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U9: CGH + CMA Flashcards

1
Q

CGH stands for?

A

Comparative Genomic Hybridization

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2
Q

CGH is primarily used to detect?

A

Copy Number Variants (CNVs)

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3
Q

These refers to alterations of the DNA of a genome that results in the cell having an abnormal number of copies of one or more sections of the DNA.

A

Copy Number Variants (CNVs)

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4
Q

CNVs i_____ or d_______ the number of copies.

A

Increase or decrease

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5
Q

Copy Number Variants (CNVs)

Larger regions have been d____ (fewer than normal number) or d_____ (more than normal number)

A

Deleted, duplicated

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6
Q

Copy Number Variants (CNVs)

Directly affect the p_____

A

phenotype

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7
Q

T/F: CNVs is helpful as phenotyping material that does not express a disease.

A

T

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8
Q

Copy Number Variants (CNVs)

These tests also rely on CNVs.

A

Fingerprinting, Paternity testing

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9
Q

Amplifications or duplications and deletions can contribute to t_____.

A

tumorigenesis

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10
Q

Why do amplifications contribute to tumorigenesis?

A
  • Position effect
  • Duplication (gain of function)
  • Deletion (loss of function)
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11
Q

This is the most common change seen in malignancies?

A

Amplification

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12
Q

Amplification is the most common change seen in?

A

malignancies

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13
Q

This provides an approach to associate an aberration with a disease phenotype and localizing critical genes-Biomarkers.

A

Detection and mapping

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14
Q

CGH provides us with?

A

Early screening for Amplifications or Deletions

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15
Q

T/F: CGH is not a pre-FISH technique.

A

F ; it is a pre-FISH technique

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16
Q

T/F: You can use CGH if you have an idea if there is a deletion or duplication for standalone confirmation (meaning no need for FISH).

A

T

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17
Q

CGH is sensitive enough for?

A

Duplications and deletions

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18
Q

Uses of CGH

Affected by localizing the biomarkers that would tell us the phenotype of this disease

A

Prognosis and therapeutics

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19
Q

Uses of CGH

Examples are HIV, SLE, Mental retardation, developmental delay, seizure disorders, dysmorphic features, multiple congenital anomalies, schizophrenia, autism spectrum disorder

A

Resistance and susceptibility to disease

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20
Q

Uses of CGH

SLE stands for?

A

Systemic Lupus Erythematosus-Autoimmune disease

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21
Q

Uses of CGH

Mental disorders

A

Schizophrenia, autism spectrum disorder

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22
Q

CMA stands for?

A

Chromosomal Microarray Analysis (CMA)

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23
Q

CGH Techniques

The kind which requires metaphase chromosomes.

A

Chromosomal KInd

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24
Q

CGH Techniques

PCR or hybridization on a chip

A

Genomic kind

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25
Q

This is used in targeting very small segments (less than 200-400 kilobases)

A

Microarrays

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26
Q

CGH: used on c______ or t_____ c_____, CMA; used on very small fragments of DNA

A

Chromosomes, tumor cells

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27
Q

CGH is first described in what year and by who?

A

1993, Kallioniemi

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28
Q

T/F: CGH; solid tumors, FISH; both solid and liquid specimens

A

T

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29
Q

T/F: CGH has a very targeted kind of aberrations to detect.

A

T

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30
Q

CGH cannot detect b_____ changes such as?

A

Balanced, substitutions and translocations

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31
Q

In one form of CGH, you have to bring the chromosomes to ________.

A

metaphase

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32
Q

DNA in CGH becomes unwrapped or single-stranded via what process?

A

Alkaline treatment

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33
Q

T/F: Alkaline treatment is done only for diseased chromosomes.

A

F ; done to both

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34
Q

Color of the normal control chromosome

A

Red

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35
Q

This is DNA from the same individual from areas without the tumor.

A

Normal control chromosome

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36
Q

Color of the disease control chromosome

A

Green

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37
Q

This is DNA from the same individual from areas with tumor cells.

A

Diseased chromosome

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38
Q

We are comparing h______ the same DNA coming from the same individual.

A

homologously

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39
Q

This is both used in CGH and FISH.

A

Fluorescent tags

40
Q

T/F: Labelling of the chromosomal content is separately.

41
Q

Color of the hybridized DNA

42
Q

Metaphase chromosomes are used for?

A

array- or matrix-CGH

43
Q

Used for identifying abnormal regions in the genome

A

Regional differences in the fluorescence ratio of gains/losses vs. control DNA

44
Q

Why is CGH a special FISH technique?

A

Use of dual probes

45
Q

Basics of technique

A

Total genomic DNA of the given sample DNA with total genomic DNA of normal cells

46
Q

It is called “G_______ H________” because we use the entire chromosome genome.

A

Genomic Hybridization

47
Q

T/F: Both tumor and normal DNAs must have identical amount.

48
Q

The tumor and normal DNAs are labeled with two different f_____ d____.

A

Fluorescent dyes

49
Q

The mixture is added and hybridized to a?

