clinical cytogenetics: microdeletions and genomic imbalance

Question 1

In general how do syndromes that cause genomic imbalance work?

Answer 1

a disease phenotype associated with deletion of multiple, adjacent genes in critical region that is caused by recombination between misaligned repeats and other related mechanisms

Question 2

What are the types of abnormalities of syndromes caused by genomic imbalance?

Answer 2

• microdeletions (small partial monosomy)
• microduplications (small partial trisomy)
• subtelomeric rearrangements (terminal rearrangements; mostly microdeletions at chromosome ends)

Question 3

Define microdeletion

Answer 3

chromosome deletions (partial monosomies) that may be too small for reliable detection by routine methods

Question 4

Why are microdeletion syndromes unable to be detected reliably?

Answer 4

they are too small which gives a limited resolution of routine chromosome analysis (banded chromosomes) because interstitial & terminal deletions <5Mb cannot be detected

Question 5

Describe Prader-Willi syndrome wrt type of microdeletion, phenotype characteristics

Answer 5

interstitial deletion encompassing 15q12 in 70% of patients (partial monosomy of critical region

• hypotonia in infancy,
• childhood hyperphagia & obesity
• mental retardation

Imprinting disorder

Question 6

What are Prader-Willi breakpoints?

Answer 6

• common breakpoints BP1, BP2, BP3
• Deletion of critical region
• unequal crossover of low-copy repeats at breakpoints

Question 7

Define normal crossover

Answer 7

perfect alignment of homolgous DNA on non-sister chromatids

Question 8

Describe unequal crossover

Answer 8

crossover in misaligned segments of leads to 2 abnormal products

1. duplication
2. deletion

can be critical if deleted chromosome is lacking the critical region and one copy of LCR remains

Question 9

What are the results of genomic rearrangements caused by illegitimate recombination between low-copy repeats?

Answer 9

Direct repeats => deletion and/or duplication of segment between repeats

Inverted repeats => flipped orientation of segment between repeats

Question 10

What are low-copy repeats? What what can they cause?

Answer 10

they are abundant and dispersed throughout the genome which make up 5-10% of human genome

recombination between misaligned repeats is a common mechanism leading to changes in copy number

• Normal copy number variation (CNV) or benign
• Segmental aneuploidy syndromes

Question 11

Define segmental aneuploidy syndromes

Answer 11

microdeletion syndromes are associated with partial monosomy with deletion of the critical region

Question 12

What are approaches to diagnosis microdeletions?

Answer 12

1. standard karyotype
2. FISH
3. chromosomal microarray analysis or arry comparative genome hybridization (aCGH)

Question 13

When diagnosing what are the 3 main quesitons you must ask yourself?

Answer 13

1. approach to testing => is there a suspected genetic diagnosis, and, if so, how many potential gene targets?
2. use of results => implications for potential test results? (true pos, false neg, result of uncertain significance)
3. Follow up => possible follow up testing (define recurrence risks, other family members)

Question 14

With a deletion of chromosome 22q, or DiGeorge/VCF syndrome, where does it usually come from?

Answer 14

90% of the time it is de novo

10% has the same as one of parent and leads to reproductive risk

this is a phenotypic type that presents with autosomal dominant patters so if a carrier then 50% of time will be passed down

Question 15

williams syndromeit is an interstitial deletion on the long arm of chromosome 7. What type of abnormality is this?

Answer 15

It is a partial monosomy 7q

deletion of the elastin gene

Question 16

What are some of the limitations of FISH analysis?

Answer 16

it only looks for the probe screened for

Question 17

If you wanted to test the entire genome for chromosomal imbalance, how would you accomplsh this?

Answer 17

comparative genomic hybridization by chromosomal microarray

Combines patient DNA and control DNA which is applied to microarray and evaluate relative copy number across genome

Question 18

Describe what a comparative genomic hybridization would read if a microdeletion was detected

Answer 18

partial monosomy with a ratio of patient : control

1 :2

Question 19

Describe how a microduplication will be read in a comparative genomic hybridization

Answer 19

partial trisomy with a ratio of patient : control

3 : 2

Question 20

Describe the process of array CGH (6 steps)

Answer 20

Steps 1-3 => patient and control DNA are labeled with fluorescent dyes and applied to the microarray

Step 4 => patient and control DNA compete to attach, or hybridize to the microarray (hybridization point)

Step 5 => microarray scanner measures fluorescent signal intensity

Step 6 => computer software gathers the data and generates a plot

Question 21

What does CMA provide for follow up testing?

Answer 21

precise information about the amount of genomic material relative to a reference genome

but not the nature of rearrangement

Question 22

What does FISH provide in follow-up testing?

Answer 22

provide information about the type of rearrangement and possible recurrence risks

Question 23

What are the advantages of array CGH?

Answer 23

• detects chromosome imbalances identified by traditional karyotyping in addition to imbalances that karyotyping cannot detect
• simultaneously and rapidly evaluates thousands of regions of the genome
• identifies and further characterizes chromosome imbalances identified by karyotyping

Question 24

What are the limitations of array CGH?

Answer 24

cannot detect the following

1. balanced chromosome rearrangements
2. some polyploidies
3. basepair changes in DNA sequence
4. gains or losses in regions of hte genome not covered in array

A normal array CGH result does not rule out most genetic conditions

**Abnormal array CGH results can have unclear implications **

Question 25

When do you need to test parents for chromosomal abnormalities?

Answer 25

1. parental testing is essential to determine whether the DNA dosage change is new or inherited
2. assists in clarifying whether DNA dosage alteration in the patient is causative o fhte patient’s clinical findings (de novo finding suggests that DNA dosage alteration may be causative)
3. assists in providing recurrence risks to the family
4. assists in identifying other family members at risk

Question 26

What are the advantages and disadvantages of CMA?

Answer 26

advantages

1. very sensitive detection of genomic imbalance
2. genome wide

disadvantages

1. CANNOT DETECT BALANCED REARRANGEMENTS
2. results frequently ambiguous and complex
3. expensive
4. methodology not standardized

Question 27

What is CMA a first tier diagnostic test for?

Answer 27

individuals with developmental disabilities or congenital anomalies

1. higher yield than karyotype
2. better detection of duplications than FISH
3. more precise characterization of abnormality

interpretation is complicated by normal variations in copy number