aneuploidys Flashcards
1
Q
Karyotype
A
- The number of a chromosome within a cell is called a karyotype
Chromosomes are rearranged in order of size and position of centromere to form a karyogram
2
Q
Karyotyping methods (basic)
A
- Blood, Amnionic Fluid (AFT) (or cvs) or bone marrow are common specimens
- Cells must be cultured in vitro, typically 3 days
- After incubation, colcemid is added
○ Arrests mitosis at metaphase
Cells fixed to slide and stained Giemsa
3
Q
FISH- staining
A
- Identifying small translocations using giemsa staining is almost impossible
- We use FISH staining
○ using probe DNA (labelled with dye)
○ Denature and hybridise
○ Where sequence is homologous to the probe DNA there is binding
○ Shine UV light
○
Probe bound to chromosome 1 that should come from homologous 3 - translocation
- We use FISH staining
4
Q
Pre-natal screening
A
- Genetic analysis for unborn foetus to diagnose aneuploidies or chromosomal rearrangement
- Previously relied on AFT or CVS and karyotyping
○ Dangerous
○ Require culturing - slow
Move towards DNA testing
- Previously relied on AFT or CVS and karyotyping
5
Q
Cell-free DNA
A
- Detection of foetal DNA in bloodstream - during pregnancy foetal DNA is shed
○ Apoptosis of placental cells during embryogenesis- Purification of foetal DNA obtained by epigenetic patterns
○ Foetal DNA primarily unmethylated
○ Maternal DNA displays unique epigenetic marker for the mother
Thus we can detect foetal DNA
- Purification of foetal DNA obtained by epigenetic patterns
6
Q
Detection of foetal aneuploidies
A
- Quantitative PCR methods
- E.g. Harmony
○ Probes that are unique to areas commonly aneuploidy
§ Chromosomes 13, 18, 21, x and y - Not good for rare (not in probe library)
2. Next-generation sequencing
We can detect copy number by number of contigs that come back for a chromosome result
- E.g. Harmony
7
Q
Terminology
A
- Aneuploidy ○ Loss or gain of a single chromosome ○ E.g. monosomy, trisomy, tetrasomy - Euploidy ○ An increase in a complete set of chromosomes (i.e. chromosome number doubles) (e.g.46 chr -> 92 chr) ○ E.g. § Triploidy - 3n § Tetraploidy - 4n Polyploidy - 3n, 4n, 5n, 6n
8
Q
Naming aneuploids
A
- Chromosome number, genotype
- E.g.
○ 47, XXX - 47 chromosomes in total, 3 x chromosomes
47, 21+ - 47 chromosomes in total, one extra chromosome 21
- E.g.
9
Q
Origins of aneuploidy
A
Non-disjunction (ND) during either meiosis 1 or 2
10
Q
Aneuploidy during meiosis 1
A
- If ND occurs during meiosis 1, gamete carries different recombinant chromosomes
○ Mendel - segregation
○
○ The bottom two left gametes have one too many chromosomes (called disomic)
○ The bottom two right gametes called empty
○
§ When combined with other parent can cause a trisomy (3 copies)
§ The other two are monosomy
○ 100% gametes are abnormal
§ 50% trisomy
50% monosomy
11
Q
Aneuploidy at meiosis 2
A
- If ND occurs during meiosis 1, gamete carries same recombinant chromosomes
- ○ One disomy, one empty and two normal
- ○ 25% trisomy
○ 25% monosomy
50% disomy (normal)
12
Q
Gene dosage effects
A
- Usually 2 copies are required for normal gene function
○ In some cases with monosomy you have haploinsufficiency (not enough of a gene product for normal phenotype)
In some cases having more than a disomy may lead to problems as well
13
Q
Departures from normal gene dosage
A
