) and small amounts of the flanking untranslated regions and
introns are analyzed. Therefore, although these tests are highly specific and sensitive, they do not routinely identify all of the mutations that could cause disease. •
DNA methylation analysis is used to diagnose certain genetic disorders that are caused by disruptions of
epigenetic mechanisms such as
genomic imprinting and
uniparental disomy. •
Southern blotting is an early technique basic on detection of fragments of DNA separated by size through
gel electrophoresis and detected using radiolabeled probes. This test was routinely used to detect deletions or duplications in conditions such as
Duchenne muscular dystrophy but is being replaced by high-resolution
array comparative genomic hybridization techniques. Southern blotting is still useful in the diagnosis of disorders caused by
trinucleotide repeats.
Treatments Each cell of the body contains the hereditary information (
DNA) wrapped up in structures called
chromosomes. Since genetic syndromes are typically the result of alterations of the chromosomes or genes, there is no treatment currently available that can correct the genetic alterations in every cell of the body. Therefore, there is currently no "cure" for genetic disorders. However, for many genetic syndromes there is treatment available to manage the symptoms. In some cases, particularly
inborn errors of metabolism, the mechanism of disease is well understood and offers the potential for dietary and medical management to prevent or reduce the long-term complications. In other cases,
infusion therapy is used to replace the missing enzyme. Current research is actively seeking to use
gene therapy or other new medications to treat specific genetic disorders.
Management of metabolic disorders In general, metabolic disorders arise from enzyme deficiencies that disrupt normal metabolic pathways. For instance, in the hypothetical example: A ⟶ B ⟶ C ⟶ D AAAA ⟶ BBBBBB ⟶ CCCCCCCCCC ⟶ (no D) X Y Z X Y | (no or insufficient Z) EEEEE Compound "A" is metabolized to "B" by enzyme "X", compound "B" is metabolized to "C" by enzyme "Y", and compound "C" is metabolized to "D" by enzyme "Z". If enzyme "Z" is missing, compound "D" will be missing, while compounds "A", "B", and "C" will build up. The pathogenesis of this particular condition could result from lack of compound "D", if it is critical for some cellular function, or from toxicity due to excess "A", "B", and/or "C", or from toxicity due to the excess of "E" which is normally only present in small amounts and only accumulates when "C" is in excess. Treatment of the metabolic disorder could be achieved through dietary supplementation of compound "D" and dietary restriction of compounds "A", "B", and/or "C" or by treatment with a medication that promoted disposal of excess "A", "B", "C" or "E". Another approach that can be taken is enzyme replacement therapy, in which a patient is given an infusion of the missing enzyme "Z" or cofactor therapy to increase the efficacy of any residual "Z" activity. • Diet Dietary restriction and supplementation are key measures taken in several well-known metabolic disorders, including
galactosemia,
phenylketonuria (PKU),
maple syrup urine disease, organic acidurias and
urea cycle disorders. Such restrictive diets can be difficult for the patient and family to maintain, and require close consultation with a nutritionist who has special experience in metabolic disorders. The composition of the diet will change depending on the caloric needs of the growing child and special attention is needed during a pregnancy if a woman is affected with one of these disorders. • Medication Medical approaches include enhancement of residual enzyme activity (in cases where the enzyme is made but is not functioning properly), inhibition of other enzymes in the biochemical pathway to prevent buildup of a toxic compound, or diversion of a toxic compound to another form that can be excreted. Examples include the use of high doses of
pyridoxine (vitamin B6) in some patients with
homocystinuria to boost the activity of the residual cystathione synthase enzyme, administration of
biotin to restore activity of several enzymes affected by deficiency of
biotinidase, treatment with
NTBC in
Tyrosinemia to inhibit the production of succinylacetone which causes liver toxicity, and the use of
sodium benzoate to decrease
ammonia build-up in
urea cycle disorders. •
Enzyme replacement therapy Certain
lysosomal storage diseases are treated with infusions of a recombinant enzyme (produced in a laboratory), which can reduce the accumulation of the compounds in various tissues. Examples include
Gaucher disease,
Fabry disease,
Mucopolysaccharidoses and
Glycogen storage disease type II. Such treatments are limited by the ability of the enzyme to reach the affected areas (the
blood brain barrier prevents enzyme from reaching the brain, for example), and can sometimes be associated with allergic reactions. The long-term clinical effectiveness of enzyme replacement therapies vary widely among different disorders.
Other examples • Angiotensin receptor blockers in Marfan syndrome & Loeys-Dietz • Bone marrow transplantation • Gene therapy == Career paths and training ==