Genetic Testing Flashcards
Be able to define what constitutes a genetic test
Analyzing an individual’s genetic material to determine predisposition to a particular health condition or to confirm a diagnosis of genetic disease.
Identify methods ofgenetic testing & those that do NOT involve the direct analysis of DNA sequences
biochemical tests (amino aids, organic acids as in phenylketonuria or maple syrup urine disease), enzyme activity assays (Gaucher disease), protein electrophoresis (sickle cell disease), lipid levels (familial hypercholesterolemia), X-rays (achondroplasia), ultrasound (polycystic kidney disease, hypertropic cardiomyopathy), sweat chloride test (cystic fibrosis), skin examination (albinism), medical history, family history, etc.
Interpret genetic testing results and distinguish betweeninformative and non-informative results.
An informative genetic test result is one where the information from a genetic test definitively diagnoses or excludes the disease in question. Put another way, an informative genetic test result is one that is reliably either a true positive or true negative result (ruling-in or ruling-out disease/risk, respectively).A non-informative genetic test result usually refers to a situation where the genetic test result is normal, but it is not possible to definitively exclude disease/disease risk. A non-informative genetic test result leaves open the possibility that an underlying pathogenic mutation exists, but was missed/not detected by the test.When considering ‘informativity’ ask yourself, how confident you are in your result (does a ‘positive’ result really mean disease/elevated risk and does a ‘negative’ result really mean no disease/no elevated risk). If the answer is ‘no’ then you may be dealing with a non-informative test result.
Explain how allelic heterogeneity can affect the informative nature of genetic tests.
Allelic Heterogeneity refers to the fact that multiple mutations in a particular gene (or at a particular loci) can cause disease. (Allelic heterogeneity in the research setting can also refer to the present of multiple non-pathogenic polymorphisms within a gene)Example: Cystic fibrosis is an autosomal recessive disease caused my mutations in one gene, CFTR. Over 1,000 different mutations have been reported. Cystic fibrosis shows allelic heterogeneity but is genetically homogenous (e.g. NO Genetic Heterogeneity).
Understand the basic approaches, advantages, limitations, and interpretations of chromosomal analysis.
General Uses and Indications: Suspected abnormality of chromosome number or structure (deletion, insertion, rearrangements). Frequently obtained from pregnant women > 35 years (amniocentesis or chorionic villus sampling), from patients with congenital abnormalities (dysmorphisms, structural organ defects, mental and/or growth retardation), from families with multiple miscarriages and/or fertility problems, and directly from certain cancer biopsies.Can Diagnose: aneuploidies (abnormal chromosome number), deletions, duplications, and insertions of moderate to large size (>3,000-5,000 kb / 3-5 Mb), and rearrangements.Cannot Diagnose: single gene deletions, point mutations, small deletions, duplications, and insertions, methylation defects, trinucleotide repeat abnormalities.
Understand the basic approaches, advantages, limitations, and interpretations of FISH testing.
General Uses and Indications: Used to diagnose deletions, some translocations, and abnormalities of copy number. Often used to detect cytogenetic changes that are at or beyond the limits of resolution obtained by high-resolution chromosomal analysis.Can Diagnose: recognized microdeletion syndromes, recognized chromosomal rearrangements (in cancers), and gene copy numbers (cancers). Also useful in diagnosing anueploidies (e.g. trisomy 13, 18, 21) in the prenatal setting.Cannot Diagnose: deletions, rearrangements that are not specifically tested for (i.e. FISH probes are specifically designed for each condition). FISH is not always able to detect duplications of gene regions. Point mutations and small deletions cannot be diagnosed with this approach.Examples of Microdeletion Syndromes: Cri-du-chat, Smith-Magenis, DiGeorge (22qdel), Williams syndrome, Wolf-Hirschhorn, Prader-Willi syndrome, Angelman syndrome.
Understand the basic approaches, advantages, limitations, and interpretations of restriction digests/southern blotting.