- Abnormal phenotype is characteristic for each chromosome
- Monosomy generally results in the worst phenotype (compared to trisomy)
- Aneuploidy of larger chromosomes results in more severe abnormal phenotype
- Severe imbalance of genes leads to inviability
○ Most autosomal aneuploidies aren’t tolerated in humans
Embryo doesn’t survive
14
Q
Sex aneuploidy
A
- Sex aneuploidies are better tolerated
- 4 most common (there is a total of 18)
○ Monosomy x - turner syndrome
○ XXY - Klinefelter syndrome
○ XXX - triple x syndrome
XYY - double Y syndrome
- 4 most common (there is a total of 18)
15
Q
Male and female aneuploidy are different
A
- Females only have x chromosomes
○ Non-disjunction in females only results in the case of meiosis 1 or 2 (look above)- In males there is more variety
○ In M1 you get gametes that carry both X&Y or neither (Klinefelter syndrome)
○ In M2 you get disomy x (triple x syndrome) or disomy Y (double Y syndrome) depending on which doesn’t segregate
For XXXX, XXXY, XXYY, XX - you need multiple non-disjunction events in both parents - rare
- In males there is more variety
16
Q
Why are sex-chromosomes better tolerated
A
- X-inactivated
○ XXX individuals will have two Barr bodies instead of one
○ XXY will have one Barr body
○ Increase Barr bodies to make gene dosage normal- Y chromosome encodes only a few genes
○ Only for sperm viability or spermatogenesis
Not critical
- Y chromosome encodes only a few genes
17
Q
Where do the abnormalities come from
A
- Not the entire x chromosome is inactivated
Abnormalities due to excess/deficit gene dosage with PAR1 and to a lesser extent in PAR2
18
Q
Alterations in sex chromosome number does not necessarily make the person sterile
A
klinefelter and turner syndrome are infertile - In Klinefelter most likely the testes don’t develop
- Why are two fertile
§ Possibly during embryonic development, normal genotype is restored
Possibly one sex chromosome must be lost to develop germline
19
Q
Turner syndrome (45, XO)
A
- Female (missing SRY)
- Near normal intelligence
- Short
- Webbed neck
Sterile
20
Q
Mosaic Turner syndrome
A
- In germline one chromosome is lost
- In some areas of tissue the cells come from precursor where one chromosome was last
21
Q
Klinefelter (47, XXY)
A
- Male
- Slightly lower IQ
- Taller
- 20% breast dev
- Sterile
22
Q
Triple x (47, XXX)
A
- Female
- Very mild - most don’t know they have it
- Mild reduction in IQ
- Tend to be very tall
- Occasionally behavioural problems
Fertile
23
Q
Double Y (47, XYY)
A
- Male
- Very mild
- Rarely a slight reduction in IQ
- Learning difficulties
Rarely antisocial behaviour
24
Q
Uniparental diploidy
A
- Generation of diploid set of chromosomes from a single parent
- i.e. sperm carries 46 chromosomes and egg carries 0
- Very rare requires many errors in both parents- Foetuses don’t develop correctly
- Typically dead, or with severe morbidity
- Possibly due to genetic imprinting
Maintain epigenetic markers of parents
- Foetuses don’t develop correctly
25
Q
Uniparental disomy
A
- Inheritance of both chromosomes from a single parent
- For example; you have multiple copies of a chromosome in the egg, but no copies in a normal sperm both copies would then come from one parent- A chromosome is lost during early mitotic division in foetus
- Many go undiagnosed
Abnormalities - imprinting errors?
