Cytogenetics

Question 1

numerical abnormalities

Answer 1

• change number of chromosomes

Question 2

structural abnormalities

Answer 2

• change structure of chromosomes

Question 3

robertsonian translocation

Answer 3

• fuse two small chromosomes into a very large chromosome

Question 4

historically

Answer 4

• chromosome rearrangements have involved large regions of genome because they have been detected by karyotyping

Question 5

limits of karyotyping

Answer 5

• requires viable cells

- low resolution limited to 3-5 MB or greater

Question 6

karyotyping used for

Answer 6

• permits evaluation of entire genome

- used to detect gains and losses of entire chromosomes and fairly large chromosomal regions

Question 7

why do chromosome abnormalities result in disease

Answer 7

• cause an increase and/or decrease in gene products

- alter the gene product itself by producing a fusion protein with altered function

Question 8

what phenotypes are typically associated with chromosome abnormalities

Answer 8

• cancer
• abnormal growth and development in children or pregnancies
• early death
• clinically normal individuals with a personal or a family history of clinical abnormal offspring, miscarriages, or infertility

Question 9

FISH

Answer 9

• high resolution - usually 100 KB
• requires clinically directed search
• very specific search
• interphase FISH can be performed on nonviable cells

Question 10

FISH technique

Answer 10

• chromosome prep and denaturation
• labelled probe and denaturation
• in situ hybridization
• detection

Question 11

micro deletion and micro duplicating syndromes characterized by

Answer 11

• by small, recurring interstitial deletions or duplications

- each associated with a well described phenotype

Question 12

DiGeorge syndrome

Answer 12

• facial features - prominent nose w/ squared nasal root, small yes, small ears with abnormal folding
• abnormal palate
• heart abnormalities
• learning disabilities
• hypocalcemia
• immune deficiency
• psychiatric disorders

Question 13

DiGeorge syndrome FISH

Answer 13

• green control maps just fine
• red probe which normally maps to DiGeorge critical region does not hybridize
• that region is deleted on chromosome 22

Question 14

microarray tech allows us to

Answer 14

• survey entire genome for gains and losses
• very high resolution
• can use nonviable cells
• allow us to identify consanguinity and probably uniparental disomy

Question 15

how affymextrix cytoscan array works

Answer 15

• patient DNA is labelled with fluorochrome probe and allowed to hybridize to a chip containing arrayed DNA of interest
• intensity of hybridization signal at each locus is compared to the in silico data obtained from 270 normal controls to assess copy number
• data for each locus plotted as a log 2 ratio of 0

Question 16

when above the 0 log

Answer 16

• duplication or amplification

Question 17

when below 0 log

Answer 17

• deletion

Question 18

importance of follow up by FISH due to changes identified in microarray

Answer 18

• provides info about mechanisms responsible for the gain/loss identified by microarray
• less expensive test to do follow up parental testing

Question 19

best test to determine if a parent carries a balanced translocation?

Answer 19

• metaphase FISH

Question 20

uniparental disomy

Answer 20

• the inheritance of both copies of an allele from a single parent
• detected by SNP microarray

Question 21

consanguinity

Answer 21

• mating between related individuals

- detected by SNP microarray

Question 22

importance of consanguinity

Answer 22

• related individuals more likely than unrelated individuals to carry same mutant recessive genes
• offspring more likely to manifest a recessive disorder

Question 23

hallmarks of consanguinity

Answer 23

• long stretches of homozygosity scattered throughout genome in offspring

Question 24

greater level of consanguinity

Answer 24

• the greater number and length of homozygous stretches

Question 25

what tier test is the chromosomal microarray

Answer 25

• first tier

Question 26

microarray exceptions that it can’t recognize

Answer 26

• balanced rearrangements

- low level mosaicism

Question 27

How does DNA appear in interphase?

Answer 27

The DNA in interphase is a “tangled mess” of chromatin in the nucleus of cells.

Question 28

Prep for chromosome analysis (cytogenetics)

Answer 28

1. Growing cells in culture
2. Exposing to a “mitotic spindle poison” (colchicine) that halts cells in prometaphase/metaphase
3. Exposing to a hypotonic solution to expand nucleus/spread things out
4. Staining (for G-banding) or fluorescently labelling to allow for visualization.
5. Viewing.

Question 29

What are some identifiable chromosomal anomalies?

Answer 29

1. Whole chromosome gain/loss (+/- the chrom #)
2. Insertions or deletions (add or del)
3. Translocations (t or der for “derivative”)
4. Inversions (inv)
5. Abnormal chromosome structures (e.g. r for rings)

Question 30

Benefits of FISH

Answer 30

• quicker and less expensive than full karyotype analysis
• great for common deletion or aneuploidy syndromes
• useful for confirmation of other studies or familial testing