General Uses and Indications: Used when a known mutation affects a restriction digest site.Can Diagnose: known and well-characterized mutations that occur at restriction sites and alter the size of digested fragments; can also identify some methylation defectsCannot Diagnose: anueploidies, chromosomal rearrangements, moderate-large deletions/insertions/rearrangements, mutations that do not affect restriction sites,
Understand the basic approaches, advantages, limitations, and interpretations of Linkage Analysis.
General Uses and Indications: May be used in large families to determine if at risk person (often a fetus or young patient) has inherited a disease locusCan Diagnose: can determine whether an individual has likely inherited a chromosome carrying a pathogenic mutation. Can do this, even when the exact mutation has not been clearly found. Cannot Diagnose: anueploidies, chromosomal rearrangements, point mutations; NOTE: in linkage analysis the exact mutation is unknown. (so usually does not find the exact mutation)
Understand the basic approaches, advantages, limitations, and interpretations of PCR.
Primary problem in genetic analysis of a single gene is that any single gene represents only a small fraction of the total genome.For example: DMD encodes dystrophin, the protein missing or damaged in Duchenne muscular dystrophy. DMD is a large gene and makes a transcript of ~2,400 bp in length; this is ~0.00008% of the total genome (still a virtual needle in a haystack).The Polymerase Chain Reaction (PCR) is a method for amplifying a sequence of interest (like a gene). By making millions of copies of a gene, the ‘signal’ of that gene (in relation to the genome) is much clearer
Understand the basic approaches, advantages, limitations, and interpretations of DNA Sequencing.
General Uses and Indications: Used to identify sequence changes (mutations) in specific genes.In general you need the following: You must know or suspect a specific genetic diagnosis. The gene must have been identified. The mutation must be detectable by sequencing (deletions, insertions, rearrangements are not always found by sequencing). The mutation must be located in a region of the gene that is actually sequenced (promoter and deep-intronic mutations often missed by commercial tests)Can Diagnose: Mutations in known genes (mutation can be previously reported or can be novel), polymorphic variants, small (1 to ~100 nucleotide) deletion/insertions. Ideal for looking at the sequence of a known disease geneCannot Diagnose: The technique is very specific, assaying only the region of the gene(s) for which the test has been designed. Frequently, many clinical genetic tests do NOT routinely sequence all parts of a gene (e.g. promoters, introns). This means that although the approach is often very specific, clinical sensitivity is frequently below 100% (this is an important concept to understand). This technique cannot easily detect larger deletions/insertions, rearrangements, and most chromosomal abnormalities.
Understand the basic approaches, advantages, limitations, and interpretations of Microarray analysis.
General Uses and Indications: Currently the clinical applications for expression arrays are quite limited, but changing.aCGH has become fairly routine to look for small genomic deletions/insertions.
Explain how genetic heterogeneity can affect the informativeness of genetic tests.
Genetic Heterogeneity: multiple genes (when mutated) associated with the same phenotypeExample: Hypertrophic cardiomyopathy (HCM) is an autosomal dominant disease caused by mutations in at least 10 different genes. HCM shows both allelic and genetic heterogeneity.A genetic test which cannot completely account for all possible allelic and genetic heterogeneity in a particular disorder can lead to non-informative results.
Can we cure/treat genetic disease? If so, how? If not, why not?
Some monogenetic disorders you can essentially cure (B12-responsive methylmalonic aciduria), some you can partially treat (galactosemia), and some you still can’t really treat (Tay-Sachs).Another example:Phenylketonuria: usually due to enzyme deficiency (phenylalanine hydroxylase). Treat with dietary restriction of phenylalanine.Genetic diseases are difficult to cure because we have not yet figured out how to replace bad genetic material, remove, silence, or regulate single or multiple genes, or fully control gene/environment interactions.
Identify genetic conditions that currently can be treated and those for which treatment may soon be available.
Trisomy 21: supportive care and better cardiac surgery responsible for improvements in survivalMultiple endocrine neoplasia: genetic testing triggers prophylactic surgery and improves survival
Discuss examples of genetic disorders that are treated on the basis of enzyme replacement therapy.
Recombinant AT1 therapy for deficiency of alpha 1 antitrypsin (recall elastase activity).Fabry disease: Treated with recombinant Alpha galactosidase. Pour this into patients.
