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2S CYTOGEN > U9: CGH + CMA > Flashcards

U9: CGH + CMA Flashcards

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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
This is used in targeting very small segments (less than 200-400 kilobases)
Microarrays
26
CGH: used on c______ or t_____ c_____, CMA; used on very small fragments of DNA
Chromosomes, tumor cells
27
CGH is first described in what year and by who?
1993, Kallioniemi
28
T/F: CGH; solid tumors, FISH; both solid and liquid specimens
T
29
T/F: CGH has a very targeted kind of aberrations to detect.
T
30
CGH cannot detect b_____ changes such as?
Balanced, substitutions and translocations
31
In one form of CGH, you have to bring the chromosomes to ________.
metaphase
32
DNA in CGH becomes unwrapped or single-stranded via what process?
Alkaline treatment
33
T/F: Alkaline treatment is done only for diseased chromosomes.
F ; done to both
34
Color of the normal control chromosome
Red
35
This is DNA from the same individual from areas without the tumor.
Normal control chromosome
36
Color of the disease control chromosome
Green
37
This is DNA from the same individual from areas with tumor cells.
Diseased chromosome
38
We are comparing h______ the same DNA coming from the same individual.
homologously
39
This is both used in CGH and FISH.
Fluorescent tags
40
T/F: Labelling of the chromosomal content is separately.
T
41
Color of the hybridized DNA
Yellow
42
Metaphase chromosomes are used for?
array- or matrix-CGH
43
Used for identifying abnormal regions in the genome
Regional differences in the fluorescence ratio of gains/losses vs. control DNA
44
Why is CGH a special FISH technique?
Use of dual probes
45
Basics of technique
Total genomic DNA of the given sample DNA with total genomic DNA of normal cells
46
It is called "G_______ H________" because we use the entire chromosome genome.
Genomic Hybridization
47
T/F: Both tumor and normal DNAs must have identical amount.
T
48
The tumor and normal DNAs are labeled with two different f_____ d____.
Fluorescent dyes
49
The mixture is added and hybridized to a?
Normal lymphocyte metaphase slide
50
The fluorescent microscope used for evaluation must be equipped with?
CCD camera and image analysis system
51
CCD stands for?
Charged Coupled Device
52
This is a capture device camera that can count and interpret signals.
Charged Couple Device
53
CGH is based on?
Onco-hybridization of two differentially labeled genomic DNAs
54
Metaphase spreads are usually prepared from?
Peripheral blood lymphocytes
55
These reflect DNA copy number changes in the test genome relative to the reference genome.
Signal intensity ratios (two labels)
56
Resolution is limited to?
3-10 megabase pairs
57
FISH to normal diploid chromosomes Loss of chromosome in the tumor DNA shifts the color of FISH signal to?
Red
58
FISH to normal diploid chromosomes Gain of chromosomes in the tumor DNA shifts the color of FISH signal to?
Green
59
Fluorochromes used to label tumor DNA
Fluorescein isothiocyanate (FITC, green)
60
Fluorochromes used to label control DNA
Tetramethylrhodamine (TRITC, red)
61
The genome is combined with excess ______ DNA and hybridized to metaphase chromosomes.
Cot 1 DNA
62
This is derived from human male placenta, and is used to decrease the false positive signals in microarrays and CGH.
Cot 1 DNA
63
This is used to extinguish background fluorescence or remove false positives.
Cot 1 DNA
64
This refers to removal of false positives.
Background reduction
65
This happens due to repetitive DNA sequences and prevents nonspecific hybridization.
Background Hybridization
66
Lines in CGH are read?
vertically
67
For CGH, the count is?
Per chromosome
68
T/F: The reading for CGH can be both interchromosomal and intrachromosomal.
F ; Intrachromosomal is already CMA because analyzing occurs in the chromosome itself (own DNA)
69
Moving towards the green region means?
There is duplication (gaini of function)
70
Moving towards the red region means?
There is deletion (loss of function)
71
This sets to capture the FITC and TRITC fluorescence.
Fluorochrome-specific optical filter
72
This measures fluorescence intensity values along length of chromosomes and translates ratio into chromosome profiles.
CGH analysis software
73
The ratio of these values is used to quantitate genetic imbalances in tumor samples.
Green to red fluorescence values
74
What DNA is used in CMA?
Individual DNA
75
T/F: In CMA, you already have a solid well material support for capturing DNA.
T
76
ARRAY CGH: The Complete Process Steps 1-3
Labelling with fluorescent dyes and applied to the microarray
77
ARRAY CGH: The Complete Process Step 4
Attach or hybridize to microarray
78
ARRAY CGH: The Complete Process Step 5
Measuring of fluorescent signals
79
ARRAY CGH: The Complete Process Step 6
Generation of plot
80
Microarrays can be done on both?
DNA or mRNA (transcriptome)
81
This refers to the transcriptome, or also called as gene expression since it will be the protein later on.
mRNA
82
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.
Reverse transcription
83
Gene expression analysis is used more on?
Cause of susceptibility, research
84
Why can we not use mRNA directly for microarray analysis?
* Unstable molecule * Create loops with itself
85
This is also known as DNA chips, which are tools used for gene expression analysis and genotyping.
DNA microarrays
86
T/F: DNA chips do not come in different types.
F ; come in different flavors
87
Steps of Microarray Analysis Step 1
Sample Preparation
88
Steps of Microarray Analysis ____ is extracted from both samples then transcribed into cDNA using r_______ t________
RNA, reverse transcription
89
Steps of Microarray Analysis Step 2
Microarray chip
90
Steps of Microarray Analysis The chip has many spots, and each spot is coated with?
Multiple identical probes
91
Steps of Microarray Analysis These spots cover the sequence of a specific gene
Short oligonucleotide probes
92
If sample 1 is expressed in the Gene X spot as green and sample 2 is washed away, what does it indicate?
Gene X is expressed in sample 1 but not in sample 2
93
If sample 2 is expressed in the Gene X spot as red and sample 1 is washed away, what does it indicate?
Gene Y is not expressed in sample 1 but expressed in sample 2
94
If both sample 1 and sample 2 is expressed in the Gene Z spot, what does it indicate?
Gene Z is expressed in both samples
95
T/F: The cDNA sample is added to the whole plate in one step.
T
96
Microarray Chip Analysis What excites a fluorescent dye?
laser
97
Microarray Chip Analysis What is measured by a detector?
Emission levels

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