Microdeletions and Genomic Imbalance

Question 1

Where are the genes associated with a disease phenotype found?

Answer 1

critical region

Question 2

What happens to the critical region to cause a disease phenotype

Answer 2

deletion of multiple adjacent genes

Question 3

What causes deletion of genes in the critical region?

Answer 3

recombination between misaligned repeats

Question 4

What is caused by abnormalities of 2 or more genes that are located next to each other on a chromosome

Answer 4

contiguous gene syndrome (i.e. Prader-Willi Syndrome (interstitial deletion)

Question 5

What is the inappropriate dosage of critical genes within a discrete genomic segment?

Answer 5

segmental aneuploidy syndrome

Question 6

What are microdeletions?

Answer 6

small partial monosomy

Question 7

What are microduplications?

Answer 7

small partial trisomy

Question 8

What are subtelomeric rearrangements?

Answer 8

terminal rearrangements and mostly microdeletions at chromosome ends

Question 9

What are chromosome deletions (partial monosomies) that may be too small for detection by routine methods (light microscopy) ?

Answer 9

microdeletions

Question 10

Interstitial and terminal deletions ____ Mb cannot be detected reliably.

Answer 10

less than 5 Mb

Question 11

Almost all patients with a microdeletion syndroms exhibit ______ plus syndrome specific anomalies.

Answer 11

developmental/intellectual disability

Question 12

What causes Prader-Willi syndrome?

Answer 12

interstitial deletion of q12 on chromosome 15

= imprinting disorder (covered in later lecture)

Question 13

What are the symptoms of Prader-Willi?

Answer 13

• hypotonia (low muscle tone) in infancy
• childhood hyperphagia (obesity)
• metal retardation

Question 14

What defines the breakpoints on a chromosome that result in the loss of the critical region?

Answer 14

presence of low copy repeats that flank the critical region

Question 15

What occurs at these breakpoints?

Answer 15

unequal crossing over of low copy repeats (due to misalignement of low copy repeats on chromosomes)

Question 16

Crossover in misaligned segments leads to 2 abnormal products…

Answer 16

duplication and deletion

Question 17

When in the cll cycle does this unequal crossing over occur?

Answer 17

meiotic pairing of chromosomes (metaphase)

Question 18

____ repeats cause a gene segment to have a flipped orientation between repeats.

Answer 18

inverted

Question 19

_____ repeats cause a gene deletion/duplication of the segment between the repeats

Answer 19

direct

Question 20

T or F: genomic rearrangement is caused by illegitimate recombination between low copy repeats

Answer 20

true

Question 21

T or F: low copy repeats are not abundantly distributed throughout the genome.

Answer 21

F: they are abundant (5-10% of genome)

Question 22

What 2 changes can recombination between misaligned repeats cause?

Answer 22

• normal copy number variation (CNV)

- segmental aneuploidy syndromes

Question 23

What are the 3 diagnostic tests used to determine genomic imbalance?

Answer 23

1. std karyotype
2. FISH
3. Chromosomal Microarray Analysis (CMA)/Array Comparative Genome Hybridization (aCGH)

Question 24

If you have already identified the disorder and know the gene duplication causing it, what diagnostic test would you perform to confirm your suspicion?

Answer 24

FISH

Question 25

Describe how a FISH work?

Answer 25

add 2 probes to pt DNA

1. ID the chromosome of interest (and works as a control)
2. Test probe that is specific to the deletion you are looking for

if there is only 1 test probe showing up, the Dx is confirmed

Question 26

What genomic imbalance leads to WIllis syndrome?

Answer 26

interstitial deletion of q11 on chromosome 7

Question 27

Describe how a comparative genome hybridization by microarray can Dx a genomic imbalance?

Answer 27

• combine pt DNA with control DNA

- apply to microarray and evaluate ratio of patient:control copy numbers

Question 28

What is the ratio of pt:control copy numbers that indicates a normal/balanced genome?

Answer 28

1:1

Question 29

What is the ratio of pt:control copy numbers that indicates a genome with a microdeletion?

Answer 29

1:2

Question 30

What is the ratio of pt:control copy numbers that indicates a genome with a microduplication?

Answer 30

2:1

Question 31

What are the limitations of CMA/aCGH?

Answer 31

1. it cannot detect balanced chromosome rearrangements
2. it can tell you if there is an imblanance by not the mechanism of the imbalance
3. does not detect some polyploidies, base pair changes in DNA

Question 32

T or F: A balanced genome will result in a normal CMA

Answer 32

true

Question 33

T or F: A normal aCGH can rule out most of the known genetic syndromes

Answer 33

False: many genetic changes are not caused my deletions or duplications of chromosome material

Question 34

T or F: aCGH simultanously and rapidly evaluates thousands of regions of the genome

Answer 34

true

Question 35

Why would you want to perform an aCGH when a std karyotype was sufficient for Dx?

Answer 35

to confirm and further characterize the chromosome imbalance

Question 36

What can you deduce from a FISH assay in which the test probe is identified in 3 places, 2 of which are very close together?

Answer 36

there is an interstitial/microdupication of the tested gene segment (=partial trisomy NOT full)

Question 37

What can you deduce from a FISH assay in which the test probe is identified in 3 places, none of which are very close together?

Answer 37

There is an extra chromosome (if extra control probe present)
OR possibly a supernumerary chromosome if control probe present but produces a small signal

Question 38

Can a CMA identify the gene segment on a chromosome that is duplicated or deleted?

Answer 38

yes; the entire genome is used and ordered so that the exact segment can be identified

Question 39

What is the major adv to CMA over FISH?

Answer 39

If you do not have a specific deletion or duplication as the cause of a pt’s phenotype, you can use the CMA to examine the entire genome for imbalances

Question 40

Which test will provide parents with recurrence risk?

Answer 40

FISH (or std karyotype)

Question 41

Why are parents tested?

Answer 41

to determine if the imbalance is de novo or inherited

-if inherited other family members can be tested for their reproductive risk

Question 42

What is the major disadv to CMA?

Answer 42

it cannot detect balanced rearrangements