Flashcards in Genetic Testing 1 Deck (7):
Briefly define different types of genetic testing
1. Diagnostic – confirms diagnosis in an affected person, and may be prognostic as well
2. Predictive – testing of unaffected individuals, usually in the absence of corroborating evidence, for:
- pre-symptomatic (will they develop the disease?)
- prenatal/pre implantation
3. Screening – testing of individuals at population-level risk of disease (i.e. newborn), where there is an advantage of detecting conditions early
4. Somatic – testing of tumor tissue (not germline) for:
- choice of therapeutic agents
5. Pharmacogenetic – metabolism/drug toxicity
Be aware of appropriate sample sources for genetic testing
1. Peripheral blood (whole blood)
- DNA extracted from WBCs
- preferred source of DNA for testing – plentiful and easy to access, minimally invasive
2. Buccal cells, urine, skin
- collected by swab inside cheek, early morning urine or biopsy
- used as a second source of DNA is suspicion of mosaicism,
- used for comparison of tumor DNA to constitutional DNA, OR
- used when it is difficult to get blood for some reason
3. Chorionic villus Sampling (placenta, 11-14 weeks) and Amniocentesis (amniotic fluid, 15-18 weeks)
- invasive, therefore risks of bleeding, infection, loss of pregnancy and incorrect results due to contamination with maternal cells
- used for chromosomal or molecular testing
- used for studying metabolic diseases
4. Cell free DNA (cfDNA)
- DNA not contained by membranes but floating free in circulation can be isolated
- Sources of cfDNA:
- haematopoeitic cells
- foetal cells
- tumor cells
- used for non-invasive prenatal screening – aneuploidies, can be used early in pregnancy
- used for tumor detection and monitoring – not widely available
How do we choose what to test within the DNA sample?
1. Change to be detected
- where it occurs
- type of change
2. Volume of samples being tested
3. Purpose of testing (known or unknown mutation). If you know where it is, focus on that region on which the variant occurs, i.e. Sanger sequencing of a single exon.
Explain the difference between targeted and untargeted genetic testing
Targeted – specific alleles of copy number variants are tested for
Untargeted – whole or multiple genes, whole genome. More than one variant may be found – which is the mutation?
What are the key factors in determining whether a genetic variant is disease-causing or benign ?
5 tier classification system:
Class 1 - Benign
Class 2 – Likely Benign
Class 3 – Uncertain significance
Class 4 – Likely pathogenic
Class 5 – Pathogenic
- public resources – literature and databse
- in silico prediction – algorithms
- Key, powerful factors:
- segregation of genotype with disease
- functional studies
Segregation of genotype:
- testing of proband’s parents usually recommended to test this
- based on family history and inheritance pattern expected to be observed
- AD: i. de novo – neither parent
ii. Inherited – an affected parent should have variant
- AR: both parents should be carriers
RNA and functional studies:
- focus on dynamic effects of changes at the DNA level on gene transcription, translation and protein-protein interaction
- tests on cells, animal models etc
Understand the concept of clinical utility, using example clinical scenarios
Utility: How can genetic testing actually improve patient management?
- why am I requesting this test?
- how does it help my patient? BRCA genes – can get prophylactic surgery, but there is nothing you can do about Huntington’s.
- can the result harm my patient or their family?
- is there a better approach or test I could use?
- could I be using resources more wisely?
- Eg – full genome testing as last resort