19. Chromosome Abnormalities

Question 1

What are the possible causes of cytogenic structural abnormalities?

Answer 1

Translocations, inversions, deletions, duplications, insertion, rings, marker chromosomes, isochromosomes.

Question 2

How do reciprocal translocations occur?

Answer 2

A two break rearrangement - there’s a break in one chromosome and a break in another and the two segments swap over.

Question 3

What gametes are a result of carriers of reciprocal translocations?

Answer 3

Either balanced or unbalanced (abnormal phenotype).

Question 4

Decode the following karyotype: 46,XY,t(2;18)(q12;q22).

Answer 4

Male, with a translocation of break points on chromosome 2 and 18 respectively on their q/long arms.

Question 5

What are the balanced and unbalanced segragation types of meiotic disjunction?

Answer 5

Balanced - alternate
Unbalanced - adjacent 1 (non homologous centromeres), adjacent 2 (homologous centromeres), 3:1 disjunction and 4:0 disjunction.

Question 6

How are unbalanced segregant outcomes assessed?

Answer 6

The likely segregation is established. The imbalance is looked up to see if it’s been reported before in the literature. The risks are then quotes if they have been established.

Question 7

What is Robertsonian translocation?

Answer 7

Two acrocentric chromosomes fused together. There is a chromosome count of 45 as an unstable trivalent is formed at meiosis. So there is an aneuploidy risk.

Question 8

Of the following, which are viable and which are not?

Trisomy 14, trisomy 21, monosomy 14 and monosomy 21.

Answer 8

Viable - monosomy 14, monosomy 21 and trisomy 21

Non-viable - trisomy 14.

Question 9

What causes deletions?

Answer 9

Uneven pairing and recombination in meiosis.

Question 10

What is the difference between terminal and interstitial deletions?

Answer 10

Terminal deletions are at the ends of chromosomes but interstitial deletions are within the chromosome.

Question 11

What is needed to confirm a micro deletion?

Answer 11

FISH technique.

Question 12

How are abnormal results from karyotyping reported?

Answer 12

The correct ISCN is given and then the abnormality is described in words and related to a clinical problem. A parental or family sample is taken if required and they’re referred to clinical genetics. Appropriate literature is provided for the clinician if available.

Question 13

What is Fluorescent in situ hybridisation?

Answer 13

A molecular cytogenic technique that allow very specific questions to be answered using probes for specific chromosomes or loci.

Question 14

How is FISH performed?

Answer 14

The DNA probe and target material and added together then denatured and hybridised. It undergoes stringency and then goes to washing to remove unbound probes. The results can then be visualised.

Question 15

What are the four FISH probe types?

Answer 15

For microdeletion syndromes:
Locus/gene specific probes - small dots on specific regions
Telomere probes - individual ones of the short and long arms.
For identification of the chromosome of origin:
Centromere probes - hybridise to the individual centromeres (not for acrocentric chromosomes)
Whole chromosome paints - to identify a chromosome in rearrangement.

Question 16

When are centromere probes used in FISH?

Answer 16

In metaphase and interphase for copy number analysis.

Question 17

What can whole chromosome paints be used for?

Answer 17

Identification of individual chromosomes even when they’re rearranged.

Question 18

What are locus specific probes used for in FISH?

Answer 18

For microdeletion/duplication syndromes. Often used to rule out DiGeorge (immune problems) before surgery.

Question 19

What do prenatal aneuploidy screenings do?

Answer 19

They test for common aneuploidies in 24-48 hours.

Question 20

Why are prenatal aneuploidy screenings chosen over PND?

Answer 20

They take a lot less time - 1-2 days rather than up to 14 days.

Question 21

How do Vysis Aneuvysion probes work?

Answer 21

There is one single microscope slide but two distinct areas with uncultured amniotic fluid. There is one probe for each area. 30 cells are scored by 2 blinded analysts.

Question 22

What is microarray methodoloy?

Answer 22

Examining the whole genome at high resolution using the patients’ DNA rather than chromosomes. Only used for comparison of copy numbers.

Question 23

How is microarray performed?

Answer 23

Equal amount of patient (green) and reference (red) DNA are mixed with COT-1. This is added to an array slide spotted with oligonucleotides and hybridised for 48 hours. The slide is then washed and scanned, the scanned images are put into an analysis software.

Question 24

What do the results of microarrays suggest?

Answer 24

If it’s yellow, then it’s normal. If there are not equal amounts of red and green, then it’s abnormal. More red means deletion of test DNA and more green means duplication of test DNA.

Question 25

What are the advantages of aCGH?

Answer 25

Examines the whole genome at high resolution, targetted against known conditions, 1 array is equivalent to thousands of FISH and can be automated, there is detailed information on genes in deletion/duplication regions and better phenotype/genotype correlation.

Question 26

What are the disadvantage of aCGH?

Answer 26

More expensive (although perhaps cheaper in the long run), doesn’t detect balanced rearrangements, copy number variation (what is pathogenic?) and mosaicism may be missed.

Question 27

What are the possible results from aCGH?

Answer 27

Normal, clearly abnormal or uncertain.

Question 28

How can microarrays be used instead of karyotyping in prenatal testing?

Answer 28

Non invasive prenatal testing - cell free foetal DNA in maternal plasma used at 9 weeks gestation.

Question 29

What are the benefits and problems with using microarrays in prenatal testing?

Answer 29

Benefits - prevents need for invasive testing, removes risk of miscarriage, earlier in gestation.
Problems - technically challenging as DNA quality deteriorates quickly so special tubes are used to stabilise samples.

Question 30

What future developments could come from sequencing technologies?

Answer 30

Next generation sequencing, whole genome sequencing and massively parallel sequencing.