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BF - MM5

Testing for Genetic Disease

Why do genetic testing? Diagnostic, mutation detection, predictive testing, prenatal testing
Why is counselling and consent needed? 1. Info can be...? 2. Can indicated individual's...? 3. Can have serious implications for...? 4. Test can give.../...results? 1. Complex 2. Future health 3. Pregnancy/ children/ relatives 4. Unexpected/ uncertain
Where can the sample be taken from? Any tissue with nucleated cells (normally blood)
Cytogenetic testing - What is added to blood sample first? Anticoagulant
Cytogenetic testing - What is purified? Lymphocytes -> cultured for 3-4 days
Cytogenetic testing - What needs to be done during mitosis of sample lymphocytes? Disrupt mitotic spindle to prevent completion
Cytogenetic testing - The cells are then harvested and treated with what kind of solution? Hypotonic
Cytogenetic testing - What is then done with these swelled cells? Fix to a microscope slide and stain
Cytogenetic testing - What is then constructed from the images seen down the microscope? Karyotype
FISH - What does it stand for? Fluorescence in situ hybridization
FISH - What is first constructed? A DNA 'probe' (copy of target region)
FISH - How is this DNA 'probe' labelled? Fluorescently
FISH - What is the probe applied to? A target chromosome
FISH - What two things are done during application of probe to chromosome? Incubate and hybridize
FISH - Wash step. What is seen in a normal result? Probe binds twice to expected chromosomes
ARRAY-CHG - What does this test allow us to do? Test thousands/ millions of genomic regions at a time
ARRAY-CHG - What must be used as a containing to carry out this test? Inert (glass or metal) welled tray
ARRAY-CHG - What are fixed to specific wells? Multiple DNA probes
ARRAY-CHG - What is added to the well? Patient DNA sample and reference DNA sample added in equal amounts
ARRAY-CHG - How is the patient sample and reference sample distinguished? Different colours
ARRAY-CHG - How can different coloured wells identify genetic abnormalities? If reference = test (mixture of two colours), if the colour is predominantly that of reference = deletion in patients DNA, if colour is predominantly that of patients sample = duplication in patients DNA
DNA Sequencing - How many reactions are set up? 4
DNA Sequencing - What are each of these 4 reactions based on? A,T,C,G - deoxynucleotides for each base with radio labels
DNA Sequencing - Why are deoxynucleotides used? They will terminate any existing DNA sequence they are added to
DNA Sequencing - What must be first done to test DNA? PCR -> cleaved into fragments of different lengths
DNA Sequencing - What other 4 components are added to the reaction? DNA polymerase, nucleotides (normal), primers, fragemented test DNA
DNA Sequencing - What is produced? Different fragments of DNA with a deoxynucleotide base terminating each fragment
DNA Sequencing - What is then done to these fragments? Electrophoresis to sort them by length
DNA Sequencing - Those of the same length...? Will move the same distance in the gel and have the same terminal base
DNA Sequencing - How is sequence read from gel? Autoradiography (x-ray), to detect the radio labelled bases, sequence is then determined
DNA Sequencing - How are modern techniques different? Flourescently labelled ddNTP terminators that can be read automatically
DNA Mutations - What does VUS mean in terms of mutations? Variance of unknown significance
DNA Mutations - How can you decide if a mutation is pathogenic, benign or VUS? (4) 1. Significant protein change (nonsense/ frameshift) 2. Other affected family members 3. Not present in control/ normal population 4. The residue is functionally important (e.g. binding site)
Why do genetic tests have varying sensitivity? 1. Test rarely covers...? 2. Test may miss...? 3. Disease may be due to...? 4. Mutation may be present in only some...? 1. All of a gene 2. Certain types of changes 3. Changes in another gene 4. Of patients cells (e.g. mosaicism)
Extras - DNA testing focuses more on introns/exons/boundries? Exons and intron/exon boundaries
Extras - Why is DNA testing focused more on exons? Thought to contain more pathogenic changes
Extras - Is DNA testing sensitive to larger deletions? No
Extras - What does MLPA stand for? Multiplex Ligation-dependant Probe Amplification
Extras - What does MLPA show? Large deletions or duplications
Extras - Do negative results from DNA testing exclude a diagnoses? (what is exception) No - except when testing for specific known familial mutation
Extras - What can gene tests do to assess probability? e.g. Some are good at giving negative predictive values e.g. for CF and HD
Extras - What are the two methods of obtaining prenatal genetic information? Chrionic Villus Smapling (CVS) and Amniocentesis
Extras - When and how is CVS done? 10-12 weeks -> placenta biopsy
Extras - When and how is amniocentesis done? 15+ weeks -> amniotic fluid
Extras - CVS/amniocentesis have greatest risk? CVS (2%), Amnio (1%)
Created by: benfenner1