01 Chromosomal Abnormalities Flashcards
Chromosomes, genes, non genes etc.
What is the Paris convention?
Naming the chromosome of the chromosome with p and q for the arms
Which is the short arm?
p
Which is the long arm?
q
Which is near the centromere? 1p1 or 1p3?
1p1 is near the centromere
Which is near the telomere? 12p1 or 12q4
12q4 is near the telomere
How much DNA in each cell? (Length)
2 metres
How big is a cell?
10um across
What’s the purpose of the centromere?
It’s where 2 sister chromatids are joined together
What’s the sequence of the centromere like and why?
It has a long stretch of repetitive DNA. This provides an attachment point for the spindle fibres at the kinetochore
What do telomeres do?
Prevents the chromosome ends being treated as broken ends
What is the telomere sequence and structure?
TTAGGG repeated for 10-15kb with a loop at the end
What’s the order of the cell cycle?
G1 (creating more cell contents), S (duplicating chromosomes), G2 (checking DNA for errors and repairing them), M (separating duplicated DNA), cytokinesis
What’s the order of mitosis?
Interphase, Prophase, Metaphase, Anaphase and Telophase
Why is is tougher to study meiosis over mitosis?
For meiosis you either need a male biopsy or a fetal ovary
What are the three stages of meiosis?
Synapsis, recombination, segregation
What is synapsis?
In Meiosis where homologous chromosomes are paired during prophase I. The chromosomes are duplicated in this state, consisting of two sister chromatids joined by the centromere.
What is the structure called of the homologous pairs together in meiosis?
A four stranded bivalent or a tetrad
What happens at the meiosis stage called recombination
Any of the 4 strands in the bivalent swap segments over at cross over events
How many cross over events take place in males meiosis?
Approximately 60
What is segregation in meiosis?
Where the bivalents separate, cytokinesis occurs, and each 4 gametes are carrying a unique combination of parental alleles
What stage of the cell cycle do you need for conventional karyotyping and why?
Metaphase of meiosis. Chromosomes are most condensed here so easier to analyse their number, size and structure
What is the resolution of karyotyping?
4-5Mb
Why is karyotyping bad?
Needs a lot of skill, it’s slow, and it’s expensive
What questions does FISH answer?
Is this specific sequence in my patient and if so, where?
How do you do FISH?
You have a fluorescent probe for the sequence of interest, you slightly denature the chromosomes so they keep their structure, but let the probe hybridise.
What’s good about FISH?
Has a high resolution. And you can use multiple colours at a time. Can see balanced translocations.
What phase of the cell cycle do you need for FISH?
Interphase or metaphase is fine.
What’s bad about FISH?
You need to know what you’re looking for ahead of time
What question does array CGH answer?
Is there any sequence that my patient has a CNV of in their genome?
How do you do array CGH?
Fragment the patient DNA and stain it red. Stain a control green. Hybridise to a microarray with many probes from a normal genome. Read the fluorescence.
What does a yellow well mean on array CGH?
There is equal patient and control DNA. No CNV
What does a red well mean on array CGH?
There is more patient DNA than control DNA at that location. Patient has a copy number gain
What does a green well mean on array CGH?
There is less patient DNA than control DNA at that location. Patient has a copy number loss
What’s the resolution of array CGH?
Can be varied. You can change your probes. Depends on if you’re looking at the whole genome, or just a chromosome etc.
What’s good about array CGH?
Quantitative information. You don’t need to know where you’re looking by default.
What’s bad about array CGH?
Can’t detect balanced translocations as it provide no locational information.
Explain SNP arrays
Patient’s DNA is hybridised to an array. Standard SNPs are assessed. The genotype is called and clustered. Can identify CNVs
What’s good about SNP arrays?
Good coverage of the genome, can change resolution
What’s bad about SNP arrays?
Can’t measure anything under a certain size (maybe 50 or 100Kb). Don’t get positional information
What is DNA sequencing used for?
Well lots… Can use for comparing tumour cells to normal cells. Mainly used for NIPD in clinical genetics.
