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CTGN Finals > FISH > Flashcards

FISH Flashcards

1
Q

FISH uses ___ light

A

excitation

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2
Q

A cytogenetic technique that uses fluorescent probes that bind specifically to a part of chromosomes complimentary to its sequence

A

FISH

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3
Q

Small strips of single stranded DNA complimentary to the sites we want to examine

A

Probes

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4
Q

Probes are ___ (natural/artificial) DNA

A

artificial

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5
Q

Target chromosomes are ___ (natural/artificial) DNA

A

natural

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6
Q

Useful in detecting and mapping the presence or absence of particular DNA sequence within chromosomes

A

FISH

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7
Q

Number of kb used in FISH

A

200-400

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8
Q

Applied to provide specific localization of genes on chromosomes

A

FISH

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9
Q

FISH is also used for the rapid diagnosis of ___ and ___ which is acquired using specific probes

A

trisomies
microdeletions

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10
Q

FISH is ___ (more/less) cost effective than PCR

A

more

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11
Q

FISH has ___ (short/long) turn around time

A

short

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12
Q

The basic requirement for FISH is for the DNA to be ___/___/___

A

undenatured
preserved
intact

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13
Q

The target DNA is also called as the ___

A

template

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14
Q

To separate DNA strands and allow probe access to target DNA

A

Denature

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15
Q

Binding the probe to target DNA

A

Hybridize

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16
Q

Specimens used for metaphase cell FISH

A

Blood
Bone Marrow
Skin Fibroblast
Chorionic villi
Amniocytes
Tumors

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17
Q

Specimens used for interphase FISH

Direct preparation

A

Uncultured cells from blood, bone marrow, cytospins

Smears made from blood, buccal cells, bone marrow

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18
Q

Specimens used for interphase FISH

Indirect preparation (Paraffin Embedded Tissue Sections)

A

Tumors
Products of conceptions

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19
Q

FFPE means ___

A

Formalin fixed paraffin embedded tissue

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20
Q

Metaphase/Interphase FISH:

Gold standard and routinely done

A

Metaphase

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21
Q

Metaphase/Interphase FISH:

Done on cultured cells

A

Metaphase

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22
Q

Metaphase/Interphase FISH:

Allows direct visualization of chromosomes and exact position of signals

A

Metaphase

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23
Q

Metaphase/Interphase FISH:

Useful in the detection of structural changes in the genokme

A

Metaphase

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24
Q

Metaphase/Interphase FISH:

More rigorous procedure

A

Metaphase

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25
Q

Metaphase/Interphase FISH:

Used for copy number changes

A

Metaphase

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26
Q

Metaphase/Interphase FISH:

Can be modified for de novo detection

A

Metaphase

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27
Q

Metaphase/Interphase FISH:

May also be done on uncultured specimens

A

Interphase

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28
Q

Metaphase/Interphase FISH:

Advantageous in the rapid screening of many nuclei for prenatal diagnosis and newborn studies

A

Interphase

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29
Q

Metaphase/Interphase FISH:

Also beneficial in the study of samples with a low mitotic index such as most solid tumors

A

Interphase

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30
Q

Metaphase/Interphase FISH:

Major disadvantage is the inability to detect unknown structural chromosomal changes

A

Interphase

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31
Q

Metaphase/Interphase FISH:

Same day turn around time

A

Interphase

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32
Q

Metaphase/Interphase FISH:

Translocation can be detected

A

Interphase

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33
Q

Metaphase/Interphase FISH:

Used for screening

A

Interphase

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34
Q

Sample for interphase fish:

For ploidy analysis during prenatal studies

A

Amniocytes

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35
Q

Sample for interphase fish:

For ploidy analysis in newborns

A

Peripheral blood smears

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36
Q

Sample for interphase fish:

Translocation or copy number analysis in cancer studies

A

Bone marrow aspirate smear or direct harvest

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37
Q

Complementary sequences of target nucleic acids tagged or labeled with fluorophores

A

FISH probes

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38
Q

FISH probes can be (3):

