Lecture 5: Diagnostic Technologies

Question 1

What are the three basic types of FISH?

Answer 1

Repeat sequences
Single copy DNA - subtelomere FISH
Chromosome painting - multi-color

Question 2

Where are repeated sequence FISH probes isolated from?

Answer 2

temlomere or centromere

Question 3

Where are single copy FISH probes isolated from?

Answer 3

unique sequence
cloned DNA of a disease-causing gene, or fragment of DNA of known location associated with a particular disease-causing gene

Question 4

Where are subtelomere FISH probes isolated from?

Answer 4

distal ends of chromosomes, proximal to actual telomere regions

Question 5

Why is subtelomere FISH very useful?

Answer 5

subtelomere regions are gene-rich

can see cryptic (very small) deletions and rearrangements which cannot be seen by standard karyotype analysis

Question 6

Which FISH technique is useful for seeing cryptic (very small) deletions and rearrangements which cannot be seen by standard karyotype analysis?

Answer 6

Subtelomere FISH

Question 7

Which FISH technique is used to detect the source extra material of unknown origin in a chromosome, complex rearrangements, or marker chromosomes?

Answer 7

Chromosome painting

Question 8

Why can’t some deletions be seen by karyotype analysis? what technique should be used instead?

Answer 8

too small

subtelomere FISH

Question 9

What size are typical FISH probes?

Answer 9

10Kb

Question 10

What size FISH probe is necessary to detect velocardiofacial syndrome (VCFS)? What is the problem with this size?

Answer 10

3Mb - too big; probe is only 10Kb

Question 11

What are regions in the genome with clusters of closely associate genes (all related to a clinical outcome) whose functions are usually unrelated?

Answer 11

Continuous Gene Syndromes

Question 12

What is FISH used to detect within Continuous Gene Syndromes?

Answer 12

microdeletions or microduplications

Question 13

What is the lower limit of abnormalities detected by karyotype analysis?

Answer 13

3Mb

Question 14

How large are microdeletions and microduplications?

Answer 14

0.5-6Mb

Question 15

How large is the common delta F508 mutation in cystic fibrosis?

Answer 15

3bp

Question 16

What are 6 Continuous Gene Syndromes?

Answer 16

WAGR - 11p
Miller-Dieker/Lissencephaly - 17p
Williams syndrome - 7q
Velocardialfacial syndrome - 22q
1p-syndrome
Prader Willi/Andelman Syndrome

Question 17

What causes coarse skin and hair, lack of flexibility in the aorta, and supravalvular aortic stenosis associated with Williams syndrome?

Answer 17

Deletion on elastin gene (ELN) on xs 7

Question 18

What causes autistic-like behavioral problems associated with Williams syndrome?

Answer 18

deletion on a gene adjacent to elastin gene

Question 19

How is Williams syndrome classified?

Answer 19

Continuous gene syndrome - deletion of several adjacent genes
connective tissue disease (deletion of elastin gene)

Question 20

What are the 1st and 2nd most common syndromes known in humans?

Answer 20

Down syndrome
Velocardiofacial syndrome (VCFS)

Question 21

Where is the deletion in velocardiofacial syndrome? How is it detected?

Answer 21

xs 22

FISH

Question 22

Difficulty feeding, cardiac defects, facial dysmorphologies are all seen infants, and learning disabilities, short stature, and conductive hearing loss as an individual ages are seen in what condition? How is this syndrome characterized?

Answer 22

Velocardiofacial syndrome

Continuous gene syndrome

Question 23

How does the deletion associated with velocardiofacial syndrome arise?

Answer 23

misalignment during meiotic crossing over

Question 24

Why do 10-15% of patients with velocardiofacial syndrome have a more severe condition than their parents with the same deletion?

Answer 24

Parent’s normal chromosome 22 can compensate

Affected child’s second chromosome 22 doesn’t have the alleles which can compensate

Question 25

In a genetic microarray, what does a green signal mean?

Answer 25

excess of reference DNA

–> deletion in test DNA

Question 26

In a genetic microarray, what does a red signal mean?

Answer 26

excess test DNA

–> duplication in test DNA

Question 27

polymorphisms, mutations, and copy number variations (CNVs) can all be detected by _______

Answer 27

gene arrays

Question 28

Will gene arrays detect balanced rearrangements?

Answer 28

no - total amount of DNA is conserved, no change in relative amounts detected

Question 29

What does a red signal in an expression array mean?

Answer 29

increased expression

Question 30

What does a green signal in an expression array mean?

Answer 30

decreased expression

Question 31

What does a peak mean in a chromosome microarray?

Answer 31

gain of segments - duplication

Question 32

What does a valley mean in a chromosome microarray?

Answer 32

loss of segments - deletion

Question 33

What do chromosome microarrays view?

Answer 33

copy number variants

Question 34

What is the SOX5 gene involved in?

Answer 34

development - mutation can cause dysmorphic features

Question 35

What kind of next gen sequencing is used for genetic disorders, oncology, infectious disease, reproductive health, population genetics, forensics, and agriculture?

Answer 35

target sequencing

Question 36

Next gen sequencing has been used to develop panels. What information do these provide?

Answer 36

particular genes or regions of genome known to be associated with particular classes of disease

Question 37

Which type of genetic technology is used for relatively large (>3Mb) numerical and structural abnormalities, and is genome wide?

Answer 37

karyotype analysis

Question 38

Which type of genetic technology is used for well-defined, specific, very small (1-300bp) mutations, with targeted testing?

Answer 38

molecular diagnostics

Question 39

Which type of genetic technology is used for well-defined, specific, medium sized (10Kb-10Mb) mutations, with targeted testing?

Answer 39

FISH

Question 40

Which type of genetic technology is used for generalized genome-wide screening for small (1Kb) to large mutations, and will not detect balanced rearrangements?

Answer 40

microarray

Question 41

Which type of genetic technology is used for high resolution for targeted regions to detect mutations to a single base level?

Answer 41

DNA sequencing