26
Q
Prader-Willi syndrome
A
- Deletion of paternal 15q11-13
- Or uniparental disomy where both copies of Chr 15 come from the mother
- Maternal copies of this region are silent due to imprinting- Conversely, Angelman syndrome - maternal deletion of the same region
- Symptoms
- Poor muscle tone
- Insatiable appetite
Cognitive delays
27
Q
Autosomal aneuploidy
A
Autosomal aneuploidies have the same proportions as sex aneuploidies
28
Q
Why are they so badly tolerated
A
- Autosomal Monosomies (2n-1) ○ Not tolerated in humans ○ Die in utero ○ Better tolerated in plants Tend to be less viable and less sterile
29
Q
Monosomies unmask recessive alleles
A
- In empty (seen above) they will have one chromosome (i.e. monosomic) - the phenotype will be determined by that chromosome (dominant or recessive)
○ Tendency to shoer greater expression of recessive phenotypes- Lethal alleles can be tolerated if non-lethal homolog available
Traits more common in males
- Lethal alleles can be tolerated if non-lethal homolog available
30
Q
Haploinsufficiency
A
- Accumulation of an additional chromosome
- Better tolerated in humans than monosomy
○ More likely to survive - Survivability increased if trisomy is in small chromosome
- Trisomy in all chromosomes can occur, but only 3 survive
Trisomy accounts for 35% of spontaneous abortions
- Better tolerated in humans than monosomy
31
Q
Trisomy in plants
A
- viable but infertile
Phenotypic differences
32
Q
Down syndrome (trisomy 21 or 47, 21+)
A
- Phenotypic variable
- Short stature
- Mental retardation
- Epicanthic fold
- Heart and nervous system abnormalities
Life expectancy not common after 60s
33
Q
Down syndrome critical region (DSCR)
A
- hypothetical region on chr 21 thought to be involved in abnormal phenotype
○ 21q22.2 = DSCR- In mouse DS model, identified candidate genes
○ DYRK - reproduces dosage-sensitive learning defects in fly and mice
DSCAAM - reproduces heart and nervous system defects
- In mouse DS model, identified candidate genes
34
Q
Maternal age down syndrome
A
- Prevalence od DS births increases with maternal age
○ Ovum the source of extra chr 21 in 95%
○ Most ND events occur at anaphase 1- Paternal age not important
○ Spermatogenesis continuous doesn’t arrest - Maternal oogenesis arrests at diplotene
○ Reduction in spindle fibers - don’t function properly
ND more likely
- Paternal age not important
35
Q
smal syndrome (Trisomy 13 or 47, 13+)
A
- Risk increases with maternal age
- Few survive beyond 1 yr
Mental defects
- Few survive beyond 1 yr
36
Q
Edwards syndrome (trisomy 18 or 47, 18+)
A
- Most spontaneous abortions
- Few survive beyond 1 yr
- Skull deformity, clenched hands
37
Q
Polyploidies
A
- Duplication of every chromosome in a set
- Not tolerated in humans
- In other animals some times tolerated
○ In toads
○ Fish or lizards
Much more stable in plants
38
Q
Autopolyploidy
A
- More than 2 sets of chromosomes all derived from one ancestral species
- Can happen naturally if
○ Fusion of non-diploid gametes
○ Cell re-enters interphase after prophase - Can induce experimentally using colchicine
Tolerated in plants
- Can happen naturally if
39
Q
Experimentally induced polyploidy
A
- During prophase add colchicine - arrests at metaphase
○ Reversible
○ Cell re-enters interphase when colchicine is removed - duplication (results in tetraploid)- Can result in larger fruit
Sterile due to the imbalance of chromosomes cant synapse correctly during meiosis
- Can result in larger fruit
40
Q
In salmon
A
- Randomly duplication occurred and produced tetraploid (4n)
○ If mated with diploid ancestor they would produce triploid (sterile)- Tetraploid reproductively isolated from its diploid ancestor
41
Q
Allopolyploidy
A
- Generation of polyploid from the fertilisation of two closely related but different species
- Progeny only fertile if:
○ The progeny has a diploid number of chromosomes AND
○ There is sufficient similarity between genes for synapsis to occur - For example
○ Radage
Combination between radish and cabbage similar enough genes
- Progeny only fertile if:
42
Q
