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MedGen (Personal) > FISH > Flashcards

FISH Flashcards

1
Q

Steps of FISH

A

denature, hybridize, analyze

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2
Q

Steps of FISH

A

denature, hybridize, analyze

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3
Q

Types of repetitive DNA probes

A

beta satellite, alpha satellite, classical satellite, telomere

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4
Q

Types of unique DNA probes

A

microdeletion

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5
Q

Types of paint probes

A

whole chromosome, arm specific, band specific

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6
Q

Paint (whole chromosome paints, WCPs)

A

hybridize to unique sequences which cover the length of an entire chromosome
useful for studying: marker chromosomes, translocations, and aneuploidy in metaphase
Not useful for interphase

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7
Q

Alpha satellite probes - centromere

A

hybridize to alpha-satellite DNA
give large, bright signal
useful for detecting aneuploidy

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8
Q

Telomere probes

A

hybridize to DNA tandem repeat TTAGGG sequences at terminal ends of chromosomes
non-specific probes target this sequence
Subtelomeric probes bind to unique DNA sequences immediately proximal to telomere repeats

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9
Q

Locus specific probes

A

identify specific gene or locus on a chromosome and hybridize to the target DNA at that location
Unique sequences in the genome

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10
Q

Direct preparations

A

uncultured cells from blood or amniotic fluid sample
smears made from blood, buccal cells, bone marrow

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11
Q

Paraffin embedded tissue sections

A

tumors
products of conception samples

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12
Q

Chromosomes that use centromere probes in prenatal samples

A

x, y, 18

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13
Q

Chromosomes that use probes on large arm to FISH prenatal samples

A

13, 21

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14
Q

Structural abnormalities may produce a _________ or _________ during prenatal interphase FISH

A

false abnormal or false normal

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15
Q

Percent of aneuploidies in interphase fish prenatally that are normal

A

0-10%

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16
Q

Percent of aneuploidies in interphase fish prenatally that are mosaicism/abnormal inconclusive

A

11-60%

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17
Q

Percent of aneuploidies in interphase fish prenatally that are abnormal

A

> 60%

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18
Q

Limitations of prenatal interphase FISH

A

only common aneuploidies
20-35% of visible chromosome abnormalities will go undetected (mostly numerical and structural abnormalities of untested chromosomes or chromosomal regions)
Need karyotyping and metaphase FISH to verify abnormals
It is a screening

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19
Q

Microdeletion syndromes

A

small recurring interstitial deletions each of which is associated with specific phenotype

20
Q

DiGeorge/Velocardiofacial Syndrome features

A

Facial (prominent nose with squared nasal root, small eyes, small ears with abnormal folding)
Abnormal palate (70%) (overt/submucous cleft)
Congenital heart disease (75%) (conotruncal malformations)
Learning problems (70-90%)
Hypocalcemia (40-50%)
Immune deficiencies
Psychiatric disorders

21
Q

Percent of 22q deletions that are de novo and recurrence risk

A

90%
<1%
risk for germline mosaicism unknown

22
Q

Percent of 22q deletions that are inherited and recurrence risk

A

10%
50%

23
Q

Limitations of FISH for 22q

A

can only detect very large deletions
some DiGeorge microdeletions are outside of the critical region

24
Q

Complementary duplications and deletions occur due to

A

NAHR (nonallelic homologous recombination)

25
Q

Counseling points for deletions

A

Most deletions are de novo
Some occur secondary to unequal segregation of balanced parental translocation
If the deletion is small and/or associated with mild phenotype, parent may also carry it
Need parental karyotyping and/or FISH for clarity on mechanism of deletion

26
Q

Counseling for duplications

A

Most duplications are de novo
If duplication is small and/or associated with mild phenotype, one of the parents may carry it (more common for duplications than deletions)
Some occur secondary to unequal segregation of balanced parental rearrangement

27
Q

FISH can be used to

A

Confirm CNV
Provide information about mechanism responsible for gain and/or loss

28
Q

FISH is performed before signing out CMA when

A

family history, G-band and/or CMA findings suggest presence of something other than likely pure interstitial deletion or tandem duplication
mosaicism is identified

29
Q

Break apart FISH probes

A

To see if the locus are separated (if together, will show up yellow)
Will have one yellow signal, one small green, and one small red
Useful for rearrangements where there are multiple known partners

30
Q

Dual FISH probe

A

If moved, will have two yellow signals, one large red, and one large green

31
Q

Extra signal, single fusion FISH probe

A

If abnormal, will have one large green, one large red, one yellow, and one small extra red or green

32
Q

Most common mechanism for genome rearrangements

A

NAHR (non-allelic homologous recombination)

33
Q

NAHR is mediated by

A

LCRs (low copy repeat sequences)

34
Q

LCRs

A

aka - segmental duplications/duplicons/paralogous duplications
at least 1 kb in length
share >90% sequency identity
Usually occur twice or a few times within genome
preferential to pericentromeric and subtelomeric regions

35
Q

LCRs rearrangement frequency positively correlated to

A

increased length, close proximity, and high sequence identity between the segmental duplications mediating the rearrangement

36
Q

Tandem (direct) LCRs mediate

A

duplications and deletions (translocations)

37
Q

Inverted LCRs mediate

A

inversions (isochromosomes)

38
Q

Palindromic sequences

A

inverted sequences that are complementary to each other and capable of forming secondary structures

39
Q

AT-rich palindromes are present

A

within the breakpoint regions of both chromosomes

40
Q

Palindromic sequences mediate translocation through

A

NHEJ (non-homologous end joining)

41
Q

Replication Fork Stalling and Template Switching (FoSTeS)

A

replication fork invades various regions of same and different replication forks

42
Q

With a break-apart probe design for FISH, which of the following signals would you be most likely to see under a microscope if a balanced translocation involving this region has occurred

A

A yellow signal, a red signal, and a green signal

43
Q

Hereditary neuropathy with liability to pressure palsy (HNLPP) causes numbness, tingling, pain, and muscle weakness in the limbs. It is caused by a deletion on 17p12 in an area flanked by low copy repeats (Timmerman & Lupski, 2006). Based on this information, SELECT ALL of the following that are TRUE

A

Non-allelic homologous recombination is a mechanism leading to this deletion
Charcot-Marie Tooth disease type 1A is the corresponding duplication in the 17p12
region

44
Q

A patient presents with clinical features of conotruncal malformation, hypocalcemia, and microphthalmia consistent with DiGeorge syndrome. However, FISH studies return a
negative result. Which of the following reflects appropriate guidance for next steps

A

FISH testing may not be accurate for DiGeorge syndrome, these results should be confirmed using a microarray

45
Q

Pelizaeus-Merzbacher disease is characterized by complex duplications of the PLP1
gene involving three duplications flanking smaller segments with no copy number
change. Which of the following methods of genetic rearrangement is most likely to
explain this phenomenon

A

Replication Fork Stalling and Template Switching (FoSTeS)

MedGen (Personal) (12 decks)

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