20.05.15 Marker chromosome at PND - strategy and management

Question 1

What is a marker chromosome

Answer 1

• Extra chromosomal piece found during karyotyping that are usually derived from a structural rearrangement.
• Present in addition to normal chromosome complement
• Also called supernumerary marker chromosome (SMC)

Question 2

Criteria for a marker chromosome

Answer 2

• Structurally abnormal, smaller or equal to the size of chromosome 20 on the same metaphase spreads.
• Cannot be identified/characterised by conventional banding cytogenetics.

Question 3

Review of marker chromosome

Answer 3

• Found in individuals with normal and abnormal clinical phenotypes.
• Effect on phenotypes depends on: size, gene content, level of mosaicism, eu/heterochromatic, UPD.
• Result in copy number gain of affected genomic sequence

Question 4

Which chromosome are marker chromosomes most frequently derived

Answer 4

Chromosome 15 (30-50%)

Question 5

What percentage of marker chromosomes are inherited

Answer 5

30%

Question 6

How many syndromes are associated with marker chromosomes

Answer 6

• 8

- e.g. Cat eye syndrome, Emanuel syndrome

Question 7

Which 4 groups of patients are marker chromosomes generally identified

Answer 7

1. Prenatally (with and without abnormal scan)
2. Adults with fertility issues
3. Children/adults with unexplained developmental delay or dysmorphism
4. Incidental findings when cytogenetic analysis is performed for other reasons.

Question 8

Incidence of marker chromosomes in live births

Answer 8

0.04%

Question 9

Incidence of marker chromosomes in intellectual disability

Answer 9

0.28%

Question 10

Incidence of marker chromosomes in infertility

Answer 10

0.125%

Question 11

Problem with best practice guidelines for investigating marker chromosomes in prenatal setting

Answer 11

• Published in 2009 and is focused on marker chromosomes found by prenatal karyotyping
• Doesn’t reflect current practices which are testing by arrayCGH as a front line test for samples with abnormal scans

Question 12

Reasons to characterise a marker chromosome

Answer 12

• Determine gene content.

- Allows better understanding of phenotypic consequence and recurrence

Question 13

Methods of characterising a marker chromosome

Answer 13

-Banding, FISH, array CGH to identify chromosomal origin, breakpoints, gene content.

Question 14

2 reasons why array isn’t as good at detecting marker chromosomes compared to banding cytogenetics and FISH

Answer 14

• array would miss low level mosaicism (<20%)

- Array would miss marker chromosomes that contain only heterochromatin

Question 15

What considerations should be made regarding characterisation of a marker chromosome

Answer 15

• Is it de novo or inherited, could UPD be involved (if derived from an imprinted chromosome)
• What is the chromosomal origin, size and gene content
• Is euchromatic material involved
• Is there mosaicism

Question 16

Pros and cons of using cytogenetic banding to investigate a marker chromosome

Answer 16

• Pro: can provide information regarding structure of marker, may reveal mosaicism
• Cons: limited resolution (analysis of small markers is difficult), limited power to identify origin of marker
• C banding can be used to establish absence/presence of heterochromatin (C+ve) or euchromatin (C-ve). If mainly heterochromatin then less risk as little active gene content.
• Silver staining: identifies NORs (nucleolar organisation regions). Distributed across short arms of 5 acrocentric chromosomes (13, 14, 15, 21, 22)

Question 17

Pros and cons of using FISH to investigate a marker chromosome

Answer 17

• Pros: can determine chromosome origin, e.g. X chromosome (markers in 7-16% of Turner syndrome cases), chr15 (56-60% of markers)
• Cons: limited accuracy and resolution, costly and inefficiency to do sequential testing.

Question 18

What two types of chromosome 15-derived supernumerary marker chromosomes (SMCs) are there

Answer 18

1. Small sSMC(15)s: without euchromatic material. Do NOT contain Prader-Willi/Angelman critical region. Usually no phenotype
2. Large SMC(15)s: acrocentric chromosomes containing copies of PWS critical region, so associated with abnormal phenotypes.

Question 19

If origin of marker not determined, should cell cultures be kept

Answer 19

Yes, you can keep for FISH or DNA extraction (array and UPD studies)

Question 20

Benefit to using array over FISH

Answer 20

• FISH can only confirm presence of regions covered by probes, unlike array.
• arrayCGH can detect chromosome imbalance
• Array can detect complex markers, where material is derived from multiple chromosomes.
• Limitations of array: may miss mosaics, won’t detect heterochromatic material.

Question 21

Do ring marker chromosomes have higher or lower risk than non-ring marker

Answer 21

Higher risk, due to instability at meiosis, may manifest features of ring syndrome.