Allopolyploidy in animals
A
- Mules ○ Donkey x horse § Donkey = 62 chr § Horse = 64 chr Mule = 63 chr (infertile) not balanced
43
Q
Creation of Allopolyploidy
A
- Interspecies hybris can be made fertile if made polyploidic
- Use colchicine to arrest mitosis then remove
Generate fertile amphidiploid
- Use colchicine to arrest mitosis then remove
44
Q
Somatic cell hybrid
A
- The fusion of two somatic cells from 2 different species into a single hybris cell
○ Hybrid that contains the genetic material of both species- Valuable technique for mapping genes and determining gene function
- Example
○ Mouse cell line defect in thymidine kinase (TK gene)
○ Generate SCH with human cell line with functional TK gene
Redundant human chromosomes lost
45
Q
Endopolploidy
A
- Certain cells within diploid organism become polyploidic
○ Tissue mosaicism- Can happen if
○ Cells enter mitotic division (prophase), without progressing through the other stages - re-enter interphase
○ The cell can progress through normal steps of mitosis, except the nuclear membrane will form over all DNA during telophase - Humans liver cells can be polyploidic
○ 3n, 4n or 8n
Unclear why
- Can happen if
46
Q
Chromosomal rearrangements
A
- Chromosomes are fragile, regions can ○ Break off ○ Invert ○ Duplicate - Changes to chromosome structure have varies phenotypes ○ Sometimes nothing happens Sometimes disease results
47
Q
Chromosome fragile sites
A
- Littered with tiny gaps or ‘pinches’ which tend to break
- Not prone to spontaneous breaks
○ Unless other factors influence chromosomal instability
○ Such as alcohol
Interest to cancer genetics
- Not prone to spontaneous breaks
48
Q
5 main types of chromosomal aberrations
A
- Deletions
- Duplications
- Inversions
- Ring chromosomes
Translocations
49
Q
Deletions
A
- Region of chromosome breaks off and is lost
○ Terminal deletion
○ Intercalary deletion
§ Internal- Severity depends on size of deletion
- Also depends on what genes are deleted
○ Important regulatory systems of later genes
i.e. loss of gene C affects gene E expression
50
Q
What is the outcome of an acentric deletion
A
Acentric chromosome would be lost coz it cant bind to the spindle
51
Q
Mitosis or meiosis with deletion chromosomes
A
- Partial chromosomes can’t pair properly
- Leads to formation of a deletion loop
○ Aka compensation loop
Allows for synapsis to occur
- Leads to formation of a deletion loop
52
Q
Cri du Chat syndrome
A
- Partial deletion of chr 5 ○ 46, 5p- - Partial monosomy - Affected tend to be: ○ Anatomical deformities glottis and larynx § Results in unique cry ○ Mental retardation ○ Normal life expectancy
53
Q
Duplication
A
- Abnormal crossover
- Where a portion of a chromosome is duplicated
- Commonly produced by
○ Un-even cross over
○ Errors in DNA replication
High degree of phenotypic variation
54
Q
Positives affects of duplication
A
- Gene redundancy
○ Having a backup copy of that gene
§ Can complement mutation or increase the production of certain gene products
○ Having multiple copies of the rRNA gene allows for significant numbers to be generated- Evolution
Paralogous genes arose from a genetic duplication event
- Evolution
55
Q
selective pressure on duplication
A
- If selective pressure is on both genes
○ The genes stay similar- If selective pressure is on just one of the genes
○ One copy degrades
Or one copy can undergo spontaneous mutation and acquire a new function
- If selective pressure is on just one of the genes
56
Q
Negatives of duplication
A
- MECP2 duplication syndrome ○ Duplication of a region on x, q-arm ○ X-linked inheritance (100% penetrant) - Twice the amount of MECP2 can result in overexpression of overactivation which down regulates key neuronal genes - Presents with ○ Intellectual disability ○ Hypotonia ○ Predisposition to infections Epileptic seizures
57
Q
Inversions
A
- Occurs when a chr breaks at two points and flips
- 2 types
○ Paracentric - centromere outside inverted regions
○ Pericentric - centromere inside inverted region - Arise from unusual looping of chr