A

DNA
RNA
Nucleic acid analogs

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39
Q

FISH probes size ranges from __ to __ base pairs

A

20-1000

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40
Q

Direct/Indirect labeling:

Fluorophores are directly attached to the probe

A

Direct

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41
Q

Direct/Indirect labeling:

Less sensitive

A

Direct

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42
Q

Direct/Indirect labeling:

FITC, rhodamine, cyanines

43
Q

Direct/Indirect labeling:

Chemical conjugation of the nucleic acid with a nonfluorescent molecule that can bind fluorescent material after hybridization

44
Q

Direct/Indirect labeling:

Biotin & digoxigenin

45
Q

Partner molecule of biotin

46
Q

A process of sticking DNA back to its original double stranded structure which requires the lowering of temperature

A

Reannealing

47
Q

This is usually washed off that can cause background fluorescence/”noise” and lessens sensitivity

A

Excess unbound probe

48
Q

Allows the visualization of nuclear boundaries and morphology

A

counterstain

49
Q

Examples of counterstain

A

Propidium iodide
DAPI

50
Q

T/F: Repetitive target does not brighten the fluorescence because they are often small

A

F (may brighten fluorescence even with small prove because of repetitive sequence)

51
Q

In denaturing the DNA, ___ and ___ are used

A

heat
denaturing chemical (formamide/salt solution)

52
Q

Most commonly used FISH probes (3)

A

Whole chromosome paints (WCPs)
Chromosome enumeration probes (CEPs)
Locus-specific identifiers (LSIs)

53
Q

Most commonly used FISH probe:

Hybridize to the unique sequences which cover the length of an entire chromosome or chromosome arm

54
Q

Most commonly used FISH probe:

Useful in studying marker chromosomes, translocations, and aneuploidy in metaphase

55
Q

Most commonly used FISH probe:

NOT useful in interphase cells

56
Q

Most commonly used FISH probe:

Collection of smaller probes that bind to the whole length of chromosome

57
Q

Most commonly used FISH probe:

Useful in the examination of chromosomal aberrations

58
Q

Most commonly used FISH probe:

Also known as alpha-satellite probes as they bind to highly repetitive DNA

59
Q

Most commonly used FISH probe:

Applicable for both metaphase & interphase FISH

60
Q

Most commonly used FISH probe:

Frequently hybridized to centromere regions

61
Q

Most commonly used FISH probe:

Most often used as control probes

62
Q

Most commonly used FISH probe:

Most probes give large, bright signal

63
Q

Most commonly used FISH probe:

Useful for detecting aneuploidy

64
Q

Most commonly used FISH probe:

Generated from repetitive sequences found in the middle of each chromosome

A

Alphoid/Centromeric repeat

65
Q

Most commonly used FISH probe:

Used to determine whether an individual has the correct number of chromosomes or if there is aneuploidy in the patient’s genome

A

Alphoid/Centromeric repeat

66
Q

Most commonly used FISH probe:

More gene/region specific

67
Q

Most commonly used FISH probe:

Hybridize to unique sequences in the genome

68
Q

Most commonly used FISH probe:

Probes span the specific region and average 200-300 kb in size

69
Q

Most commonly used FISH probe:

Useful diagnostic tool to detect deletions, duplications, rearrangements, amplifications

70
Q

Most commonly used FISH probe:

Can also be used in fusion-type probe strategies

71
Q

Most commonly used FISH probe:

Binds to a particular regions of a chromosome

72
Q

Most commonly used FISH probe:

Used when only a small portion of a gene is isolated and want to determine on which chromosome the gene is located, or how many copies of a gene exist within a particular genome

73
Q

Specialize and evolving technologies:

A technique that allows the investigator to view a karyotype so that each chromosome is “painted” with a different color

A

Multiplex FISH (M-FISH)

74
Q

Specialize and evolving technologies:

Ratio-labeled probes are used to create a distinct computer-generated false color for each chromosome

A

Multiplex FISH (M-FISH)

75
Q

Specialize and evolving technologies:

Useful for complex rearrangements, such as those seen in neoplastic disorders and solid tumors

A

Multiplex FISH (M-FISH)

76
Q

Specialize and evolving technologies:

Uses chromosome-specific mixtures of partial chromosome paints that are labeled with various fluorochromes

A

Multicolor Banding (mBAND) Analysis

77
Q

Specialize and evolving technologies:

A computer program analyzes metaphase chromosome data and procedures a pseudocolored banded karyotype with an estimated resolution of 550 bands, regardless of chromosome length

A

Multicolor Banding (mBAND) Analysis

78
Q

Specialize and evolving technologies:

Advantageous for the determination of breakpoints and the analysis of intrachromomal rearrangements and can be particularly useful in preparations with shorter chromosomes

A

Multicolor Banding (mBAND) Analysis

79
Q

Single/Dual color FISH probe:

Designed to cover a gene of interest

80
Q

Single/Dual color FISH probe:

Allows simultaneous detection of numerical abnormalities of two to three regions ins one FISH assay

81
Q

Probe strategies:

Probes span specific regions of interest, typically regions with recurring breakpoints

A

Dual fusion FISH probe strategies

82
Q

Probe strategies:

Used to identify specific chromosome rearrangements, typically involving 2 chromosomes

A

Dual fusion FISH probe strategies

83
Q

Probe strategies:

Probes will flank the specific region of interest

A

Break apart (BAP) FISH probe strategies

84
Q

Probe strategies:

Used to detect chromosomal rearrangements

A

Break apart (BAP) FISH probe strategies

85
Q

Probe strategies:

Useful in FFPE sample

A

Break apart (BAP) FISH probe strategies

86
Q

Probe strategies:

Useful for rearrangements where there are multiple known partners

A

Break apart (BAP) FISH probe strategies

87
Q

Probe strategies:

Applicable for knowing the source of translocation material

A

Break apart (BAP) FISH probe strategies

88
Q

Types of FISH probes:

Specific to the subtelomere region of chromosome

A

Subtelomere

89
Q

Types of FISH probes:

Useful in the detection of subtelomere deletions and rearrangements

A

Subtelomere

90
Q

Types of FISH probes:

Comprise of different combinations of fluorophore-labeled probes specific for chromosomes 13, 18, 21, X, and/or Y

91
Q

T/F:

Cell scoring in FISH: If there are two nuclei with one signal each or one twisted nuclei, do not count

92
Q

T/F:

Cell scoring in FISH: If there is one diffused and one clustered signal, do not count

A

F (must be counted as two signals)

93
Q

T/F:

Cell scoring in FISH: If there is one normal and one split signal, count as two signals

94
Q

Specialized and evolving technologies:

A technique that is almost entirely used for research

A

Fiber FISH

95
Q

Specialized and evolving technologies:

Allows the chromosomes to be stretched out and elongated

A

Fiber FISH

96
Q

Specialized and evolving technologies:

Provides a much higher spatial resolution and allows for correct orientation and placement of probes and for precise mapping of proves

A

Fiber FISH

97
Q

Specialized and evolving technologies:

Essentially PCR on a slide

A

Primed In Situ Labeling (PRINS)

98
Q

Specialized and evolving technologies:

Primers of interest are hybridized on a slide and then subjected to cycles of denaturation, reannealing, and elongation that are used to incorporate labeled nucleotides

A

Primed In Situ Labeling (PRINS)

99
Q

Specialized and evolving technologies:

Can differentiate hybridizaton with the alpha satellite sequences for chromosomes 13 and 21, something that cannot be done with traditional FISH

A

Primed In Situ Labeling (PRINS)

100
Q

Specialized and evolving technologies:

Used to identify material of unknown origin

A

Reverse FISH

101
Q

Specialized and evolving technologies:

A technique that uses DNA from the cells of interest, rather than using a standard karyotype, for chromosomal analysis

102
Q

Specialized and evolving technologies:

Can be very useful, especially in some cancers when only DNA is available rather than any growing cells

103
Q

Specialized and evolving technologies:

Used successfully for clinical analysis, particularly with cases that have a low (or no) mitotic index

104
Q

Specialized and evolving technologies:

Not useful for detecting balanced rearrangements

CTGN Finals (6 decks)

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