A

Normal lymphocyte metaphase slide

50
Q

The fluorescent microscope used for evaluation must be equipped with?

A

CCD camera and image analysis system

51
Q

CCD stands for?

A

Charged Coupled Device

52
Q

This is a capture device camera that can count and interpret signals.

A

Charged Couple Device

53
Q

CGH is based on?

A

Onco-hybridization of two differentially labeled genomic DNAs

54
Q

Metaphase spreads are usually prepared from?

A

Peripheral blood lymphocytes

55
Q

These reflect DNA copy number changes in the test genome relative to the reference genome.

A

Signal intensity ratios (two labels)

56
Q

Resolution is limited to?

A

3-10 megabase pairs

57
Q

FISH to normal diploid chromosomes

Loss of chromosome in the tumor DNA shifts the color of FISH signal to?

58
Q

FISH to normal diploid chromosomes

Gain of chromosomes in the tumor DNA shifts the color of FISH signal to?

59
Q

Fluorochromes used to label tumor DNA

A

Fluorescein isothiocyanate (FITC, green)

60
Q

Fluorochromes used to label control DNA

A

Tetramethylrhodamine (TRITC, red)

61
Q

The genome is combined with excess ______ DNA and hybridized to metaphase chromosomes.

62
Q

This is derived from human male placenta, and is used to decrease the false positive signals in microarrays and CGH.

63
Q

This is used to extinguish background fluorescence or remove false positives.

64
Q

This refers to removal of false positives.

A

Background reduction

65
Q

This happens due to repetitive DNA sequences and prevents nonspecific hybridization.

A

Background Hybridization

66
Q

Lines in CGH are read?

A

vertically

67
Q

For CGH, the count is?

A

Per chromosome

68
Q

T/F: The reading for CGH can be both interchromosomal and intrachromosomal.

A

F ; Intrachromosomal is already CMA because analyzing occurs in the chromosome itself (own DNA)

69
Q

Moving towards the green region means?

A

There is duplication (gaini of function)

70
Q

Moving towards the red region means?

A

There is deletion (loss of function)

71
Q

This sets to capture the FITC and TRITC fluorescence.

A

Fluorochrome-specific optical filter

72
Q

This measures fluorescence intensity values along length of chromosomes and translates ratio into chromosome profiles.

A

CGH analysis software

73
Q

The ratio of these values is used to quantitate genetic imbalances in tumor samples.

A

Green to red fluorescence values

74
Q

What DNA is used in CMA?

A

Individual DNA

75
Q

T/F: In CMA, you already have a solid well material support for capturing DNA.

76
Q

ARRAY CGH: The Complete Process

Steps 1-3

A

Labelling with fluorescent dyes and applied to the microarray

77
Q

ARRAY CGH: The Complete Process

Step 4

A

Attach or hybridize to microarray

78
Q

ARRAY CGH: The Complete Process

Step 5

A

Measuring of fluorescent signals

79
Q

ARRAY CGH: The Complete Process

Step 6

A

Generation of plot

80
Q

Microarrays can be done on both?

A

DNA or mRNA (transcriptome)

81
Q

This refers to the transcriptome, or also called as gene expression since it will be the protein later on.

82
Q

This is the first step in gene expression analysis on microarrays using mRNA, in which we create complementary DNA sequences from mRNA to be used in the microarray.

A

Reverse transcription

83
Q

Gene expression analysis is used more on?

A

Cause of susceptibility, research

84
Q

Why can we not use mRNA directly for microarray analysis?

A
  • Unstable molecule
  • Create loops with itself
85
Q

This is also known as DNA chips, which are tools used for gene expression analysis and genotyping.

A

DNA microarrays

86
Q

T/F: DNA chips do not come in different types.

A

F ; come in different flavors

87
Q

Steps of Microarray Analysis

Step 1

A

Sample Preparation

88
Q

Steps of Microarray Analysis

____ is extracted from both samples then transcribed into cDNA using r_______ t________

A

RNA, reverse transcription

89
Q

Steps of Microarray Analysis

Step 2

A

Microarray chip

90
Q

Steps of Microarray Analysis

The chip has many spots, and each spot is coated with?

A

Multiple identical probes

91
Q

Steps of Microarray Analysis

These spots cover the sequence of a specific gene

A

Short oligonucleotide probes

92
Q

If sample 1 is expressed in the Gene X spot as green and sample 2 is washed away, what does it indicate?

A

Gene X is expressed in sample 1 but not in sample 2

93
Q

If sample 2 is expressed in the Gene X spot as red and sample 1 is washed away, what does it indicate?

A

Gene Y is not expressed in sample 1 but expressed in sample 2

94
Q

If both sample 1 and sample 2 is expressed in the Gene Z spot, what does it indicate?

A

Gene Z is expressed in both samples

95
Q

T/F: The cDNA sample is added to the whole plate in one step.

96
Q

Microarray Chip Analysis

What excites a fluorescent dye?

97
Q

Microarray Chip Analysis

What is measured by a detector?

A

Emission levels

2S CYTOGEN (16 decks)

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