20.03.19 Abnormal phenotypes in balanced karyotypes

Question 1

Can arrays detect balanced changes?

Answer 1

No

Question 2

Can karyotyping detect balanced changes?

Answer 2

Yes

Question 3

List 8 reasons why a balanced rearrangement may show an abnormal phenotype

Answer 3

1) Disruption of a gene by breakpoints
2) Cryptic imbalance
3) Position effect
4) Disruption of imprinting
5) UPD
6) Balanced rearrangements involving the X chromosome
7) Mosaicism
8) Co-incidental findings

Question 4

1) Disruption of a gene by breakpoints

Answer 4

• Can cause truncated or no protein/RNA to be produced
• Dominant gene - if its function is disrupted by a breakpoint - usually occurs de novo
• Recessive gene - the non-disrupted gene carries a recessive pathogenic variant and the other copy of the gene is disrupted by a rearrangement breakpoint, resulting in a recessive condition being unmasked
• FISH is normally helpful
• NGS (paired end reads) can map breakpoints
• Also get fusion genes in HODs

Question 5

2) Cryptic imbalance

Answer 5

• 37% of balanced rearrangements by karyotype were found to be unbalanced by array
• Often occur at breakpoints (but can be coincidental at other locations)
• Can be complex (inv, inser, del)
• Dels more common than dups
• Most de novo changes arise on PAT allele - ?spermatogeneis is more susceptible to changes than oogensis?

Question 6

3) Position effect

Answer 6

• Deleterious change in the level of gene expression brought about by a change in the position of the gene relative to its normal chromosomal environment, but not associated with an intragenic pathogenic variant or deletion
• important for dosage sensitive genes
• Some specific DNA elements are required in cis to affect transcription
• Thereby by translocation changing location of gene, it’s gene expression can also be affected

Question 7

Examples of position effects

Answer 7

1) Genes moves away from enhancer = reducing expression
2) Gene moves away from inhibitor/silencer element = inappropriate activation and expression
3) Gene moves closer to enhancer of another gene = inappropriate activation and expression
4) Gene and regulatory elements move close to another gene causing competition for the regulatory element = changes in expression for both genes
5) Position effect variegation (PEV) - silencing of a gene in some cells through its abnormal juxtaposition with heterochromatin via rearrangement or transposition. It is also associated with changes in chromatin conformation

Question 8

4) Disruption of imprinting

Answer 8

• A breakpoint removes a chromosome region which is subject to imprinting away from its imprinting centre (IC)

Question 9

5) UPD

Answer 9

• Robertsonian and reciprocal translocation carriers can have offspring with UPD
• Clinically relevant when chromosome involved has imprinted genes on or when it carriers an AR pathogenic variant
• Both are rare

Question 10

6) Balanced rearrangements involving the X chromosome

Answer 10

• inv(X) - if breakpoint is in the critical region (Xq13-q22 or Xq22-q26) then can cause infertility and gonadal dysfunction
• t(Y;autosome) - carriers usually infertile (but some exceptions)
• t(X;autosome)

Question 11

Translocations involving X and autosome - are males and females both in fertile?

Answer 11

1) males normally infertile
2) Female carriers very variable:
- 75% have random X inactivation but only functionally balanced cells survive - so cells where normal X is inactivated survive to protect the autosomal genes from being inactivated and to maintain normal dosage
- 25% of cases have some functionally disomic cells survive leading to abnormal phenotype

Question 12

Translocations involving X and autosome - what happens is XIC is on the derivative X?

Answer 12

If XIC is on der X and it is inactivated, then autosomal material on der X will also be inactivated and X material on der A will not be inactivated - can lead to abnormal phenotype (or lethal if regions are too large)

Question 13

Translocations involving X and autosome - what happens is XIC is on the derivative autosome?

Answer 13

If XIC is present on der A then part of the autosome can become inactivated and the der X remains active - can get functional disomy for some of the X chromosome and loss of autosome function - can also cause abnormal phenotype

Question 14

7) Mosaicism

Answer 14

• Can be balanced in blood, but mosaic for unbalanced in other tissues (i.e. Pallister-Killian)
• Can occur due to 3:1 segregation at meiosis - results in interchange trisomy (two derivative and one normal chromosome)
• Then get post zygotic loss of normal chromosome leading to mosaicism

Question 15

8) Co-incidental findings

Answer 15

• The balanced rearrangement is a co-incidental finding and the abnormal phenotype is caused by a point mutation in a gene, environmental factors etc

Question 16

What is the most common consequences of a balanced rearrangement?

Answer 16

Recurrent miscarriage or infertility

• Disturbs the process of gamete formation, especially in males
• Due to failing of pairing of homologous regions in the quadrivalent formed at meiosis 1 by a reciprocal translocation
• With robertsonian trans, the heterochromatic regions of the short arms of the acrocentric chromosomes in the trivalent doe not pair at meiosis 1
• Must be careful when interpreting ‘balanced’ translocations in one family, as there are some cases where one familial rearrangement can give rise to multiuple larger and smaller dels/dups

Question 17

Prenatals who carry apparently balanced translocations - what worry is there?

Answer 17

• that there are smaller copy number changes at breakpoint
• could do array to be certain of this
• Large study carried out over 10 years only found 16 children with balanced translocations who had a phenotype
• so risk of this is low but can’t be ruled out