What is long read seq good for?
Identifying large rearrangements. Transcriptomics.
What are the two broad ways chromosomes can go wrong?
In number (aneuploidy) or in structure
Name some types of structural abnormalities in chromosomes
Deletions, duplications, inversions, tranlocations (Both reciprocal or robertsonian).
How does triploidy come about?
66% -
24% -
10% -
66% - 2 sperm
24% - A 2n sperm
10% - A 2n egg
How do most aneuploidies come about?
A failure of chromosomes to segregate correctly during cell division.
Aneuploidies can either be consitutional or mosaic, how?
Either have a failure during meiosis leading to a constitutional abnormality, or a failure during mitosis, this will lead to a clone of cells with aneuploidy creating a mosaic.
What are the three constitutional trisomies that are compatible with life?
Downs (21), Edwards (18) and Patau (13) syndromes
How could you live with an aneuploidy of say, chromosome 1
By it being a mosaic
Why are sex chromosome aneuploidies less damaging?
There’s a small overlap between the X and Y, there are few shared genes.
What aneuplodies exist with the sex chromosomes?
XXY Klinefelters, XYY Jacob’s syndrome, XXX, X Turner syndrome
What is the general effect of someone having an aneuploidy?
Risk of infertility and miscarriages or abnormal babies
Why are balanced translations or inversions not as bad as unbalanced translocations?
Because there is no overall change in the amount of DNA.Wh
What is the sample type in Non Invasive Prenatal Diagnosis?
Cell free DNA from the baby that is naturally in the mother’s blood
What can NIPD be used to detect?
Trisomies, because the cfDNA from the child will be slightly more abundant from the triploid chromosome.
What do you have to adjust for in NIPD?
Chromosome length
How do structural chromosomal abnormalities come about?
When there are two breaks in chromsomes and the areas are misrepaired giving an inversion, deletion, translocation etc.
What can occur from aberrant recombination from mis-paired low-copy repeats?
Either deletions, duplications, or translocations
What can stalled replication forks from DNA damage cause?
Complex chromosomal rearrangements
What is replicative template switching?
When DNA replication forks stall, it’s a way for the DNA replication machinery to use microhomologies (of 3-5 nucleotides) to try and recontinue the process.
What are the possible products of reciprocal translocations
Either two chromosomes with just a bit of DNA switched from each one. OR an acentric chromosome (no centromere) that gets degraded, and a dicentric chromosome which can be pulled in two directions at mitosis and break and cause a mess
What is a robertsonian translocation?
The fusion of two chromosomes that have their cetromeres very close to the chromosome end.
What chromosomes are usually involved in robertsonian translocations?
13, 14, 15, 21 and 22.
What is true of the p arms involves in robertsonian translocations?
They share similar sequences
What happens to the two chromosomes created from robertsonian translocations?
The double p arm chromosome can be degraded, but this can be OK because they have little on them and the p arms are all similar of chr 13, 14, 15, 21 and 22. And the double q chromsome can be kept healthily. But leads to issues at meiosis.
When there’s been a reciprocal translocation, what are the possible results in meiosis?
1/4 completely normal
1/4 phenotypically normal carrier
1/4 partial trisomy of chrA and partial monosomy of chrB
1/4 partial trsiomy of chrB and partial monosomy of chrA
When you’ve had a robertsonian translocation, say between one chr14, and one chr21, and the double p arm chromosome is lost, what are the 6 results when the gametes take part in fertilisation with a normal other gamete?
(You start with one chr14, one chr21, and a chr14/21 split)
1/6 Normal
1/6 balanced carrier
1/6 trisomy 14
1/6 monosomy 14
1/6 trisomy 21
1/6 monosomy 21
What percentage of embryos abort spontaneously in the first trimester due to chromosomal abnormalities?
> 50%
How many newborns have multiple congenital abnormalities due to chromosomal abnormalities?
1 in 200
What’s one final topic that chromosomal abnormalities are important to but we haven’t mentioned yet?
Cancer
