Chromosomal abnormalities

Question 1

What does a genome look like?

Answer 1

Chromosomes are condensed and can be karyotyped during metaphase.

At this point, each chromosome comprises two chromatids. One chromosome comes from father and one from mother.

4n at this point prior to cell division.

Question 2

What is DNA compaction?

Answer 2

DNA compaction is very fundamental to the expression of genes within the compaction.

1. Starts off with the DNA double helix.
2. DNA is wrapped around histones. DNA + histone is called a nucleosome.
3. Nucleosomes are coiled into a chromatin fiber.
4. Chromatin further condensed around a protein core forming the chromosome.

Question 3

What is the G-banded architecture of a chromosome?

Answer 3

Chromosomes are analysed using ideograms. Giemsa staining leaves a recognizable pattern of bands:

top Telomere

p-arm - always the small arm

centromere

q-arm

g-dark - more tightly bound making it ‘gene poor’ so genes are less accessible.

g-light - less tightly bound making it ‘gene rich’ so genes are more accessible therefore more expression.

bottom telomere

Question 4

What is the normal karyotype?

Answer 4

46,XX or 46,XY

Question 5

What sort of abnormality do these show?
1. 46,XX,t(5;10)(q34.1;q11.2)

2. 46,XX,del(5)(q21q23)
3. 45,XX,-7
4. 47,XX,+8
5. 46,XX,inv(3)(q21q26)

Answer 5

1. Translocation
2. Deletion
3. Monosomy
4. Trisomy
5. Inversion

Question 6

What are haploinsufficient, imprinted and haplosufficient genes?

Answer 6

Haploinsufficient - both alleles of gene required for normal phenotype

Imprinted - methylation pattern that is parent of origin specific that must be inherited correctly

Haplosufficient - only one allele needed for normal phenotype

Question 7

When might genes be expressed?

Answer 7

Tissue specific - only expression in specific tissues

Can be at a specific time in development

Can be in response to an event

Question 8

How are chromosomes cultured and harvested in order to identify karyotype? (6 steps)

Answer 8

1. 0.5ml of blood sample from patient in 5ml culture medium
2. Add phytohemagglutinin which stimulates lymphocytes to divide
3. Culture for 24 hours
4. Add colcemid which arrests cells in metaphase
5. Culture briefly, add hypotonic KCl to swell cells, fix in methanol and acetic acid in the ration 3:1 and drop on to microscope slide
6. Brief digestion with trypsin then stain with Giemsa.

Question 9

What is the purpose of mitosis and meiosis?

Answer 9

Mitosis - Create two identical daughter cells for growth and repair/ replace exhausted cells.
2n - 2n

Meiosis - Ensures genetic variation in gametes and enables random assortment of homologues and recombination
2n - n

Question 10

When can non-disjunction occur?

Answer 10

Non-disjunction can occur during anaphase 1 of meiosis 1. This means atleast one pair of homologous chromosomes didn’t separate correctly resulting in 2 cells with an extra chromosome and 2 cells missing that chromosome.

Non-disjunction can also occur during anaphase 2 of meiosis 2. This means atleast one pair of sister chromatids didn’t separate correctly resulting in two normal haploid cells, one cell with an extra copy of a chromosome and one cell missing that chromosome.

Question 11

Why is non-disjunction more likely to occur during female meiosis?

Answer 11

Meiosis 1 occurs in utero and is then paused until puberty in women.
There is also a sort of unbalanced division since one primary oocyte yields one ovum and 3 polar bodies .
Finally there is also a finite number of primary oocytes.

In men spematogenesis begins at puberty and continues lifelong. Each spermatocyte yields 4 spermatids.

Question 12

Why does the risk of non-disjunction increase along with maternal age?

Answer 12

Most aneuploidy is caused by non-disjunction in oogenesis because there is a degradation of the factors that hold homologous chromosomes together therefore as maternal age increases the risk of non-disjunction occuring also increases.

Question 13

What is trisomy 21?

Answer 13

Trisomy 21 causes down syndrome. 85-90% caused by non-disjunction in maternal meiosis.

Question 14

How is trisomy 21 identified?

Answer 14

Study of karyotype takes a long time therefore quantitive fluorescence PCR is used. Number of peaks shows number of chromosomes. Height of peak shows ratio.

3 peaks of same height = trisomy caused be meiosis 1.

2 peaks in a 1:2 height ratio = trisomy caused by meiosis 2 .

Question 15

Are there trisomies other than 13, 18 and 21?

Answer 15

Yes, trisomies for all chromosomes have been identified prenatally but many are not compatible with life.

Monosomies are poorly tolerated and miscarriage occurs almost straight after conception or before the pregnancy is identified.

Question 16

Why is sex aneuploidy well tolerated?

Answer 16

X - inactivation of excess X chromosomes. One X gene is fully methylated and shut down.

Low gene content of Y

Question 17

What are the 3 types of reciprocal chromosomal abnormalities?

Answer 17

1. Translocations
2. Insertions
3. Inversion

Carriers are usually phenotypically normal. However, chromosomes have to contort into unusual figurations to achieve synapsis which is the fusion of chromosome pairs at the start of mitosis and meiosis increasing the chance of unbalanced gametes.

Question 18

Difference between de novo and parent abnormality

Answer 18

de novo = new to individual

parent abnormality = inherited from parent

Question 19

What are contiguous gene deletion syndromes?

Answer 19

A clinical phenotype caused by a chromosomal abnormality, such as a deletion or duplication that removes several genes lying in close proximity to one another on the chromosome.

Question 20

What is aCGH?

Answer 20

Array comparative genome hybridisation

Works by taking a patient sample and a reference sample and hybridising them together. A computer will read the hybridisation and looks for regions of imbalance.

Question 21

Mechanism of contiguous gene sydrome

Answer 21

When chromosomes undergo recombination they look for regions of homology (similarity) to ensure they are recombining with the correct part of the chromosome. Low copy repeats show some homology (enough to trick enzymes into thinking it is the an allele) but are not actually the correct part of the chromsome leading to recombination that causes one chromatid to have a duplication and one to have a deletion. This is because the allele on one chromatid has been exchanged for an LCR leaving that chromatid with a deletion and the other chromatid with a duplication.

Question 22

What is the ‘genotype first’ era?

Answer 22

Instead of looking at karyotypes we can now look at arrays with automated analysis allowing the cost of genomic analysis to be greatly reduced. They are also able to detect smaller imbalances.

Question 23

How does next generation sequencing occur?

Answer 23

1. Library preparation
2. Cluster formation
3. Sequencing
4. Sequence identification

Question 24

What is the main vulnerability in male meiosis?

Answer 24

There is no equivalent menopausal limit on reproductive span. Primary spermatocytes undergo 23 mitotic division per year potentially life long and can accumulate defects over time.

Question 25

How is rare disease defined in the UK?

Answer 25

Affects 1 in 2000 or less of the population