Hodgson - history of clinical cytogenetics, human karyotyping and main tech used to detect disease Flashcards
What are the 3 main referral reasons for couples to fertility services?
- couples who believe they are infertile as trying and cannot get pregnant (don’t have clinically detectable pregnancies)
- couples who have had frequent miscarriages
- patients w/ serious risk of genetic disease likely to affect fetus
How are chroms visualised?
- staining and visualised by G banding
- all from single nucleus captured from metaphase
How are chroms organised by morphology?
- position of centromere
- large metacentric, large submetacentric, medium submetacentric, large acrocentric, small submetacentric, small metacentric, small acrocentric (groups A-G respectively)
What is the protocol for G banding?
- cells cultured to gen mitotic cells (need dividing cells)
- arrest cell cycle in metaphase (high mitotic index)
- swell nuclei w/ hypotonic solution (so no overlapping)
- kill cells using fixative (3:1 methanol:acetic acid) –> fixed
- drop fixed sample onto glass slide
- trypsin digest (protease) –> creates pale bands
- wash, then Leishman’s stain
- wash, then image analysis
Why are cells fixed in G banding?
- to stop chromosomes from condensing, otherwise would be so small wouldn’t be able to see bands, and also helps sep chroms
- also kills everything in sample (ie. minimises risk of staff being infected w/ any infectious disease)
What do the dark and pale band represent in G banding?
- dark bands = AT rich
- pale bands = GC rich
What diff samples can be received in the clinic, and what are the sources of these samples?
- blood sample from parents
- fetal epithelial cells –> taken from amniotic fluid samples
- placental material –> chorionic villus sample
- (also fetal blood samples but signif risk of spont abortion, so gen last resort)
Are most cells received actively growing and diving, what is the consequence of this?
- no (except cancers, usually actively growing and dividing)
- so need to culture in order to grow so can gen metaphases to analyse
Why in light microscopy of chroms does 1 side largely appears pale and other dark?
- wherever dye has stained chroms heavily, conformation of chromatin quite open –> theory is this means dye can access binding pocket
- chromatin collapsed in on itself where pale staining –> dye cannot access binding pocket as well
- v likely that structure of chromatin determines type of staining you get
- trypsin wash determines this step
What is an idiogram?
- diag of chrom
In what order are chrom bands numbered?
- no.s increase further away from centromere
What is ISCN?
- standardised nomenclature system for describing chroms and chrom abnormalities
What can affect banding resolution?
- stage of cell cycle cell in when added mitotic blocking agent
- type of tissue received from patient
- G banding protocol
Why are chroms analysed in metaphase?
- as move through cell cycle from interphase to metaphase, chroms become longer and more spaced out
- if more condensed chrom see fewer bands, 2 homologs don’t necessarily condense in perfect synchronicity
- want to analyse when chroms long enough, so can see all bands, but not too long otherwise will overlap and need more cells
Why does morphology differ dep on type of tissue (ie. type of sample)?
- not fully understood but does slightly correlate w/ maturity of cells –> long chroms when cells terminally differentiated (ie. leucocytes from peripheral blood), but SCs not terminally differentiated and tend to be a lot shorter
Why does trypsin cause pale bands in G banding?
- controls how much of chromatin is collapsing
- longer add trypsin get paler band as cleaving peptide bonds, causing partial collapse of chromatin, so ends up collapsed and smooth, preventing Leishman’s dye from getting to binding pocket
What happens if leave trypsin on too long in G banding?
- eventually chroms fall to pieces
Why is it important that chroms are optimally stained?
- amount of time to analyse chroms signif quicker if optimally stained, so get patient quicker result which is v important
Apart from trypsin digest, what other factors can influence quality of slide?
- ageing –> let slides dry out, longer = better banding quality
- staining time w/ Leishman’s, too long can blur dark bands together = bad
- chromosome spread –> too overlapping then can’t see bandin structure properly
What are the 2 types of FISH?
- direct labelling = DNA/RNA probes directly mod by fluorescent nts
- indirect labelling = fluorescent dyes added after probe hybridised to patient sample
Which type of FISH is used in the NHS, why?
- direct
- much quicker and brighter as labels already manufactured
How is FISH carried out?
- take microscope slide –> DNA in metaphase chrom spread or interphase nucleus (both same protocol)
- 1st step is like PCR, make patient DNA ss so can hybridise another NA to it
- -> but lower temps (75-78°), so denatures but doesn’t destroy DNA structures
- anneal probe
- series of stringent washes to remove any probe bound to non-complementary regions of sample
- DAPI is intercalating agent (blue background colour in images), used as counter-stain for both methods
What are the 3 main probes used for FISH in clinical setting?
1) FISH probe itself is specific clinical service, ie. if abnormality in fetus suspected go straight to FISH not G-banding, as usually due to gains and losses of chroms (aneuploidy), so need to check chrom no.
2) when querying specific section of chrom that is poss abnormal, after seeing something specific from G-banding
3) whole chrom painting, when unsure about origin of certain piece of DNA
How big are probes?
- tend to be v large (sometimes 100s of kb)
Why is a bright signal of a probe in FISH beneficial?
- allows rapid hybridisation times and rapid, less ambiguous analysis
What are the most common aneuploidies seen in samples?
