Techniques of Cytogenetic Analysis Flashcards
Which out of the following tests would you use for whole genome and targeted testing?
G-Banding Microarrays FISH MLPA QF-PCR or qPCR
G-banding and Microarrays are used for whole genome analysis
FISH, MLPA and QF-PCR/ qPCR are used for targetted testing
What is the difference between conventional cytogenetics and molecular cytogenetics?
Conventional cytogenetics involves the analysis of chromosomes at metaphase down a light microscope or image (g-banding)
Molecular cytogenetics involves chromosome analysis at the molecular resolution of all stages (FISH, array CGH)
What three categories of samples can be taken for cytogenetics?
Prenatal- amniotic fluid, placenta and other foetal tissue
Postnatal- peripheral blood
Cancer- bone marrow, tumour
How is blood in cytogenetics prepared and analysed?
5-10ml unclotted
culture t-lymphocytes 2-3 days using incubator to help division of cells
G-banding analysis can then be done
How do you prepare and analyse amniotic fluid in cytogenetic ?
Portion for DNA extraction (QF-PCR) Separate cells from remaining fluid Culture cells as monolayer 7-14 days incubation G-banded analysis
Spontaneous abortions can provide tissue such as placenta, lungs, cartilage etc. What may be the problems with using this sort of tissue in cytogenetics and how can it be analysed?
It may be old and so macerated tissue (deteriorating)
Either way you can make it into a monolayer then G-banded analysis
How does G-banding work? What preparation is needed?
Cell culture -> mitotic arrest -> hypotonic (swells and spreads out) -> fixation -> trypsin and leishman’s stain -> G-banding- AT (stain lighter) and GC (stain darker) rich regions
What are four molecular cytogenetic techniques used for target areas?
Fluorescent in situ hybridisation (FISH)- used in conjunction with G-banding
Multiplex ligation dependent probe amplification (MLPA)
Microarray comparative genomic hybridisation (array CGH)
Quantitative Fluorescence-PCR (QF-PCR)
What is Flourescent in situ hybridisation (FISH)? What are the steps and which colours mean what?
Detection of DNA material on slides using fluorescent
dyes & UV light. First step is to label them (flourochrome), denature them, hybridise, then after washing, you can visualise them. Blue is the chromosome and pink/green are the flourescent probes
What types of probes are used in FISH?
What are each used for?
Unique sequence- locus specific + microdeletions/duplications & rearrangements in oncology
Centromeric- large regions of repetitive DNA + used much more in oncology
Chromosome paint- rearrangements/translocations and recombination
What is MLPA used for?
DNA-based multiplex PCR test which identifies copy number changes in up to 50 different genomic locations simultaneously. It’s an alternative to FISH and detects deletions at ends of chromosomes which may be causing learning difficulties in children
What is Microarray CGH?
A front line test for children with learning difficulties. A genome-wide screen in which hybridisation of a sample & control DNA to a microarray “chip” – BACs or SNPs or oligonucleotides (1000s of DNA spots) detects genomic imbalances (copy number variants) at high resolution (10-10000x conventional cytogenetics)
How are the results of a microarray CGH read?
Using software which measures the ratio of red to green (correlating to levels of normal and test DNA that competed for a spot on the chip) which can then show any gains or losses of certain genes
Which patients are often tested for with array CGH?
Those with learning difficulties and developmental disability (LDD). Many times the etiology is heterogeneous
What are the disadvantages of array CGH?
Only detects imbalanced rearrangements- not balanced
Limited for mosaicism
Non-pathogenic and uncertain pathogenic changes detected
Requires good quality DNA
Expensive initially (but long term cheaper than G-banding)
Doesn’t cover entire genome
What is QF-PCR?
PCR amplification of short tandem repeats (STRs) using flourescent primers. Looks at lots of different areas simultaneously and the products are visualised and quantified as peak areas using an automated DNA sequencer
How do prenatal aneuploidy detections happen? (testing for abnormalities in pregnancies)
DNA extraction from amniotic fluid
PCR amplification- primers from chromosome 13, 18 and 21
DNA dosage in 4-5 markers/chromosome
Aneuploidy= 2 markers with abnormal dosage
(Basically allows you to quantify chromosomes)
V.quick results= 24h
What is shown from prenatal testing if there is trisomy 21 or 13?
Either 3 peaks or two peaks but one is double the size of the other
What sort of patients are often send for blood chromosome studies?
Dysmorphic newborns Gender assignment if not clear Developmental and learning problems Sexual development as some people do not reach puberty when they should Heart defects Reproductive problems Family studies
How many are affected by Digeorge syndrome? What are the traits?
1/5000 10-15% familial (got it from parents) Low set ears Sloping head Facial abnormalities Absent thyroid Hypocalcaemia Nasal speech Short Stature Learning difficulties Mental health problems- schizophrenia/bipolar
What is Williams syndrome? What gene does it affect? What traits are there with this condition?
7q11.23 deletion- critical gene involved in elastin and this affects the heart. 'cocktail-party' personality Pixie-like face Hypercalcaemia Developmental delay Infantile hypercalcaemia Premature aging
When are parents referred for prenatal tests?
When mother is older
Serum screen risk
Abnormal ultrasound
FH/previous chromosome abnormality
What is the pattern/ correlation between down syndrome risk and maternal age?
From about 35 years old and older, the risk increases dramatically
What are the two sampling procedures carried out to obtain material for prenatal diagnosis?
Amniocentesis at around 16 weeks (amniotic fluid)
Chorionic villus sampling at around 12 weeks (placental tissue)
What happens to the tissue for a prenatal diagnosis?
Separate maternal from foetal tissue
Place in suspension culture for 24 hours or QF-PCR
Longer-term monolayer culture (8-20 days)
G-banded analysis
(Ideally want the QF-PCR and longer culture to be sure)
What future tests could there be for prenatal diagnosis?
Array CGH or next gen. sequencing on NHS? Exomes or whole genome?
NIFTY (Non invasive fetal trisomy test)- an advanced test based on parallel sequencing- abnormal results would still need to be verified by other tests (used from 10 weeks onwards)
How can cytogenetics help with cancer?
Can help detect chromosome changes and therefore diagnose it- leukaemia andsolid tumour tissue. Can also measure the progression or remission by measuring any more accumulating chromosome abnormalities and this may help with treatment decisions
How can cytogenetic analysis help in the diagnosis of leukaemia cancer?
1 ml unclotted bone marrow
Suspension overnight
G-banded analysis/ FISH
What is a philadelphia translocation? What are the symptoms of this?
It is an abnormality on chromosome 22 which makes it abnormally short due to a reciprocal translocation
Symptoms include tiredness and low white blood cell count
How are solid tumours analysed?
Macerate+enzyme digest tumour tissue
short-term suspension and longer term monolayers
G-banded analysis/FISH analysis