○ Odd twist that breaks the chromosome and improper repair results in flip - Genes are in balance - minimal effect on individual
○ Consequences on offspring
If the inversion interferes the expression of other genes (oncogenes)
- 2 types
58
Q
Meiosis continues normally if homozygous for inversion
A
- Genes pair up during prophase
Inversion will be passed onto offspring
59
Q
If heterozygous for inversion
A
- To allow pairing during prophase one inversion must make an inversion loop to fit with the normal chromosome
60
Q
If heterozygous for inversion- no cross-over
A
meiosis will continue normally
○ 50% will have inverted chromosome
50% will have a normal chromosome
61
Q
If heterozygous for inversion- cross-over in pericentric inversion
A
○ 50% normal gametes (1 inverted, but balanced)
○ 50% abnormal gametes ( carrying deletions )
Deletions = unbalanced = infertility
62
Q
If heterozygous for inversion- cross over in paracentric inversion
A
○ Gametes produced
§ 50%n normal, 50% abnormal
○ Acentric fragment (no centromere) get lost - cannot attach to spindle
Dicentric chromosome forms dicentric bridge - fragment lost
63
Q
Dicentric chromosome
A
- At meiosis there will be a break between the two bridges and fragment will be lost
- 2 normal gametes (with 1 balanced inversion)
2 deletion chromosomes - if fused with normal gamete foetus not viable
- 2 normal gametes (with 1 balanced inversion)
64
Q
Ring chromosomes
A
- Form when break occurs on both arms and the middle bit joins together to form a loop
○ Loss of genetic material at the terminal ends- Effects are severe
Ring chromosome 14 syndrome
- Effects are severe
65
Q
Translocations overview
A
- Transfer of genetic material from one location to another
○ Can occur within the same homologous pair (intrachromosomal)
○ Or between non-homologous pairs (interchromosomal)- Reciprocal translocations
○ Exchange of genetic material with replacement - Non-reciprocal translocations
Transfer of genetic material without replacement
- Reciprocal translocations
66
Q
Effects of translocations
A
- As long as the genetic material is balanced
○ May effect meiosis- Can disrupt important genes
○ Interrupt important genetic regulatory sequences
Origins of translocations - Chromosomal break and re-joining
Abnormal cross-over
- Can disrupt important genes
67
Q
Meiosis with chromosomes with translocations
A
- Similar to inversions, if homozygous for translocation - meiosis will continue normally
- If heterozygous, how do the chromosomes synapse
Form a translocation cross (quadrivalent)
- If heterozygous, how do the chromosomes synapse
68
Q
3 methods of segregation
A
The same kinetochore complex cannot migrate to the same pole
- alternate - two normal cells + 2 cells with balanced translocations
- adjacent-1 segregation - all 4 unbalanced cells - horizontal
- adjacent-2 segregation - all 4 unbalanced cells - vertical - exception (same kinetochore)
69
Q
Outcomes of 3 forms of segregation
A
- If unbalanced gamete fuses with a normal gamete - zygote unviable
- Therefore reduced fertility in heterozygotes
Recurrent miscarriage
- Therefore reduced fertility in heterozygotes
70
Q
Robertsonian translocation
A
- Break occur on p-arms of acrocentric chromosomes
- Will reduced chromosome number by 2
- The p-arm are lost, and the two q arms fuse
○ Only tolerated if p-arms are non-essential
E.g. familial down syndrome
71
Q
Familial down syndrome
A
- ~3% total DS births
○ Very common to give birth to many DS children
Robertsonian translocation between chr 14 & 21
72
Q
Chromosomal rearrangements
A
- Can promote speciation if spread through population
○ Heterozygotes have reduced fertility thus favours homozygous
Sometimes the homozygous translocation cannot mate with normal = new species can occur
73
Q
Reconstruction of human evolution from primates
A
- Examined G-banding patterns between closely related species
- Human chromosome
○ Chr 3 - arose from pericentric inversion on p-arm
○ Chr 2 - arose from Robertsonian translocation from primate chr
○ Chr 1 arose from a paracentric inversion on q-arm
- Human chromosome