- ChX –> fragile X (XXX), Turner syndrome (XO)
- ChY –> Klinefelter (XXY)
- Ch21 –> DS
- Ch18 –> Edwards syndrome (trisomy)
- Ch13 –> Patau syndrome (trisomy)
Can Down’s Syndrome occur w/o full trisomy?
- yes, there is critical region which can be amplified
What are micro deletion probes used for?
- usually for unbalanced foetal karyotype due to ‘abnormal’ inheritance of chroms from a parent w/ balanced rearrangement
- eg. Cri du Chat, SOTOS
- often combine multiple diagnostic probes to save money –> 1 probe used as +ve control for other
What is the effect of having a balanced rearrangement?
- gen no other phenotypes, apart from fertility problems
- can cause fertility problems because fetal karyotype unbalanced, may be so unbalanced that aborts before even realise pregnant, or if slightly imbalanced and can mature part way through dev before aborting
- if breakpoints near ends of chroms, then fetus can be viable, and dev w/ serious genetic disease
When is whole chrom painting used?
- when unsure where breakpoints are or unsure about origin of certain part of DNA
What is an asynchronous culture?
- contain dividing cells at all stages of mitosis and G0 (quiescence)
Why do patient samples need to be asynchronous cultures?
- human cells take approx 24 hrs to complete 1 cell cycle (and often longer)
- mitosis lasts for approx 1-2 hrs (4-8% cells in mitosis at any 1 point, and even lower prop in metaphase)
- therefore need to somewhat synchronise cells
How can DNA synthesis be reg for cell synchronisation?
- DIAG*
- have precursor nts (dATP/dCTP/dGTP/dTTP), used by DNA pol and added to new strand as synthesise it
- rest are some of the precursors to dCTP and dTTP
- excess dTTP inhibits reduction of CDP to dCDP (precursor for dCTP) by ribonucleotide reductase, this reduces availability of dCTP for DNA synthesis
- dCTP cellular conc becomes rate limiting –> lymphocytes remain in S-phase for extended periods
- prop of cells in S-phase increases w/ dTTP block reaction time
How is thymidine block released (part of cell synchronisation)
- by washing –> centrifugation and subsequent suspension of lymphocytes in fresh growth media
- or addition of dCTP, bypassing need for ribonucleotide reductase (used in healthcare, as centrifuging has health and safety issue)
What happens to cells after released from dTTP block?
- arrested cells process through mitosis in synchronous manner
What is an alt to cell cycle manip for cell synchronisation?
- fluorodeoxyuridylate (FdU) synchronisation
- excess FdU inhibits the synthesis of dTMP (a precursor of dTTP) –> reduces the availability dTTP for DNA synthesis
- dTTP cellular concs become rate limiting –> lymphocytes remain in S-phase for extended periods
- prop of cells in S-Phase increases w/ FdU block reaction time
- FdU block released by addition of dTTP (or wash and centrifugation, but not preferred)
- once released, arrested cells proceed through mitosis in synchronous manner
What occurs normally in meiosis?
- in early metaphase spindle fibres polymerised and bind kinetochores
- once mts connected to kinetochores get tension across spindle
- sister chromatid cohesion broken down by separase (req tension)
- immed enter anaphase and chroms condense at opp poles
- telophase, then cytokinesis
How does colcemid synchronisation work?
- mech of action at mol level not completely understood, but following gen agreed:
- colcemid binds soluble tubulin, colcemid-tubulin complex may still polymerise, but w/ signif reduced efficiency
- colcemid-tubulin complex also slows microtubule depolymerisation
- overall microtubule stability reduced, preventing functional spindle from forming, so no tension and no breakdown of sister chromatid cohesion
Why do we care about mitotic index or banding resolution?
- affects quality
What are the diff aspects of quality, and how is each of these defined?
- accuracy and precision = measure tests general reliability
- -> test accurate when true abnormality identified
- -> test precise when repeated analyses yield same result
- specificity and sensitivity = likelihood of FPs (false +ves) and FNs (false -ves)
- -> test specific when false +ve rate low, so correctly excludes ‘normal’ patients
- -> test sensitive when false -ve rate low, so correctly identifies people w/ given disorder
How is QA measured?
- look at 4 diff chroms and see clearly bands indicated for that particular QA in both homologs for 3/4 chroms
What is QA3 used for?
- oncology only –> too low for any fertility services
When is QA4 used?
- for exclusion of aneuploidy and large structural rearrangements –> eg. if prenatal diagnosis, suspected Down Syndrome
- if can get QA5 rather than QA4 then would, even if only req QA4
When is QA5 used?
- if concerned about fetal dev, for exclusion of aneuploidy and large or more subtle structural rearrangements –> eg. if prenatal diagnosis, ultrasound scan (16-20w gestation) detects morphological abnormalities
When is QA6 (highest) used, and what samples are needed?
- for parental blood samples (as achievable, but cant get QA6 from chorionic villus etc.)
- for exclusion of subtle structural rearrangements and many microdeletion syndromes –> eg. if recurrent miscarriage (>3)
What holds bivalents together in meiosis?
- COs
What % of clinically recognisable conceptions spontaneously abort, and how many of these are due to abnormal chrom complement?
- 15% of all clinically recognisable conceptions will spont abort
- approx 50% of all spont abortions have an abnormal chromosome complement
What is the most common cause of spontaneous abortion?
- polyploidy most common aborted (and triploidy most common of this)